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Nickel in PDB 3uqy: H2-Reduced Structure of E. Coli Hydrogenase-1

Enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1

All present enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1:
1.12.99.6;

Protein crystallography data

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.710, 97.400, 183.730, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 16

Nickel Binding Sites:

The binding sites of Nickel atom in the H2-Reduced Structure of E. Coli Hydrogenase-1 (pdb code 3uqy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3uqy

Go back to Nickel Binding Sites List in 3uqy
Nickel binding site 1 out of 2 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni602

b:9.0
occ:1.00
SG L:CYS576 2.2 10.2 1.0
SG L:CYS76 2.3 8.3 1.0
SG L:CYS79 2.3 6.7 1.0
SG L:CYS579 2.5 8.1 1.0
FE L:FCO601 2.6 6.8 1.0
CB L:CYS76 3.1 7.4 1.0
CB L:CYS576 3.3 7.8 1.0
CB L:CYS79 3.4 7.5 1.0
CB L:CYS579 3.5 7.4 1.0
C1 L:FCO601 3.7 5.8 1.0
C2 L:FCO601 3.7 6.4 1.0
N L:CYS79 3.7 6.7 1.0
CA L:CYS79 4.1 6.3 1.0
C3 L:FCO601 4.2 8.0 1.0
NH1 L:ARG509 4.2 7.9 1.0
CA L:CYS76 4.5 6.8 1.0
CA L:CYS579 4.6 5.7 1.0
N L:CYS579 4.6 5.7 1.0
N1 L:FCO601 4.6 6.8 1.0
N2 L:FCO601 4.6 8.9 1.0
CB L:VAL78 4.6 6.0 1.0
CZ L:ARG509 4.7 7.1 1.0
CA L:CYS576 4.7 6.3 1.0
CD L:ARG509 4.7 7.0 1.0
C L:VAL78 4.8 8.2 1.0
NE L:ARG509 4.8 7.1 1.0

Nickel binding site 2 out of 2 in 3uqy

Go back to Nickel Binding Sites List in 3uqy
Nickel binding site 2 out of 2 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:9.3
occ:1.00
SG M:CYS576 2.1 10.5 1.0
SG M:CYS79 2.3 7.3 1.0
SG M:CYS76 2.3 8.3 1.0
SG M:CYS579 2.5 7.5 1.0
FE M:FCO601 2.6 7.0 1.0
CB M:CYS76 3.1 7.4 1.0
CB M:CYS576 3.3 7.8 1.0
CB M:CYS79 3.4 6.6 1.0
CB M:CYS579 3.5 5.6 1.0
C1 M:FCO601 3.7 6.1 1.0
C2 M:FCO601 3.7 5.1 1.0
N M:CYS79 3.7 6.9 1.0
C3 M:FCO601 4.2 7.3 1.0
CA M:CYS79 4.2 7.5 1.0
NH1 M:ARG509 4.2 7.5 1.0
CA M:CYS76 4.5 6.1 1.0
CA M:CYS579 4.6 6.5 1.0
N1 M:FCO601 4.6 7.8 1.0
N M:CYS579 4.6 6.1 1.0
N2 M:FCO601 4.6 6.7 1.0
CD M:ARG509 4.6 6.6 1.0
CA M:CYS576 4.7 7.9 1.0
CZ M:ARG509 4.7 6.9 1.0
CB M:VAL78 4.7 7.0 1.0
NE M:ARG509 4.8 6.9 1.0
C M:VAL78 4.8 7.8 1.0

Reference:

A.Volbeda, P.Amara, C.Darnault, J.M.Mouesca, A.Parkin, M.M.Roessler, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Crystallographic and Computational Studies of the O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli. Proc.Natl.Acad.Sci.Usa V. 109 5305 2012.
ISSN: ISSN 0027-8424
PubMed: 22431599
DOI: 10.1073/PNAS.1119806109
Page generated: Fri Sep 25 08:36:09 2020
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