Cobalt in PDB 5nhc: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose, PDB code: 5nhc
was solved by
H.J.Rozeboom,
D.B.Janssen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.00 /
1.93
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.249,
79.332,
91.359,
115.72,
89.39,
116.87
|
|
R / Rfree (%)
|
15.7 /
18.8
|
Cobalt Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Cobalt atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
(pdb code 5nhc). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the
Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose, PDB code: 5nhc:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cobalt binding site 1 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 1 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co501
b:16.3
occ:1.00
|
OE1
|
A:GLU269
|
2.0
|
12.4
|
1.0
|
|
OD2
|
A:ASP297
|
2.1
|
11.4
|
1.0
|
|
OE2
|
A:GLU233
|
2.1
|
11.5
|
1.0
|
|
O2
|
A:XUL503
|
2.2
|
18.3
|
1.0
|
|
OD2
|
A:ASP340
|
2.2
|
12.8
|
1.0
|
|
O4
|
A:XUL503
|
2.3
|
18.4
|
1.0
|
|
CD
|
A:GLU233
|
3.0
|
10.7
|
1.0
|
|
C2
|
A:XUL503
|
3.1
|
21.4
|
1.0
|
|
CG
|
A:ASP297
|
3.1
|
10.7
|
1.0
|
|
C4
|
A:XUL503
|
3.2
|
18.9
|
1.0
|
|
CD
|
A:GLU269
|
3.2
|
10.3
|
1.0
|
|
CG
|
A:ASP340
|
3.2
|
11.4
|
1.0
|
|
OE1
|
A:GLU233
|
3.3
|
12.3
|
1.0
|
|
C3
|
A:XUL503
|
3.4
|
20.0
|
1.0
|
|
O3
|
A:XUL503
|
3.6
|
21.3
|
1.0
|
|
CB
|
A:ASP297
|
3.6
|
9.7
|
1.0
|
|
CB
|
A:ASP340
|
3.7
|
10.3
|
1.0
|
|
CO
|
A:CO502
|
3.7
|
10.9
|
0.7
|
|
OE2
|
A:GLU269
|
4.0
|
10.1
|
1.0
|
|
O
|
A:HOH824
|
4.0
|
12.6
|
1.0
|
|
CE1
|
A:HIS272
|
4.2
|
9.1
|
1.0
|
|
CG
|
A:GLU269
|
4.2
|
9.3
|
1.0
|
|
OD1
|
A:ASP297
|
4.2
|
10.9
|
1.0
|
|
CB
|
A:GLU269
|
4.3
|
8.6
|
1.0
|
|
OD1
|
A:ASP340
|
4.3
|
12.9
|
1.0
|
|
CG
|
A:GLU233
|
4.4
|
10.1
|
1.0
|
|
NE2
|
A:HIS272
|
4.4
|
8.9
|
1.0
|
|
C1
|
A:XUL503
|
4.5
|
21.7
|
1.0
|
|
C5
|
A:XUL503
|
4.5
|
18.4
|
1.0
|
|
ND2
|
A:ASN267
|
4.8
|
8.4
|
1.0
|
|
