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Nickel in PDB 6ehs: E. Coli Hydrogenase-2 Chemically Reduced Structure

Enzymatic activity of E. Coli Hydrogenase-2 Chemically Reduced Structure

All present enzymatic activity of E. Coli Hydrogenase-2 Chemically Reduced Structure:
1.12.99.6;

Protein crystallography data

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

Resolution Low / High (Å) 86.08 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.885, 100.065, 168.801, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 16.3

Other elements in 6ehs:

The structure of E. Coli Hydrogenase-2 Chemically Reduced Structure also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the E. Coli Hydrogenase-2 Chemically Reduced Structure (pdb code 6ehs). 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 Chemically Reduced Structure, PDB code: 6ehs:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6ehs

Go back to Nickel Binding Sites List in 6ehs
Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni602

b:17.8
occ:1.00
O L:HOH1014 1.8 23.3 1.0
SG L:CSO546 2.1 23.0 1.0
SG L:CYS61 2.2 16.8 1.0
SG L:CYS549 2.4 13.0 1.0
SG L:CYS64 2.5 14.3 1.0
FE L:FCO601 2.8 12.2 1.0
CB L:CYS61 3.0 14.7 1.0
CB L:CSO546 3.2 17.4 1.0
OD L:CSO546 3.3 25.6 0.5
CB L:CYS549 3.5 10.8 1.0
CB L:CYS64 3.6 14.8 1.0
C1 L:FCO601 3.8 10.9 1.0
N L:CYS64 3.8 19.4 1.0
C2 L:FCO601 4.0 12.5 1.0
CA L:CYS64 4.3 15.2 1.0
N L:CYS549 4.4 12.3 1.0
C3 L:FCO601 4.4 12.8 1.0
CA L:CYS549 4.5 12.1 1.0
CA L:CYS61 4.5 12.6 1.0
CB L:VAL63 4.5 15.0 1.0
CA L:CSO546 4.6 12.2 1.0
NH1 L:ARG479 4.6 13.7 1.0
N1 L:FCO601 4.7 12.1 1.0
C L:VAL63 4.9 16.8 1.0
CD L:ARG479 4.9 12.6 1.0
CZ L:ARG479 4.9 12.8 1.0
NE L:ARG479 4.9 12.2 1.0
CG L:GLU14 5.0 21.9 1.0
N L:VAL63 5.0 15.3 1.0
OE1 L:GLU14 5.0 25.3 1.0

Nickel binding site 2 out of 2 in 6ehs

Go back to Nickel Binding Sites List in 6ehs
Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni602

b:19.9
occ:1.00
O M:HOH976 1.8 24.5 1.0
SG M:CSO546 2.1 26.1 1.0
SG M:CYS61 2.2 18.3 1.0
SG M:CYS549 2.4 14.4 1.0
SG M:CYS64 2.5 15.6 1.0
FE M:FCO601 2.8 13.8 1.0
CB M:CYS61 3.0 17.3 1.0
CB M:CSO546 3.3 19.4 1.0
OD M:CSO546 3.3 25.0 0.5
CB M:CYS549 3.5 12.9 1.0
CB M:CYS64 3.6 19.3 1.0
C1 M:FCO601 3.8 12.4 1.0
N M:CYS64 3.8 17.8 1.0
C2 M:FCO601 4.1 13.2 1.0
CA M:CYS64 4.3 16.4 1.0
N M:CYS549 4.3 13.5 1.0
C3 M:FCO601 4.4 13.8 1.0
CA M:CYS549 4.4 13.7 1.0
CA M:CYS61 4.5 15.6 1.0
CB M:VAL63 4.5 18.4 1.0
CA M:CSO546 4.6 15.1 1.0
NH1 M:ARG479 4.6 14.4 1.0
N1 M:FCO601 4.7 14.1 1.0
C M:VAL63 4.9 18.0 1.0
CD M:ARG479 4.9 14.8 1.0
CG M:GLU14 4.9 24.1 1.0
CZ M:ARG479 4.9 13.6 1.0
NE M:ARG479 5.0 14.3 1.0
N M:VAL63 5.0 15.7 1.0
OE1 M:GLU14 5.0 32.4 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 08:23:37 2024

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