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Magnesium 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:

Nickel (Ni) 2 atoms
Iron (Fe) 24 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Hydrogenase-2 Chemically Reduced Structure (pdb code 6ehs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E. Coli Hydrogenase-2 Chemically Reduced Structure, PDB code: 6ehs:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ehs

Go back to Magnesium Binding Sites List in 6ehs
Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg603

b:9.2
occ:1.00
O L:HOH732 2.1 15.1 1.0
OE2 L:GLU42 2.1 12.5 1.0
O L:HOH720 2.1 12.7 1.0
O L:ALA498 2.1 14.7 1.0
O L:HOH737 2.1 13.0 1.0
NE2 L:HIS552 2.2 12.1 1.0
CD L:GLU42 3.1 13.4 1.0
CE1 L:HIS552 3.1 12.7 1.0
CD2 L:HIS552 3.2 12.0 1.0
C L:ALA498 3.3 12.2 1.0
OE1 L:GLU42 3.5 14.5 1.0
N L:ALA498 3.7 11.5 1.0
CA L:ALA498 4.0 11.5 1.0
OE1 L:GLN497 4.0 17.4 1.0
OE2 L:GLU329 4.1 17.3 1.0
OE1 L:GLU329 4.2 20.7 1.0
O L:HOH788 4.2 14.1 1.0
O L:HOH924 4.3 12.3 1.0
ND1 L:HIS552 4.3 11.8 1.0
NZ L:LYS366 4.3 16.0 1.0
CG L:HIS552 4.3 11.5 1.0
CB L:ALA498 4.4 13.1 1.0
N L:VAL499 4.4 12.5 1.0
CG L:GLU42 4.5 14.1 1.0
CD L:LYS366 4.5 15.5 1.0
CD L:GLU329 4.6 17.2 1.0
C L:GLN497 4.7 12.7 1.0
CA L:VAL499 4.7 12.8 1.0
CE L:LYS366 4.7 14.9 1.0
CA L:GLN497 4.9 13.3 1.0

Magnesium binding site 2 out of 2 in 6ehs

Go back to Magnesium Binding Sites List in 6ehs
Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:11.5
occ:1.00
O M:HOH713 2.1 17.0 1.0
O M:HOH758 2.1 16.2 1.0
OE2 M:GLU42 2.1 15.1 1.0
O M:ALA498 2.1 15.0 1.0
O M:HOH733 2.1 16.2 1.0
NE2 M:HIS552 2.2 14.7 1.0
CE1 M:HIS552 3.1 12.9 1.0
CD M:GLU42 3.1 16.3 1.0
CD2 M:HIS552 3.3 15.0 1.0
C M:ALA498 3.3 13.8 1.0
OE1 M:GLU42 3.5 16.6 1.0
N M:ALA498 3.8 14.3 1.0
OE1 M:GLN497 4.0 20.4 1.0
CA M:ALA498 4.0 13.9 1.0
OE2 M:GLU329 4.1 21.1 1.0
OE1 M:GLU329 4.2 21.8 1.0
O M:HOH782 4.2 14.8 1.0
ND1 M:HIS552 4.2 12.9 1.0
O M:HOH894 4.3 14.3 1.0
NZ M:LYS366 4.3 17.5 1.0
CG M:HIS552 4.4 13.6 1.0
N M:VAL499 4.4 14.3 1.0
CB M:ALA498 4.4 14.1 1.0
CG M:GLU42 4.5 15.6 1.0
CD M:LYS366 4.6 18.2 1.0
CD M:GLU329 4.6 20.0 1.0
CA M:VAL499 4.7 14.1 1.0
C M:GLN497 4.7 14.1 1.0
CE M:LYS366 4.7 18.3 1.0
CA M:GLN497 4.9 13.5 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: Mon Sep 30 23:58:22 2024

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