O1
|
A:XUL503
|
5.0
|
22.6
|
1.0
|
|
Cobalt binding site 2 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 2 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co502
b:4.6
occ:0.30
|
CO
|
A:CO502
|
0.0
|
4.6
|
0.3
|
|
OD2
|
A:ASP308
|
1.5
|
14.8
|
0.6
|
|
CO
|
A:CO502
|
1.8
|
10.9
|
0.7
|
|
CG
|
A:ASP308
|
2.2
|
12.9
|
0.6
|
|
OE2
|
A:GLU269
|
2.2
|
10.1
|
1.0
|
|
OD1
|
A:ASP308
|
2.3
|
13.7
|
0.6
|
|
OD1
|
A:ASP310
|
2.4
|
11.2
|
1.0
|
|
O
|
A:HOH824
|
2.9
|
12.6
|
1.0
|
|
NE2
|
A:HIS272
|
2.9
|
8.9
|
1.0
|
|
O1
|
A:XUL503
|
3.3
|
22.6
|
1.0
|
|
CG
|
A:ASP310
|
3.3
|
10.2
|
1.0
|
|
CD2
|
A:HIS272
|
3.3
|
8.6
|
1.0
|
|
CD
|
A:GLU269
|
3.4
|
10.3
|
1.0
|
|
CB
|
A:ASP308
|
3.4
|
9.6
|
0.4
|
|
OD2
|
A:ASP308
|
3.4
|
9.4
|
0.4
|
|
OD2
|
A:ASP310
|
3.4
|
11.0
|
1.0
|
|
CB
|
A:ASP308
|
3.7
|
12.0
|
0.6
|
|
CG
|
A:ASP308
|
3.9
|
9.4
|
0.4
|
|
O
|
A:HOH688
|
4.1
|
35.1
|
1.0
|
|
OE1
|
A:GLU269
|
4.1
|
12.4
|
1.0
|
|
O2
|
A:XUL503
|
4.1
|
18.3
|
1.0
|
|
ND2
|
A:ASN299
|
4.1
|
7.9
|
1.0
|
|
CE1
|
A:HIS272
|
4.2
|
9.1
|
1.0
|
|
NZ
|
A:LYS235
|
4.3
|
11.1
|
1.0
|
|
C1
|
A:XUL503
|
4.4
|
21.7
|
1.0
|
|
CB
|
A:ASN271
|
4.4
|
8.2
|
1.0
|
|
CG
|
A:GLU269
|
4.5
|
9.3
|
1.0
|
|
CG
|
A:HIS272
|
4.6
|
8.5
|
1.0
|
|
C2
|
A:XUL503
|
4.6
|
21.4
|
1.0
|
|
CE
|
A:LYS235
|
4.6
|
10.2
|
1.0
|
|
CB
|
A:ASP310
|
4.7
|
9.9
|
1.0
|
|
CA
|
A:ASP308
|
4.7
|
11.0
|
0.6
|
|
OD1
|
A:ASN271
|
4.7
|
8.6
|
1.0
|
|
CA
|
A:ASP308
|
4.8
|
9.7
|
0.4
|
|
CG
|
A:ASN271
|
4.8
|
8.4
|
1.0
|
|
Cobalt binding site 3 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 3 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co502
b:10.9
occ:0.70
|
CO
|
A:CO502
|
0.0
|
10.9
|
0.7
|
|
CO
|
A:CO502
|
1.8
|
4.6
|
0.3
|
|
O
|
A:HOH824
|
2.1
|
12.6
|
1.0
|
|
OE2
|
A:GLU269
|
2.2
|
10.1
|
1.0
|
|
O1
|
A:XUL503
|
2.2
|
22.6
|
1.0
|
|
NE2
|
A:HIS272
|
2.2
|
8.9
|
1.0
|
|
O2
|
A:XUL503
|
2.3
|
18.3
|
1.0
|
|
OD2
|
A:ASP308
|
2.7
|
14.8
