Cobalt in PDB 5vej: High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase
Protein crystallography data
The structure of High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase, PDB code: 5vej
was solved by
C.Selleck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.74 /
1.30
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.072,
109.072,
62.790,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13.1 /
14.4
|
Other elements in 5vej:
The structure of High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase
(pdb code 5vej). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the
High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase, PDB code: 5vej:
Jump to Cobalt binding site number:
1;
2;
Cobalt binding site 1 out
of 2 in 5vej
Go back to
Cobalt Binding Sites List in 5vej
Cobalt binding site 1 out
of 2 in the High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase
![](/pictures/CO/pdb/ve/5vej-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/ve/5vej-CO-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co403
b:10.2
occ:0.85
|
HD1
|
A:HIS201
|
1.3
|
15.3
|
1.0
|
OQ1
|
A:KCX169
|
2.0
|
12.6
|
1.0
|
NE2
|
A:HIS230
|
2.0
|
11.5
|
1.0
|
ND1
|
A:HIS201
|
2.1
|
12.8
|
1.0
|
F
|
A:F405
|
2.1
|
15.6
|
0.9
|
O
|
A:HOH738
|
2.3
|
15.8
|
1.0
|
CE1
|
A:HIS201
|
3.0
|
14.1
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
12.8
|
1.0
|
CX
|
A:KCX169
|
3.0
|
13.2
|
1.0
|
CD2
|
A:HIS230
|
3.1
|
10.8
|
1.0
|
HB2
|
A:HIS201
|
3.1
|
14.5
|
1.0
|
HE1
|
A:HIS201
|
3.1
|
16.9
|
1.0
|
HE1
|
A:TRP131
|
3.2
|
16.5
|
1.0
|
HE1
|
A:HIS230
|
3.2
|
15.4
|
1.0
|
CG
|
A:HIS201
|
3.2
|
12.3
|
1.0
|
HD2
|
A:HIS230
|
3.2
|
12.9
|
1.0
|
OQ2
|
A:KCX169
|
3.4
|
11.6
|
1.0
|
HH21
|
A:ARG254
|
3.6
|
17.3
|
0.7
|
HE1
|
A:HIS55
|
3.6
|
11.7
|
1.0
|
CB
|
A:HIS201
|
3.6
|
12.1
|
1.0
|
CO
|
A:CO404
|
3.7
|
9.8
|
1.0
|
HE2
|
A:HIS55
|
3.8
|
12.0
|
1.0
|
NH2
|
A:ARG254
|
3.8
|
14.4
|
0.7
|
HH22
|
A:ARG254
|
3.9
|
17.3
|
0.7
|
NE1
|
A:TRP131
|
4.0
|
13.7
|
1.0
|
HA
|
A:HIS201
|
4.0
|
13.7
|
1.0
|
ND1
|
A:HIS230
|
4.1
|
12.1
|
1.0
|
NE2
|
A:HIS201
|
4.2
|
15.3
|
1.0
|
CE1
|
A:HIS55
|
4.2
|
9.7
|
1.0
|
CG
|
A:HIS230
|
4.2
|
10.7
|
1.0
|
OD2
|
A:ASP301
|
4.2
|
11.4
|
1.0
|
NE2
|
A:HIS55
|
4.2
|
10.0
|
1.0
|
NZ
|
A:KCX169
|
4.3
|
11.9
|
1.0
|
CD2
|
A:HIS201
|
4.3
|
14.5
|
1.0
|
HE2
|
A:PHE132
|
4.3
|
17.2
|
1.0
|
HD1
|
A:TRP131
|
4.3
|
15.5
|
1.0
|
HB3
|
A:HIS201
|
4.4
|
14.5
|
1.0
|
CA
|
A:HIS201
|
4.4
|
11.4
|
1.0
|
O
|
A:HOH774
|
4.5
|
43.7
|
1.0
|
CZ
|
A:ARG254
|
4.5
|
11.4
|
0.7
|
CD1
|
A:TRP131
|
4.6
|
12.9
|
1.0
|
HE
|
