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Nickel in PDB 2yiv: Ni,Fe-Codh with N-Butylisocyanate State

Enzymatic activity of Ni,Fe-Codh with N-Butylisocyanate State

All present enzymatic activity of Ni,Fe-Codh with N-Butylisocyanate State:
1.2.99.2;

Protein crystallography data

The structure of Ni,Fe-Codh with N-Butylisocyanate State, PDB code: 2yiv was solved by J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.900 / 1.28
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.700, 75.240, 71.220, 90.00, 111.38, 90.00
R / Rfree (%) 11.23 / 14.33

Nickel Binding Sites:

The binding sites of Nickel atom in the Ni,Fe-Codh with N-Butylisocyanate State (pdb code 2yiv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Ni,Fe-Codh with N-Butylisocyanate State, PDB code: 2yiv:

Nickel binding site 1 out of 1 in 2yiv

Go back to Nickel Binding Sites List in 2yiv
Nickel binding site 1 out of 1 in the Ni,Fe-Codh with N-Butylisocyanate State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni,Fe-Codh with N-Butylisocyanate State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ni5002

b:9.4
occ:0.73
NI X:WCC5002 0.0 9.4 0.7
C X:YIV5003 2.0 12.8 0.8
SG X:CYS526 2.1 10.0 1.0
S3 X:WCC5002 2.2 12.2 1.0
FE X:FE5004 2.2 25.6 0.3
S1 X:WCC5002 2.3 11.1 1.0
H1A X:YIV5003 2.7 17.3 0.8
O1 X:YIV5003 2.8 13.2 0.8
FE4 X:WCC5002 2.9 9.0 0.9
N X:YIV5003 2.9 12.8 0.8
O X:HOH5100 3.1 14.6 0.9
FE X:FE5004 3.1 8.7 0.7
C1 X:YIV5003 3.2 14.4 0.8
CB X:CYS526 3.3 8.4 1.0
HB3 X:CYS526 3.3 10.1 1.0
HB2 X:CYS526 3.5 10.1 1.0
FE1 X:WCC5002 3.6 8.9 0.9
HA2 X:GLY445 3.6 11.2 1.0
H1 X:YIV5003 3.7 17.3 0.8
FE3 X:WCC5002 3.8 9.3 0.9
S4 X:WCC5002 4.0 12.1 1.0
HZ3 X:LYS563 4.0 12.0 1.0
SG X:CYS295 4.4 8.2 0.6
HA3 X:GLY475 4.4 9.3 1.0
O X:HOH2691 4.4 7.9 1.0
SG X:CYS295 4.5 10.0 0.4
CA X:GLY445 4.5 9.3 1.0
H X:CYS476 4.5 9.1 1.0
C2 X:YIV5003 4.5 15.8 0.8
H2A X:YIV5003 4.6 18.9 0.8
HE3 X:LYS563 4.6 10.5 1.0
SG X:CYS446 4.6 8.4 1.0
CA X:CYS526 4.6 8.0 1.0
HB2 X:LYS563 4.7 9.0 1.0
S2 X:WCC5002 4.7 12.0 1.0
HD13 X:ILE567 4.7 17.5 0.6
HA X:CYS526 4.7 9.6 1.0
HE2 X:HIS93 4.7 24.2 0.3
H X:GLY445 4.7 12.5 1.0
NZ X:LYS563 4.8 10.0 1.0
HZ2 X:LYS563 4.8 12.0 1.0
H X:CYS526 4.8 8.1 1.0
HB3 X:LYS563 4.8 9.0 1.0
C X:GLY445 4.9 8.7 1.0
NE2 X:HIS261 4.9 18.8 1.0
HB3 X:ALA564 4.9 11.3 1.0

Reference:

J.H.Jeoung, H.Dobbek. N-Butyl Isocyanide Oxidation at the [NIFE4S4OH(X)] Cluster of Co Dehydrogenase. J.Biol.Inorg.Chem. V. 17 167 2012.
ISSN: ISSN 0949-8257
PubMed: 21904889
DOI: 10.1007/S00775-011-0839-Y
Page generated: Fri Sep 25 08:18:26 2020
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