|
0.6
|
|
C2
|
A:XUL503
|
2.9
|
21.4
|
1.0
|
|
CD
|
A:GLU269
|
2.9
|
10.3
|
1.0
|
|
C1
|
A:XUL503
|
2.9
|
21.7
|
1.0
|
|
OE1
|
A:GLU269
|
3.0
|
12.4
|
1.0
|
|
CE1
|
A:HIS272
|
3.1
|
9.1
|
1.0
|
|
CD2
|
A:HIS272
|
3.3
|
8.6
|
1.0
|
|
CO
|
A:CO501
|
3.7
|
16.3
|
1.0
|
|
CG
|
A:ASP308
|
3.8
|
12.9
|
0.6
|
|
OD1
|
A:ASP310
|
3.8
|
11.2
|
1.0
|
|
OD2
|
A:ASP340
|
3.9
|
12.8
|
1.0
|
|
OD1
|
A:ASP308
|
4.0
|
13.7
|
0.6
|
|
OD2
|
A:ASP310
|
4.2
|
11.0
|
1.0
|
|
ND1
|
A:HIS272
|
4.2
|
8.8
|
1.0
|
|
NZ
|
A:LYS235
|
4.3
|
11.1
|
1.0
|
|
CG
|
A:GLU269
|
4.3
|
9.3
|
1.0
|
|
C3
|
A:XUL503
|
4.3
|
20.0
|
1.0
|
|
CG
|
A:HIS272
|
4.3
|
8.5
|
1.0
|
|
OD2
|
A:ASP308
|
4.4
|
9.4
|
0.4
|
|
CG
|
A:ASP310
|
4.4
|
10.2
|
1.0
|
|
OE2
|
A:GLU233
|
4.4
|
11.5
|
1.0
|
|
CG
|
A:ASP340
|
4.4
|
11.4
|
1.0
|
|
O
|
A:HOH997
|
4.5
|
22.5
|
1.0
|
|
O3
|
A:XUL503
|
4.6
|
21.3
|
1.0
|
|
OD1
|
A:ASP340
|
4.7
|
12.9
|
1.0
|
|
O
|
A:HOH688
|
4.7
|
35.1
|
1.0
|
|
CE
|
A:LYS235
|
4.7
|
10.2
|
1.0
|
|
ND2
|
A:ASN299
|
4.8
|
7.9
|
1.0
|
|
CD
|
A:LYS235
|
4.9
|
9.6
|
1.0
|
|
CZ
|
C:PHE61
|
5.0
|
23.8
|
1.0
|
|
CB
|
A:GLU269
|
5.0
|
8.6
|
1.0
|
|
Cobalt binding site 4 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 4 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co501
b:15.6
occ:1.00
|
OE1
|
B:GLU269
|
2.1
|
10.8
|
1.0
|
|
OD2
|
B:ASP297
|
2.1
|
8.3
|
1.0
|
|
O2
|
B:XUL503
|
2.1
|
17.6
|
1.0
|
|
OD2
|
B:ASP340
|
2.2
|
11.1
|
1.0
|
|
O4
|
B:XUL503
|
2.2
|
17.5
|
1.0
|
|
OE2
|
B:GLU233
|
2.2
|
10.2
|
1.0
|
|
C2
|
B:XUL503
|
3.1
|
20.9
|
1.0
|
|
CD
|
B:GLU233
|
3.1
|
9.9
|
1.0
|
|
CG
|
B:ASP297
|
3.1
|
7.9
|
1.0
|
|
CG
|
B:ASP340
|
3.2
|
9.5
|
1.0
|
|
C4
|
B:XUL503
|
3.2
|
19.9
|
1.0
|
|
CD
|
B:GLU269
|
3.3
|
9.7
|
1.0
|
|
OE1
|
B:GLU233
|
3.3
|
10.5
|
1.0
|
|
C3
|
B:XUL503
|
3.4
|
21.0
|
1.0
|
|
O3
|
B:XUL503
|
3.5
|
21.7
|
1.0
|
|
CB
|
B:ASP297
|
3.6
|
7.6
|
1.0
|
|
CB
|
B:ASP340
|
3.7
|
8.7
|
1.0
|
|
CO
|
B:CO502