A:ARG254
|
4.7
|
13.6
|
0.7
|
CE
|
A:KCX169
|
4.7
|
12.2
|
1.0
|
HD1
|
A:HIS230
|
4.9
|
14.5
|
1.0
|
NE
|
A:ARG254
|
4.9
|
11.3
|
0.7
|
O
|
A:HOH692
|
5.0
|
18.8
|
0.8
|
OD1
|
A:ASP301
|
5.0
|
10.5
|
1.0
|
CG
|
A:ASP301
|
5.0
|
10.6
|
1.0
|
O
|
A:HOH818
|
5.0
|
64.8
|
1.0
|
|
Cobalt binding site 2 out
of 2 in 5vej
Go back to
Cobalt Binding Sites List in 5vej
Cobalt binding site 2 out
of 2 in the High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase
![](/pictures/CO/pdb/ve/5vej-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/ve/5vej-CO-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of High Resolution Crystal Structure of A Fluoride-Inhibited Organo- Phosphate-Degrading Metallohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co404
b:9.8
occ:1.00
|
HE2
|
A:HIS55
|
1.3
|
12.0
|
1.0
|
F
|
A:F405
|
2.0
|
15.6
|
0.9
|
NE2
|
A:HIS57
|
2.1
|
9.8
|
1.0
|
OQ2
|
A:KCX169
|
2.1
|
11.6
|
1.0
|
OD1
|
A:ASP301
|
2.1
|
10.5
|
1.0
|
NE2
|
A:HIS55
|
2.2
|
10.0
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
9.6
|
1.0
|
CG
|
A:ASP301
|
3.0
|
10.6
|
1.0
|
CX
|
A:KCX169
|
3.0
|
13.2
|
1.0
|
CD2
|
A:HIS55
|
3.1
|
9.8
|
1.0
|
CD2
|
A:HIS57
|
3.1
|
9.0
|
1.0
|
HD2
|
A:HIS55
|
3.2
|
11.7
|
1.0
|
HE1
|
A:HIS57
|
3.2
|
11.5
|
1.0
|
CE1
|
A:HIS55
|
3.2
|
9.7
|
1.0
|
HD2
|
A:HIS57
|
3.3
|
10.8
|
1.0
|
OD2
|
A:ASP301
|
3.3
|
11.4
|
1.0
|
HE1
|
A:HIS55
|
3.4
|
11.7
|
1.0
|
HE1
|
A:HIS230
|
3.5
|
15.4
|
1.0
|
OQ1
|
A:KCX169
|
3.5
|
12.6
|
1.0
|
HG23
|
A:VAL101
|
3.7
|
12.7
|
1.0
|
CO
|
A:CO403
|
3.7
|
10.2
|
0.8
|
HG21
|
A:VAL101
|
4.0
|
12.7
|
1.0
|
NZ
|
A:KCX169
|
4.2
|
11.9
|
1.0
|
CG2
|
A:VAL101
|
4.2
|
10.6
|
1.0
|
ND1
|
A:HIS57
|
4.2
|
10.1
|
1.0
|
CE1
|
A:HIS230
|
4.2
|
12.8
|
1.0
|
HA
|
A:ASP301
|
4.2
|
11.6
|
1.0
|
CG
|
A:HIS57
|
4.2
|
9.4
|
1.0
|
HG22
|
A:VAL101
|
4.2
|
12.7
|
1.0
|
CG
|
A:HIS55
|
4.3
|
9.2
|
1.0
|
ND1
|
A:HIS55
|
4.3
|
10.1
|
1.0
|
O
|
A:HOH738
|
4.3
|
15.8
|
1.0
|
CB
|
A:ASP301
|
4.4
|
10.2
|
1.0
|
NE2
|
A:HIS230
|
4.4
|
11.5
|
1.0
|
HB2
|
A:ASP301
|
4.6
|
12.3
|
1.0
|
O
|
A:HOH692
|
4.6
|
18.8
|
0.8
|
HH21
|
A:ARG254
|
4.8
|
17.3
|
0.7
|
CA
|
A:ASP301
|
4.8
|
9.6
|
1.0
|
HD13
|
A:ILE106
|
4.9
|
14.6
|
1.0
|
HD1
|
A:HIS201
|
4.9
|
15.3
|
1.0
|
HD1
|
A:HIS57
|
4.9
|
12.2
|
1.0
|
|
Reference:
C.Selleck,
L.W.Guddat,
D.L.Ollis,
G.Schenk,
M.M.Pedroso.
High Resolution Crystal Structure of A Fluoride-Inhibited Organophosphate-Degrading Metallohydrolase. J. Inorg. Biochem. V. 177 287 2017.
ISSN: ISSN 1873-3344
PubMed: 28673485
DOI: 10.1016/J.JINORGBIO.2017.06.013
Page generated: Tue Jul 30 18:16:13 2024
|