Cobalt in PDB 2gve: Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
Enzymatic activity of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
All present enzymatic activity of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase:
5.3.1.5;
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
(pdb code 2gve). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the
Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase, PDB code: 2gve:
Jump to Cobalt binding site number:
1;
2;
Cobalt binding site 1 out
of 2 in 2gve
Go back to
Cobalt Binding Sites List in 2gve
Cobalt binding site 1 out
of 2 in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co390
b:11.6
occ:1.00
|
OD2
|
A:ASP255
|
1.9
|
8.6
|
1.0
|
O
|
A:DOD1018
|
2.0
|
10.0
|
1.0
|
DE2
|
A:HIS220
|
2.0
|
9.5
|
0.4
|
D1
|
A:DOD1018
|
2.0
|
15.0
|
1.0
|
OE2
|
A:GLU217
|
2.1
|
5.9
|
1.0
|
OD1
|
A:ASP257
|
2.2
|
6.6
|
1.0
|
D2
|
A:DOD1018
|
2.3
|
15.0
|
1.0
|
CG
|
A:ASP255
|
2.6
|
9.1
|
1.0
|
OD1
|
A:ASP255
|
2.6
|
6.8
|
1.0
|
NE2
|
A:HIS220
|
2.7
|
7.9
|
1.0
|
D1
|
A:DOD1174
|
2.8
|
38.2
|
1.0
|
HD2
|
A:HIS220
|
2.9
|
7.6
|
1.0
|
D1
|
A:DOD3452
|
3.0
|
59.8
|
1.0
|
CD
|
A:GLU217
|
3.0
|
8.5
|
1.0
|
CD2
|
A:HIS220
|
3.1
|
6.3
|
1.0
|
CG
|
A:ASP257
|
3.1
|
10.8
|
1.0
|
OD2
|
A:ASP257
|
3.3
|
12.1
|
1.0
|
OE1
|
A:GLU217
|
3.3
|
7.1
|
1.0
|
D2
|
A:DOD1021
|
3.4
|
10.9
|
1.0
|
O
|
A:DOD1174
|
3.6
|
25.4
|
1.0
|
DD22
|
A:ASN247
|
3.6
|
10.1
|
1.0
|
O
|
A:DOD3452
|
3.7
|
39.9
|
1.0
|
DD21
|
A:ASN247
|
3.8
|
10.1
|
1.0
|
HD21
|
A:ASN247
|
3.8
|
10.1
|
0.0
|
CE1
|
A:HIS220
|
3.9
|
9.6
|
1.0
|
CB
|
A:ASP255
|
4.1
|
6.2
|
1.0
|
ND2
|
A:ASN247
|
4.1
|
8.4
|
1.0
|
HE3
|
A:LYS183
|
4.2
|
16.1
|
1.0
|
O
|
A:DOD1021
|
4.2
|
7.3
|
1.0
|
HE1
|
A:HIS220
|
4.3
|
11.5
|
1.0
|
DZ3
|
A:LYS183
|
4.3
|
19.5
|
1.0
|
D2
|
A:DOD3452
|
4.3
|
59.8
|
1.0
|
HB3
|
A:ASP255
|
4.3
|
7.4
|
1.0
|
D2
|
A:DOD1174
|
4.3
|
38.2
|
1.0
|
CG
|
A:HIS220
|
4.4
|
8.1
|
1.0
|
CG
|
A:GLU217
|
4.4
|
5.5
|
1.0
|
HA
|
A:ASP257
|
4.4
|
11.0
|
1.0
|
CB
|
A:ASP257
|
4.5
|
5.2
|
1.0
|
HB2
|
A:ASP255
|
4.5
|
7.4
|
1.0
|
HG2
|
A:GLU217
|
4.5
|
6.6
|
1.0
|
ND1
|
A:HIS220
|
4.7
|
7.9
|
1.0
|
DZ1
|
A:LYS183
|
4.7
|
19.5
|
1.0
|
D1
|
A:DOD1116
|
4.8
|
52.0
|
1.0
|
CO
|
A:CO391
|
4.8
|
16.8
|
1.0
|
NZ
|
A:LYS183
|
4.8
|
16.3
|
1.0
|
OD2
|
A:ASP287
|
4.8
|
17.7
|
1.0
|
HA3
|
A:GLY219
|
4.9
|
9.7
|
1.0
|
D
|
A:HIS220
|
4.9
|
11.2
|
0.1
|
H
|
A:HIS220
|
4.9
|
11.2
|
0.9
|
HB2
|
A:ASP257
|
4.9
|
6.3
|
1.0
|
CA
|
A:ASP257
|
4.9
|
9.2
|
1.0
|
H
|
A:ASP257
|
4.9
|
12.3
|
0.2
|
D
|
A:ASP257
|
4.9
|
12.3
|
0.8
|
HA
|
A:ASP255