|
3.8
|
9.9
|
0.7
|
|
OE2
|
B:GLU269
|
4.0
|
10.7
|
1.0
|
|
O
|
B:HOH758
|
4.1
|
14.0
|
1.0
|
|
OD1
|
B:ASP297
|
4.2
|
8.3
|
1.0
|
|
CE1
|
B:HIS272
|
4.2
|
8.3
|
1.0
|
|
OD1
|
B:ASP340
|
4.3
|
10.2
|
1.0
|
|
CG
|
B:GLU269
|
4.3
|
8.7
|
1.0
|
|
CB
|
B:GLU269
|
4.3
|
8.1
|
1.0
|
|
CG
|
B:GLU233
|
4.4
|
9.1
|
1.0
|
|
C1
|
B:XUL503
|
4.4
|
22.5
|
1.0
|
|
C5
|
B:XUL503
|
4.5
|
20.5
|
1.0
|
|
NE2
|
B:HIS272
|
4.5
|
8.3
|
1.0
|
|
ND2
|
B:ASN267
|
4.8
|
8.2
|
1.0
|
|
O1
|
B:XUL503
|
4.9
|
24.1
|
1.0
|
|
CZ2
|
B:TRP50
|
5.0
|
6.8
|
1.0
|
|
Cobalt binding site 5 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 5 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co502
b:7.5
occ:0.30
|
CO
|
B:CO502
|
0.0
|
7.5
|
0.3
|
|
OD2
|
B:ASP308
|
1.5
|
8.7
|
0.2
|
|
CO
|
B:CO502
|
1.9
|
9.9
|
0.7
|
|
CG
|
B:ASP308
|
2.1
|
8.8
|
0.2
|
|
OE2
|
B:GLU269
|
2.2
|
10.7
|
1.0
|
|
OD1
|
B:ASP308
|
2.3
|
8.6
|
0.2
|
|
OD1
|
B:ASP310
|
2.3
|
8.9
|
1.0
|
|
O
|
B:HOH758
|
2.7
|
14.0
|
1.0
|
|
NE2
|
B:HIS272
|
3.0
|
8.3
|
1.0
|
|
O1
|
B:XUL503
|
3.1
|
24.1
|
1.0
|
|
CG
|
B:ASP310
|
3.2
|
8.8
|
1.0
|
|
OD2
|
B:ASP308
|
3.3
|
11.8
|
0.8
|
|
CB
|
B:ASP308
|
3.4
|
10.6
|
0.8
|
|
CD2
|
B:HIS272
|
3.4
|
8.0
|
1.0
|
|
OD2
|
B:ASP310
|
3.4
|
9.4
|
1.0
|
|
CD
|
B:GLU269
|
3.5
|
9.7
|
1.0
|
|
CB
|
B:ASP308
|
3.6
|
8.9
|
0.2
|
|
CG
|
B:ASP308
|
3.8
|
11.0
|
0.8
|
|
O
|
B:HOH755
|
4.0
|
30.1
|
1.0
|
|
OE1
|
B:GLU269
|
4.1
|
10.8
|
1.0
|
|
ND2
|
B:ASN299
|
4.1
|
6.6
|
1.0
|
|
O2
|
B:XUL503
|
4.1
|
17.6
|
1.0
|
|
CE1
|
B:HIS272
|
4.3
|
8.3
|
1.0
|
|
NZ
|
B:LYS235
|
4.3
|
9.5
|
1.0
|
|
C1
|
B:XUL503
|
4.3
|
22.5
|
1.0
|
|
CB
|
B:ASN271
|
4.4
|
7.2
|
1.0
|
|
CG
|
B:GLU269
|
4.6
|
8.7
|
1.0
|
|
C2
|
B:XUL503
|
4.7
|
20.9
|
1.0
|
|
CB
|
B:ASP310
|
4.7
|
8.5
|
1.0
|
|
CA
|
B:ASP308
|
4.7
|
9.0
|
0.2
|
|
CE
|
B:LYS235
|
4.7
|
8.7
|
1.0
|
|
CG
|
B:HIS272
|
4.7
|
7.6
|
1.0
|
|
OD1
|
B:ASN271
|
4.7
|
7.3
|
1.0
|
|
CA
|
B:ASP308
|
4.7
