Cobalt in PDB 1qt1: Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
Enzymatic activity of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
All present enzymatic activity of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution, PDB code: 1qt1
was solved by
L.Niu,
M.Teng,
X.Zhu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
5.00 /
1.85
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.976,
98.836,
93.927,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.6 /
21.9
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
(pdb code 1qt1). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution, PDB code: 1qt1:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 1qt1
Go back to
Cobalt Binding Sites List in 1qt1
Cobalt binding site 1 out
of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
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 Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co400
b:16.1
occ:1.00
|
OD2
|
A:ASP244
|
1.9
|
17.6
|
1.0
|
OE1
|
A:GLU216
|
1.9
|
3.4
|
1.0
|
OD2
|
A:ASP286
|
2.1
|
12.3
|
1.0
|
OE2
|
A:GLU180
|
2.2
|
13.0
|
1.0
|
CD
|
A:GLU180
|
2.9
|
7.9
|
1.0
|
CG
|
A:ASP244
|
3.0
|
10.2
|
1.0
|
CG
|
A:ASP286
|
3.1
|
7.2
|
1.0
|
CD
|
A:GLU216
|
3.1
|
7.0
|
1.0
|
OE1
|
A:GLU180
|
3.1
|
10.4
|
1.0
|
CB
|
A:ASP286
|
3.4
|
8.4
|
1.0
|
CB
|
A:ASP244
|
3.5
|
8.4
|
1.0
|
O
|
A:HOH1288
|
3.6
|
18.6
|
1.0
|
CG
|
A:GLU216
|
3.8
|
4.5
|
1.0
|
O
|
A:HOH1290
|
3.8
|
36.7
|
1.0
|
CB
|
A:GLU216
|
3.9
|
3.5
|
1.0
|
O
|
A:HOH1635
|
4.0
|
45.0
|
1.0
|
OD1
|
A:ASP244
|
4.0
|
10.0
|
1.0
|
OE2
|
A:GLU216
|
4.1
|
7.5
|
1.0
|
OD1
|
A:ASP286
|
4.2
|
9.3
|
1.0
|
CE1
|
A:HIS219
|
4.2
|
4.6
|
1.0
|
CG
|
A:GLU180
|
4.2
|
6.9
|
1.0
|
NE2
|
A:HIS219
|
4.7
|
4.4
|
1.0
|
ND1
|
A:HIS219
|
4.8
|
2.9
|
1.0
|
CO
|
A:CO401
|
4.9
|
10.2
|
1.0
|
CA
|
A:ASP286
|
4.9
|
5.8
|
1.0
|
ND2
|
A:ASN214
|
5.0
|
10.2
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 1qt1
Go back to
Cobalt Binding Sites List in 1qt1
Cobalt binding site 2 out
of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
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 Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co401
b:10.2
occ:1.00
|
OD2
|
A:ASP254
|
2.0
|
9.4
|
1.0
|
OD1
|
A:ASP256
|
2.2
|
7.4
|
1.0
|
OE2
|
A:GLU216
|
2.2
|
7.5
|
1.0
|
O
|
A:HOH1635
|
2.4
|
45.0
|
1.0
|
NE2
|
A:HIS219
|
2.5
|
4.4
|
1.0
|
CG
|
A:ASP254
|
2.7
|
10.0
|
1.0
|
OD1
|
A:ASP254
|
2.8
|
13.0
|
1.0
|
CG
|
A:ASP256
|
3.1
|
8.3
|
1.0
|
CD
|
A:GLU216
|
3.2
|
7.0
|
1.0
|
OD2
|
A:ASP256
|
3.2
|
13.3
|
1.0
|
CD2
|
A:HIS219
|
3.3
|
2.0
|
1.0
|
O
|
A:HOH1275
|
3.3
|
58.8
|
1.0
|
OE1
|
A:GLU216
|
3.3
|
3.4
|
1.0
|
CE1
|
A:HIS219
|
3.5
|
4.6
|
1.0
|
ND2
|
A:ASN246
|
4.1
|
5.2
|
1.0
|
CB
|
A:ASP254
|
4.2
|
5.9
|
1.0
|
CB
|
A:ASP256
|
4.5
|
4.6
|
1.0
|
CG
|
A:HIS219
|
4.5
|
4.0
|
1.0
|
O
|
A:HOH1018
|
4.5
|
7.6
|
1.0
|
CG
|
A:GLU216
|
4.5
|
4.5
|
1.0
|
ND1
|
A:HIS219
|
4.6
|
2.9
|
1.0
|
OD2
|
A:ASP286
|
4.7
|
12.3
|
1.0
|
NZ
|
A:LYS182
|
4.9
|
5.5
|
1.0
|
CO
|
A:CO400
|
