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Nickel in PDB 6ehq: E. Coli Hydrogenase-2 (As Isolated Form).

Enzymatic activity of E. Coli Hydrogenase-2 (As Isolated Form).

All present enzymatic activity of E. Coli Hydrogenase-2 (As Isolated Form).:
1.12.99.6;

Protein crystallography data

The structure of E. Coli Hydrogenase-2 (As Isolated Form)., PDB code: 6ehq was solved by S.B.Carr, S.E.Beaton, R.M.Evans, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.064, 100.090, 168.135, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19

Other elements in 6ehq:

The structure of E. Coli Hydrogenase-2 (As Isolated Form). also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 26 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the E. Coli Hydrogenase-2 (As Isolated Form). (pdb code 6ehq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the E. Coli Hydrogenase-2 (As Isolated Form)., PDB code: 6ehq:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6ehq

Go back to Nickel Binding Sites List in 6ehq
Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-2 (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 E. Coli Hydrogenase-2 (As Isolated Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni602

b:26.6
occ:1.00
O L:HOH868 1.8 23.6 1.0
SG L:CYS61 2.2 26.6 1.0
SG L:CYS546 2.2 26.5 1.0
SG L:CYS549 2.5 18.2 1.0
SG L:CYS64 2.5 24.0 1.0
FE L:FCO601 2.9 22.0 1.0
CB L:CYS61 3.0 26.5 1.0
CB L:CYS546 3.3 24.0 1.0
CB L:CYS549 3.5 19.7 1.0
CB L:CYS64 3.6 25.4 1.0
N L:CYS64 3.8 27.4 1.0
C1 L:FCO601 3.9 22.6 1.0
C2 L:FCO601 4.2 20.7 1.0
CA L:CYS64 4.3 26.2 1.0
N L:CYS549 4.4 20.5 1.0
CA L:CYS61 4.4 25.8 1.0
CB L:VAL63 4.5 28.4 1.0
C3 L:FCO601 4.5 22.1 1.0
CA L:CYS549 4.5 19.9 1.0
NH1 L:ARG479 4.6 24.3 1.0
CA L:CYS546 4.7 23.7 1.0
N1 L:FCO601 4.8 22.8 1.0
C L:VAL63 4.8 27.8 1.0
CG L:GLU14 4.9 33.4 1.0
N L:VAL63 4.9 27.7 1.0
CZ L:ARG479 4.9 23.2 1.0
CD L:ARG479 5.0 21.8 1.0
CA L:VAL63 5.0 28.3 1.0
CG1 L:VAL63 5.0 29.0 1.0

Nickel binding site 2 out of 2 in 6ehq

Go back to Nickel Binding Sites List in 6ehq
Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-2 (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 E. Coli Hydrogenase-2 (As Isolated Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:29.0
occ:1.00
O M:HOH831 1.9 23.1 1.0
SG M:CYS546 2.2 31.2 1.0
SG M:CYS61 2.2 29.8 1.0
SG M:CYS549 2.5 23.0 1.0
SG M:CYS64 2.5 25.0 1.0
FE M:FCO601 2.9 23.0 1.0
CB M:CYS61 3.0 29.5 1.0
CB M:CYS546 3.2 28.3 1.0
CB M:CYS549 3.5 22.7 1.0
CB M:CYS64 3.7 27.1 1.0
N M:CYS64 3.8 28.6 1.0
C1 M:FCO601 3.9 23.9 1.0
C2 M:FCO601 4.1 21.4 1.0
CA M:CYS64 4.3 28.5 1.0
N M:CYS549 4.4 22.6 1.0
C3 M:FCO601 4.4 22.5 1.0
CA M:CYS549 4.5 22.8 1.0
CA M:CYS61 4.5 29.2 1.0
CB M:VAL63 4.5 29.9 1.0
NH1 M:ARG479 4.5 23.3 1.0
CA M:CYS546 4.6 27.0 1.0
N1 M:FCO601 4.8 23.6 1.0
C M:VAL63 4.9 29.3 1.0
CG M:GLU14 4.9 36.3 1.0
CZ M:ARG479 4.9 23.8 1.0
CD M:ARG479 5.0 24.7 1.0
N M:VAL63 5.0 29.5 1.0
CG1 M:VAL63 5.0 29.9 1.0

Reference:

S.E.Beaton, R.M.Evans, A.J.Finney, C.M.Lamont, F.A.Armstrong, F.Sargent, S.B.Carr. The Structure of Hydrogenase-2 Fromescherichia Coli: Implications For H2-Driven Proton Pumping. Biochem. J. V. 475 1353 2018.
ISSN: ESSN 1470-8728
PubMed: 29555844
DOI: 10.1042/BCJ20180053
Page generated: Thu Oct 10 08:23:29 2024

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