|
10.0
|
0.8
|
|
CG
|
B:ASN271
|
4.8
|
7.2
|
1.0
|
|
Cobalt binding site 6 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 6 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co502
b:9.9
occ:0.70
|
CO
|
B:CO502
|
0.0
|
9.9
|
0.7
|
|
CO
|
B:CO502
|
1.9
|
7.5
|
0.3
|
|
O1
|
B:XUL503
|
2.0
|
24.1
|
1.0
|
|
O
|
B:HOH758
|
2.1
|
14.0
|
1.0
|
|
OE2
|
B:GLU269
|
2.2
|
10.7
|
1.0
|
|
NE2
|
B:HIS272
|
2.2
|
8.3
|
1.0
|
|
O2
|
B:XUL503
|
2.3
|
17.6
|
1.0
|
|
OD2
|
B:ASP308
|
2.8
|
8.7
|
0.2
|
|
C1
|
B:XUL503
|
2.9
|
22.5
|
1.0
|
|
C2
|
B:XUL503
|
2.9
|
20.9
|
1.0
|
|
CD
|
B:GLU269
|
2.9
|
9.7
|
1.0
|
|
OE1
|
B:GLU269
|
3.0
|
10.8
|
1.0
|
|
CE1
|
B:HIS272
|
3.1
|
8.3
|
1.0
|
|
CD2
|
B:HIS272
|
3.3
|
8.0
|
1.0
|
|
CO
|
B:CO501
|
3.8
|
15.6
|
1.0
|
|
CG
|
B:ASP308
|
3.8
|
8.8
|
0.2
|
|
OD1
|
B:ASP310
|
3.9
|
8.9
|
1.0
|
|
OD2
|
B:ASP340
|
3.9
|
11.1
|
1.0
|
|
OD1
|
B:ASP308
|
4.1
|
8.6
|
0.2
|
|
OD2
|
B:ASP310
|
4.2
|
9.4
|
1.0
|
|
ND1
|
B:HIS272
|
4.2
|
7.9
|
1.0
|
|
OD2
|
B:ASP308
|
4.3
|
11.8
|
0.8
|
|
CG
|
B:GLU269
|
4.3
|
8.7
|
1.0
|
|
C3
|
B:XUL503
|
4.3
|
21.0
|
1.0
|
|
NZ
|
B:LYS235
|
4.3
|
9.5
|
1.0
|
|
CG
|
B:HIS272
|
4.3
|
7.6
|
1.0
|
|
OE2
|
B:GLU233
|
4.4
|
10.2
|
1.0
|
|
CG
|
B:ASP340
|
4.4
|
9.5
|
1.0
|
|
CG
|
B:ASP310
|
4.4
|
8.8
|
1.0
|
|
O3
|
B:XUL503
|
4.5
|
21.7
|
1.0
|
|
OD1
|
B:ASP340
|
4.6
|
10.2
|
1.0
|
|
CE
|
B:LYS235
|
4.8
|
8.7
|
1.0
|
|
ND2
|
B:ASN299
|
4.8
|
6.6
|
1.0
|
|
O
|
B:HOH755
|
4.8
|
30.1
|
1.0
|
|
CD
|
B:LYS235
|
4.9
|
8.0
|
1.0
|
|
CB
|
B:GLU269
|
5.0
|
8.1
|
1.0
|
|
CZ
|
D:PHE61
|
5.0
|
24.3
|
1.0
|
|
Cobalt binding site 7 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 7 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co501
b:14.8
occ:1.00
|
OE1
|
C:GLU269
|
2.0
|
14.0
|
1.0
|
|
O2
|
C:XUL503
|
2.1
|
20.1
|
1.0
|
|
OD2
|
C:ASP297
|
2.1
|
9.5
|
1.0
|
|
OE2
|
C:GLU233
|
2.2
|
12.1
|
1.0
|
|
OD2
|
C:ASP340
|
2.2
|
9.2
|
1.0
|
|
O4
|
