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Magnesium 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

Other elements in 3uqy:

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 24 atoms
Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3uqy

Go back to Magnesium Binding Sites List in 3uqy
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:6.4
occ:1.00
O L:HOH702 2.0 7.1 1.0
O L:HOH703 2.0 6.9 1.0
O L:HOH701 2.1 6.5 1.0
O L:CYS528 2.1 7.2 1.0
OE1 L:GLU57 2.2 7.1 1.0
NE2 L:HIS582 2.2 5.9 1.0
CD L:GLU57 3.1 6.2 1.0
CE1 L:HIS582 3.1 6.4 1.0
CD2 L:HIS582 3.3 6.8 1.0
C L:CYS528 3.3 7.6 1.0
OE2 L:GLU57 3.4 7.6 1.0
N L:CYS528 3.8 6.2 1.0
CA L:CYS528 4.0 6.2 1.0
OE2 L:GLU347 4.1 8.5 1.0
OE1 L:GLU347 4.1 9.5 1.0
OE1 L:GLN527 4.2 10.0 1.0
NZ L:LYS399 4.2 7.5 1.0
O L:HOH723 4.2 6.4 1.0
ND1 L:HIS582 4.3 6.9 1.0
O L:HOH716 4.3 6.9 1.0
CB L:CYS528 4.3 7.2 1.0
N L:VAL529 4.4 6.9 1.0
CG L:HIS582 4.4 5.4 1.0
CG L:GLU57 4.4 6.0 1.0
CD L:LYS399 4.5 6.7 1.0
CD L:GLU347 4.5 9.3 1.0
CA L:VAL529 4.6 6.2 1.0
CE L:LYS399 4.7 7.2 1.0
C L:GLN527 4.9 6.8 1.0
CG2 L:VAL529 5.0 8.1 1.0

Magnesium binding site 2 out of 2 in 3uqy

Go back to Magnesium Binding Sites List in 3uqy
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:6.1
occ:1.00
O M:HOH703 2.0 8.0 1.0
O M:HOH704 2.1 8.9 1.0
O M:HOH702 2.1 7.3 1.0
O M:CYS528 2.1 7.8 1.0
OE1 M:GLU57 2.2 7.2 1.0
NE2 M:HIS582 2.2 6.5 1.0
CD M:GLU57 3.1 5.9 1.0
CE1 M:HIS582 3.2 6.1 1.0
CD2 M:HIS582 3.3 6.5 1.0
C M:CYS528 3.3 6.7 1.0
OE2 M:GLU57 3.4 8.6 1.0
N M:CYS528 3.8 6.8 1.0
CA M:CYS528 4.0 6.6 1.0
OE2 M:GLU347 4.1 10.0 1.0
OE1 M:GLN527 4.2 8.9 1.0
OE1 M:GLU347 4.2 9.2 1.0
NZ M:LYS399 4.2 6.8 1.0
O M:HOH725 4.3 7.3 1.0
O M:HOH718 4.3 7.7 1.0
ND1 M:HIS582 4.3 7.5 1.0
CB M:CYS528 4.3 8.0 1.0
N M:VAL529 4.4 6.1 1.0
CG M:HIS582 4.4 7.3 1.0
CG M:GLU57 4.5 6.4 1.0
CD M:LYS399 4.5 7.2 1.0
CD M:GLU347 4.6 8.3 1.0
CE M:LYS399 4.7 6.9 1.0
CA M:VAL529 4.7 6.2 1.0
C M:GLN527 4.9 6.9 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: Thu Aug 15 12:38:09 2024

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