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Nickel in PDB 3use: Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

Enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

All present enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use 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) 29.82 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.930, 97.790, 183.290, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 16.8

Nickel Binding Sites:

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

Nickel binding site 1 out of 2 in 3use

Go back to Nickel Binding Sites List in 3use
Nickel binding site 1 out of 2 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

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

b:11.5
occ:1.00
O L:HOH701 1.9 9.7 1.0
SG L:CYS576 2.2 10.9 1.0
SG L:CYS76 2.2 9.6 1.0
O L:HOH702 2.4 10.3 0.2
SG L:CYS79 2.5 9.2 1.0
SG L:CYS579 2.6 8.6 1.0
FE L:FCO601 2.9 8.7 1.0
CB L:CYS76 3.1 9.4 1.0
CB L:CYS576 3.2 9.6 1.0
CB L:CYS79 3.6 8.0 1.0
CB L:CYS579 3.7 8.1 1.0
N L:CYS79 3.7 8.2 1.0
C1 L:FCO601 4.0 7.8 1.0
C2 L:FCO601 4.1 8.7 1.0
CA L:CYS79 4.2 8.0 1.0
NH1 L:ARG509 4.4 9.5 1.0
C3 L:FCO601 4.4 8.8 1.0
CA L:CYS76 4.5 8.7 1.0
CB L:VAL78 4.5 7.7 1.0
N L:CYS579 4.6 8.7 1.0
CZ L:ARG509 4.6 9.1 1.0
CA L:CYS576 4.6 8.8 1.0
CA L:CYS579 4.6 7.6 1.0
C L:VAL78 4.7 9.2 1.0
NE L:ARG509 4.8 8.9 1.0
CD L:ARG509 4.9 8.0 1.0
N1 L:FCO601 4.9 9.2 1.0
N L:VAL78 4.9 7.9 1.0
CA L:VAL78 4.9 9.1 1.0

Nickel binding site 2 out of 2 in 3use

Go back to Nickel Binding Sites List in 3use
Nickel binding site 2 out of 2 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

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

b:11.7
occ:1.00
O M:HOH701 1.8 9.9 1.0
SG M:CYS576 2.2 10.0 1.0
SG M:CYS76 2.2 12.0 1.0
O M:HOH702 2.4 9.6 0.2
SG M:CYS79 2.4 8.4 1.0
SG M:CYS579 2.7 8.0 1.0
FE M:FCO601 2.9 7.9 1.0
CB M:CYS76 3.1 9.2 1.0
CB M:CYS576 3.2 8.1 1.0
CB M:CYS79 3.6 8.2 1.0
CB M:CYS579 3.7 7.3 1.0
N M:CYS79 3.7 8.2 1.0
C1 M:FCO601 4.0 8.5 1.0
C2 M:FCO601 4.1 7.1 1.0
CA M:CYS79 4.2 9.1 1.0
NH1 M:ARG509 4.3 8.1 1.0
C3 M:FCO601 4.4 8.0 1.0
CA M:CYS76 4.5 6.9 1.0
CZ M:ARG509 4.5 9.0 1.0
CB M:VAL78 4.6 10.5 1.0
CA M:CYS576 4.6 7.7 1.0
N M:CYS579 4.6 6.4 1.0
CA M:CYS579 4.6 6.3 1.0
NE M:ARG509 4.7 6.5 1.0
C M:VAL78 4.7 8.7 1.0
CD M:ARG509 4.8 6.3 1.0
N1 M:FCO601 4.9 8.5 1.0
N M:VAL78 4.9 8.3 1.0
CA M:VAL78 5.0 9.4 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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