C:XUL503
|
2.2
|
22.5
|
1.0
|
|
C2
|
C:XUL503
|
3.0
|
24.0
|
1.0
|
|
CD
|
C:GLU233
|
3.1
|
11.2
|
1.0
|
|
CG
|
C:ASP297
|
3.1
|
8.8
|
1.0
|
|
C4
|
C:XUL503
|
3.2
|
23.4
|
1.0
|
|
CG
|
C:ASP340
|
3.2
|
8.3
|
1.0
|
|
CD
|
C:GLU269
|
3.3
|
11.3
|
1.0
|
|
OE1
|
C:GLU233
|
3.3
|
12.3
|
1.0
|
|
C3
|
C:XUL503
|
3.4
|
23.8
|
1.0
|
|
CB
|
C:ASP297
|
3.6
|
8.4
|
1.0
|
|
O3
|
C:XUL503
|
3.6
|
25.2
|
1.0
|
|
CB
|
C:ASP340
|
3.7
|
7.8
|
1.0
|
|
CO
|
C:CO502
|
3.7
|
9.6
|
0.7
|
|
OE2
|
C:GLU269
|
4.0
|
12.3
|
1.0
|
|
O
|
C:HOH733
|
4.0
|
11.0
|
1.0
|
|
CE1
|
C:HIS272
|
4.2
|
8.2
|
1.0
|
|
OD1
|
C:ASP297
|
4.2
|
8.9
|
1.0
|
|
CG
|
C:GLU269
|
4.3
|
10.0
|
1.0
|
|
OD1
|
C:ASP340
|
4.3
|
8.6
|
1.0
|
|
CB
|
C:GLU269
|
4.3
|
9.0
|
1.0
|
|
CG
|
C:GLU233
|
4.4
|
10.3
|
1.0
|
|
C1
|
C:XUL503
|
4.4
|
23.5
|
1.0
|
|
NE2
|
C:HIS272
|
4.5
|
8.3
|
1.0
|
|
C5
|
C:XUL503
|
4.5
|
23.1
|
1.0
|
|
ND2
|
C:ASN267
|
4.8
|
8.9
|
1.0
|
|
O1
|
C:XUL503
|
4.9
|
22.9
|
1.0
|
|
CZ2
|
C:TRP50
|
5.0
|
8.7
|
1.0
|
|
Cobalt binding site 8 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 8 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 8 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co502
b:6.6
occ:0.30
|
CO
|
C:CO502
|
0.0
|
6.6
|
0.3
|
|
OD2
|
C:ASP308
|
1.5
|
15.8
|
0.6
|
|
CO
|
C:CO502
|
1.8
|
9.6
|
0.7
|
|
OE2
|
C:GLU269
|
2.2
|
12.3
|
1.0
|
|
CG
|
C:ASP308
|
2.3
|
14.9
|
0.6
|
|
OD1
|
C:ASP308
|
2.4
|
16.2
|
0.6
|
|
O
|
C:HOH733
|
2.5
|
11.0
|
1.0
|
|
OD1
|
C:ASP310
|
2.5
|
10.0
|
1.0
|
|
NE2
|
C:HIS272
|
2.9
|
8.3
|
1.0
|
|
O1
|
C:XUL503
|
3.0
|
22.9
|
1.0
|
|
CG
|
C:ASP310
|
3.3
|
9.4
|
1.0
|
|
CD2
|
C:HIS272
|
3.3
|
8.0
|
1.0
|
|
CD
|
C:GLU269
|
3.4
|
11.3
|
1.0
|
|
OD2
|
C:ASP308
|
3.4
|
9.6
|
0.4
|
|
OD2
|
C:ASP310
|
3.4
|
9.8
|
1.0
|
|
CB
|
C:ASP308
|
3.5
|
10.0
|
0.4
|
|
CB
|
C:ASP308
|
3.7
|
13.4
|
0.6
|
|
O2
|
C:XUL503
|
3.9
|
20.1
|
1.0
|
|
CG
|
C:ASP308
|
3.9
|
9.8
|
0.4
|
|
OE1
|
C:GLU269
|
4.0
|