4.9
|
16.1
|
1.0
|
CE
|
A:LYS182
|
5.0
|
2.1
|
1.0
|
CA
|
A:ASP256
|
5.0
|
4.0
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 1qt1
Go back to
Cobalt Binding Sites List in 1qt1
Cobalt binding site 3 out
of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
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 Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co900
b:18.0
occ:1.00
|
OD2
|
B:ASP744
|
1.9
|
9.3
|
1.0
|
OE1
|
B:GLU716
|
2.0
|
5.9
|
1.0
|
OD2
|
B:ASP786
|
2.0
|
10.6
|
1.0
|
OE2
|
B:GLU680
|
2.1
|
15.6
|
1.0
|
CD
|
B:GLU680
|
2.9
|
9.5
|
1.0
|
CG
|
B:ASP786
|
3.0
|
8.1
|
1.0
|
CG
|
B:ASP744
|
3.1
|
12.3
|
1.0
|
OE1
|
B:GLU680
|
3.1
|
10.6
|
1.0
|
CD
|
B:GLU716
|
3.2
|
7.5
|
1.0
|
CB
|
B:ASP786
|
3.5
|
5.1
|
1.0
|
O
|
B:HOH1410
|
3.5
|
17.1
|
1.0
|
CB
|
B:ASP744
|
3.6
|
7.9
|
1.0
|
CG
|
B:GLU716
|
3.8
|
7.6
|
1.0
|
O
|
B:HOH1636
|
3.9
|
48.3
|
1.0
|
CB
|
B:GLU716
|
3.9
|
2.7
|
1.0
|
O
|
B:HOH1407
|
4.1
|
34.3
|
1.0
|
OD1
|
B:ASP744
|
4.1
|
8.8
|
1.0
|
OD1
|
B:ASP786
|
4.1
|
8.7
|
1.0
|
OE2
|
B:GLU716
|
4.1
|
9.4
|
1.0
|
CG
|
B:GLU680
|
4.2
|
6.2
|
1.0
|
O
|
B:HOH1235
|
4.3
|
36.0
|
1.0
|
CE1
|
B:HIS719
|
4.3
|
5.4
|
1.0
|
NE2
|
B:HIS719
|
4.8
|
6.3
|
1.0
|
OD1
|
B:ASN714
|
4.8
|
11.6
|
1.0
|
CO
|
B:CO901
|
4.9
|
11.0
|
1.0
|
ND1
|
B:HIS719
|
4.9
|
4.4
|
1.0
|
O
|
B:HOH1627
|
5.0
|
42.5
|
1.0
|
CA
|
B:ASP786
|
5.0
|
6.0
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 1qt1
Go back to
Cobalt Binding Sites List in 1qt1
Cobalt binding site 4 out
of 4 in the Crystal Structure of Xylose Isomerase From Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution
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 Streptomyces Diastaticus No.7 M1033 at 1.85 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co901
b:11.0
occ:1.00
|
OD2
|
B:ASP754
|
2.1
|
10.5
|
1.0
|
OD1
|
B:ASP756
|
2.1
|
10.8
|
1.0
|
OE2
|
B:GLU716
|
2.2
|
9.4
|
1.0
|
O
|
B:HOH1636
|
2.2
|
48.3
|
1.0
|
NE2
|
B:HIS719
|
2.6
|
6.3
|
1.0
|
CG
|
B:ASP754
|
2.8
|
11.1
|
1.0
|
OD1
|
B:ASP754
|
2.8
|
16.1
|
1.0
|
CG
|
B:ASP756
|
3.0
|
11.9
|
1.0
|
CD
|
B:GLU716
|
3.1
|
7.5
|
1.0
|
OD2
|
B:ASP756
|
3.2
|
14.8
|
1.0
|
CD2
|
B:HIS719
|
3.3
|
2.1
|
1.0
|
OE1
|
B:GLU716
|
3.3
|
5.9
|
1.0
|
O
|
B:HOH1627
|
3.4
|
42.5
|
1.0
|
CE1
|
B:HIS719
|
3.6
|
5.4
|
1.0
|
ND2
|
B:ASN746
|
4.0
|
3.8
|
1.0
|
O
|
B:HOH1015
|
4.2
|
13.7
|
1.0
|
CB
|
B:ASP754
|
4.2
|
5.2
|
1.0
|
CB
|
B:ASP756
|
4.4
|
6.7
|
1.0
|
CG
|
B:GLU716
|
4.5
|
7.6
|
1.0
|
CG
|
B:HIS719
|
4.5
|
3.7
|
1.0
|
ND1
|
B:HIS719
|
4.6
|
4.4
|
1.0
|
OD2
|
B:ASP786
|
4.8
|
10.6
|
1.0
|
CO
|
B:CO900
|
4.9
|
18.0
|
1.0
|
CA
|
B:ASP756
|
4.9
|
5.9
|
1.0
|
NZ
|
B:LYS682
|
4.9
|
2.0
|
1.0
|
O
|
B:ASP786
|
5.0
|
6.5
|
1.0
|
|
Reference:
X.Zhu,
M.Teng,
L.Niu,
C.Xu,
Y.Wang.
Structure of Xylose Isomerase From Streptomyces Diastaticus No. 7 Strain M1033 at 1.85 A Resolution. Acta Crystallogr.,Sect.D V. 56 129 2000.
ISSN: ISSN 0907-4449
PubMed: 10666592
DOI: 10.1107/S0907444999015097
Page generated: Tue Jul 30 14:31:55 2024
|