|
4.9
|
8.1
|
1.0
|
D1
|
A:DOD1021
|
4.9
|
10.9
|
1.0
|
CE
|
A:LYS183
|
5.0
|
13.4
|
1.0
|
HB3
|
A:GLU217
|
5.0
|
5.3
|
1.0
|
|
Cobalt binding site 2 out
of 2 in 2gve
Go back to
Cobalt Binding Sites List in 2gve
Cobalt binding site 2 out
of 2 in the Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co391
b:16.8
occ:1.00
|
OE1
|
A:GLU217
|
2.0
|
7.1
|
1.0
|
OE2
|
A:GLU181
|
2.0
|
15.0
|
1.0
|
OD2
|
A:ASP287
|
2.1
|
17.7
|
1.0
|
D1
|
A:DOD1116
|
2.2
|
52.0
|
1.0
|
D2
|
A:DOD1218
|
2.2
|
13.2
|
1.0
|
O
|
A:DOD1218
|
2.2
|
8.8
|
1.0
|
O
|
A:DOD1116
|
2.5
|
34.6
|
1.0
|
OD2
|
A:ASP245
|
2.5
|
9.7
|
1.0
|
D1
|
A:DOD1218
|
2.5
|
13.2
|
1.0
|
CD
|
A:GLU181
|
2.9
|
15.1
|
1.0
|
D1
|
A:DOD1018
|
3.0
|
15.0
|
1.0
|
CG
|
A:ASP287
|
3.1
|
18.4
|
1.0
|
OE1
|
A:GLU181
|
3.2
|
16.5
|
1.0
|
CD
|
A:GLU217
|
3.2
|
8.5
|
1.0
|
D2
|
A:DOD1116
|
3.3
|
52.0
|
1.0
|
HB3
|
A:ASP287
|
3.4
|
15.4
|
1.0
|
D1
|
A:DOD1240
|
3.5
|
50.3
|
1.0
|
CG
|
A:ASP245
|
3.5
|
11.2
|
1.0
|
HB2
|
A:ASP287
|
3.6
|
15.4
|
1.0
|
HB2
|
A:GLU217
|
3.6
|
5.3
|
1.0
|
HE1
|
A:HIS220
|
3.6
|
11.5
|
1.0
|
O
|
A:DOD1018
|
3.6
|
10.0
|
1.0
|
CB
|
A:ASP287
|
3.6
|
12.9
|
1.0
|
HB3
|
A:ASP245
|
3.6
|
8.7
|
1.0
|
D2
|
A:DOD1240
|
3.7
|
50.3
|
1.0
|
HG3
|
A:GLU217
|
3.8
|
6.6
|
1.0
|
HB2
|
A:ASP245
|
3.8
|
8.7
|
1.0
|
CB
|
A:ASP245
|
3.9
|
7.2
|
1.0
|
CG
|
A:GLU217
|
3.9
|
5.5
|
1.0
|
CE1
|
A:HIS220
|
4.0
|
9.6
|
1.0
|
O
|
A:DOD1240
|
4.0
|
33.5
|
1.0
|
OE2
|
A:GLU217
|
4.1
|
5.9
|
1.0
|
HD21
|
A:ASN215
|
4.2
|
24.1
|
0.1
|
DD21
|
A:ASN215
|
4.2
|
24.1
|
0.9
|
D2
|
A:DOD1018
|
4.2
|
15.0
|
1.0
|
CB
|
A:GLU217
|
4.2
|
4.4
|
1.0
|
OD1
|
A:ASP287
|
4.2
|
14.1
|
1.0
|
CG
|
A:GLU181
|
4.3
|
10.2
|
1.0
|
DE2
|
A:HIS220
|
4.3
|
9.5
|
0.4
|
NE2
|
A:HIS220
|
4.4
|
7.9
|
1.0
|
HG2
|
A:GLU181
|
4.5
|
12.2
|
1.0
|
D1
|
A:DOD1022
|
4.5
|
5.8
|
0.5
|
HG3
|
A:GLU181
|
4.5
|
12.2
|
1.0
|
HB3
|
A:GLU217
|
4.7
|
5.3
|
1.0
|
D1
|
A:DOD1174
|
4.7
|
38.2
|
1.0
|
HZ2
|
A:TRP16
|
4.7
|
16.8
|
1.0
|
OD1
|
A:ASP245
|
4.7
|
10.3
|
1.0
|
ND1
|
A:HIS220
|
4.8
|
7.9
|
1.0
|
CO
|
A:CO390
|
4.8
|
11.6
|
1.0
|
ND2
|
A:ASN215
|
4.8
|
20.1
|
1.0
|
HG2
|
A:GLU217
|
4.8
|
6.6
|
1.0
|
HD22
|
A:ASN215
|
5.0
|
24.1
|
0.2
|
DD22
|
A:ASN215
|
5.0
|
24.1
|
0.8
|
|
Reference:
A.K.Katz,
X.Li,
H.L.Carrell,
B.L.Hanson,
P.Langan,
L.Coates,
B.P.Schoenborn,
J.P.Glusker,
G.J.Bunick.
Locating Active-Site Hydrogen Atoms in D-Xylose Isomerase: Time-of-Flight Neutron Diffraction. Proc.Natl.Acad.Sci.Usa V. 103 8342 2006.
ISSN: ISSN 0027-8424
PubMed: 16707576
DOI: 10.1073/PNAS.0602598103
Page generated: Tue Jul 30 15:14:42 2024
|