14.0
|
1.0
|
|
CE1
|
C:HIS272
|
4.1
|
8.2
|
1.0
|
|
ND2
|
C:ASN299
|
4.2
|
7.0
|
1.0
|
|
NZ
|
C:LYS235
|
4.2
|
9.5
|
1.0
|
|
C1
|
C:XUL503
|
4.3
|
23.5
|
1.0
|
|
CB
|
C:ASN271
|
4.5
|
6.8
|
1.0
|
|
C2
|
C:XUL503
|
4.5
|
24.0
|
1.0
|
|
CG
|
C:GLU269
|
4.5
|
10.0
|
1.0
|
|
CG
|
C:HIS272
|
4.6
|
7.7
|
1.0
|
|
CE
|
C:LYS235
|
4.6
|
9.1
|
1.0
|
|
CB
|
C:ASP310
|
4.8
|
9.2
|
1.0
|
|
CA
|
C:ASP308
|
4.8
|
12.1
|
0.6
|
|
CA
|
C:ASP308
|
4.9
|
10.3
|
0.4
|
|
OD1
|
C:ASN271
|
4.9
|
6.8
|
1.0
|
|
CG
|
C:ASN271
|
4.9
|
6.8
|
1.0
|
|
ND1
|
C:HIS272
|
5.0
|
7.8
|
1.0
|
|
Cobalt binding site 9 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 9 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 9 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co502
b:9.6
occ:0.70
|
CO
|
C:CO502
|
0.0
|
9.6
|
0.7
|
|
CO
|
C:CO502
|
1.8
|
6.6
|
0.3
|
|
O
|
C:HOH733
|
1.9
|
11.0
|
1.0
|
|
O1
|
C:XUL503
|
2.1
|
22.9
|
1.0
|
|
NE2
|
C:HIS272
|
2.2
|
8.3
|
1.0
|
|
OE2
|
C:GLU269
|
2.2
|
12.3
|
1.0
|
|
O2
|
C:XUL503
|
2.2
|
20.1
|
1.0
|
|
OD2
|
C:ASP308
|
2.8
|
15.8
|
0.6
|
|
CD
|
C:GLU269
|
2.9
|
11.3
|
1.0
|
|
C2
|
C:XUL503
|
2.9
|
24.0
|
1.0
|
|
C1
|
C:XUL503
|
2.9
|
23.5
|
1.0
|
|
OE1
|
C:GLU269
|
3.0
|
14.0
|
1.0
|
|
CE1
|
C:HIS272
|
3.0
|
8.2
|
1.0
|
|
CD2
|
C:HIS272
|
3.2
|
8.0
|
1.0
|
|
CO
|
C:CO501
|
3.7
|
14.8
|
1.0
|
|
CG
|
C:ASP308
|
3.8
|
14.9
|
0.6
|
|
OD2
|
C:ASP340
|
3.9
|
9.2
|
1.0
|
|
OD1
|
C:ASP310
|
3.9
|
10.0
|
1.0
|
|
OD1
|
C:ASP308
|
4.1
|
16.2
|
0.6
|
|
ND1
|
C:HIS272
|
4.1
|
7.8
|
1.0
|
|
OD2
|
C:ASP310
|
4.2
|
9.8
|
1.0
|
|
CG
|
C:GLU269
|
4.2
|
10.0
|
1.0
|
|
CG
|
C:HIS272
|
4.3
|
7.7
|
1.0
|
|
NZ
|
C:LYS235
|
4.3
|
9.5
|
1.0
|
|
C3
|
C:XUL503
|
4.3
|
23.8
|
1.0
|
|
OE2
|
C:GLU233
|
4.4
|
12.1
|
1.0
|
|
OD2
|
C:ASP308
|
4.4
|
9.6
|
0.4
|
|
O
|
C:HOH830
|
4.4
|
32.7
|
1.0
|
|
CG
|
C:ASP340
|
4.4
|
8.3
|
1.0
|
|
CG
|
C:ASP310
|
4.5
|
9.4
|
1.0
|
|
O3
|
C:XUL503
|
4.6
|
25.2
|
1.0
|
|
OD1
|
C:ASP340
|
4.7
|
8.6
|
1.0
|
|
CE
|
C:LYS235
|
4.8
|
9.1
|
1.0
|
|
ND2
|
C:ASN299
|
4.8
|
7.0
|
1.0
|
|
CD
|
C:LYS235
|
4.9
|
8.7
|
1.0
|
|
CB
|
C:GLU269
|
4.9
|
9.0
|
1.0
|
|
Cobalt binding site 10 out
of 12 in 5nhc
Go back to
Cobalt Binding Sites List in 5nhc
Cobalt binding site 10 out
of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 10 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CO2+ Ions and Xylulose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co501
b:14.5
occ:1.00
|
O2
|
D:XUL503
|
2.1
|
15.4
|
1.0
|
|
OE1
|
D:GLU269
|
2.1
|
11.3
|
1.0
|
|
OD2
|
D:ASP297
|
2.1
|
8.9
|
1.0
|
|
OD2
|
D:ASP340
|
2.1
|
10.9
|
1.0
|
|
OE2
|
D:GLU233
|
2.2
|
9.6
|
1.0
|
|
O4
|
D:XUL503
|
2.2
|
16.7
|
1.0
|
|
C2
|
D:XUL503
|
3.0
|
19.0
|
1.0
|
|
CD
|
D:GLU233
|
3.0
|
9.5
|
1.0
|
|
CG
|
D:ASP297
|
3.1
|
9.0
|
1.0
|
|
CG
|
D:ASP340
|
3.2
|
9.6
|
1.0
|
|
C4
|
D:XUL503
|
3.2
|
16.8
|
1.0
|
|
CD
|
D:GLU269
|
3.3
|
9.9
|
1.0
|
|
OE1
|
D:GLU233
|
3.3
|
10.0
|
1.0
|
|
C3
|
D:XUL503
|
3.4
|
17.9
|
1.0
|
|
O3
|
D:XUL503
|
3.6
|
19.6
|
1.0
|
|
CB
|
D:ASP297
|
3.6
|
8.6
|
1.0
|
|
CB
|
D:ASP340
|
3.7
|
8.8
|
1.0
|
|
CO
|
D:CO502
|
3.8
|
7.2
|
0.7
|
|
O
|
D:HOH761
|
3.9
|
14.1
|
1.0
|
|
OE2
|
D:GLU269
|
4.0
|
11.7
|
1.0
|
|
CE1
|
D:HIS272
|
4.2
|
6.8
|
1.0
|
|
OD1
|
D:ASP297
|
4.2
|
9.6
|
1.0
|
|
OD1
|
D:ASP340
|
4.3
|
10.8
|
1.0
|
|
CG
|
D:GLU269
|
4.3
|
8.9
|
1.0
|
|
CB
|
D:GLU269
|
4.3
|
8.0
|
1.0
|
|
C1
|
D:XUL503
|
4.4
|
19.7
|
1.0
|
|
CG
|
D:GLU233
|
4.4
|
8.8
|
1.0
|
|
NE2
|
D:HIS272
|
4.5
|
6.9
|
1.0
|
|
C5
|
D:XUL503
|
4.5
|
17.1
|
1.0
|
|
ND2
|
D:ASN267
|
4.9
|
8.9
|
1.0
|
|
CZ2
|
D:TRP50
|
5.0
|
7.6
|
1.0
|
|
O1
|
D:XUL503
|
5.0
|
20.6
|
1.0
|
|
Reference:
M.Lee,
H.J.Rozeboom,
P.P.De Waal,
R.M.De Jong,
H.M.Dudek,
D.B.Janssen.
Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777
Page generated: Sun Dec 13 10:48:15 2020
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