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Magnesium in PDB 6fpo: High Resolution Structure of Native Hydrogenase (Hyd-1)

Enzymatic activity of High Resolution Structure of Native Hydrogenase (Hyd-1)

All present enzymatic activity of High Resolution Structure of Native Hydrogenase (Hyd-1):
1.12.99.6;

Protein crystallography data

The structure of High Resolution Structure of Native Hydrogenase (Hyd-1), PDB code: 6fpo was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.55 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.786, 97.733, 183.102, 90.00, 90.00, 90.00
R / Rfree (%) 11.5 / 13.4

Other elements in 6fpo:

The structure of High Resolution Structure of Native Hydrogenase (Hyd-1) also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High Resolution Structure of Native Hydrogenase (Hyd-1) (pdb code 6fpo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High Resolution Structure of Native Hydrogenase (Hyd-1), PDB code: 6fpo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6fpo

Go back to Magnesium Binding Sites List in 6fpo
Magnesium binding site 1 out of 2 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg603

b:6.4
occ:1.00
O L:HOH754 2.1 7.5 1.0
O L:HOH735 2.1 7.5 1.0
O L:CYS528 2.1 7.0 1.0
O L:HOH740 2.1 7.4 1.0
OE1 L:GLU57 2.1 7.1 1.0
NE2 L:HIS582 2.2 6.5 1.0
CD L:GLU57 3.1 7.1 1.0
CE1 L:HIS582 3.1 6.9 1.0
CD2 L:HIS582 3.2 6.7 1.0
C L:CYS528 3.3 6.9 1.0
OE2 L:GLU57 3.4 7.5 1.0
N L:CYS528 3.8 6.7 1.0
CA L:CYS528 4.0 6.9 1.0
OE2 L:GLU347 4.1 8.4 1.0
OE1 L:GLN527 4.2 9.3 1.0
OE1 L:GLU347 4.2 8.5 1.0
NZ L:LYS399 4.2 7.8 1.0
O L:HOH1068 4.2 7.7 1.0
ND1 L:HIS582 4.3 7.0 1.0
O L:HOH805 4.3 7.6 1.0
CB L:CYS528 4.3 7.3 1.0
CG L:HIS582 4.4 6.6 1.0
N L:VAL529 4.4 7.0 1.0
CG L:GLU57 4.4 7.0 1.0
CD L:LYS399 4.5 7.7 1.0
CD L:GLU347 4.5 7.7 1.0
CA L:VAL529 4.7 6.9 1.0
CE L:LYS399 4.7 8.1 1.0
C L:GLN527 4.9 7.0 1.0

Magnesium binding site 2 out of 2 in 6fpo

Go back to Magnesium Binding Sites List in 6fpo
Magnesium binding site 2 out of 2 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:6.5
occ:1.00
O M:HOH729 2.1 7.5 1.0
O M:HOH727 2.1 7.5 1.0
O M:CYS528 2.1 7.1 1.0
O M:HOH731 2.1 7.6 1.0
OE1 M:GLU57 2.1 6.9 1.0
NE2 M:HIS582 2.2 6.8 1.0
CD M:GLU57 3.1 6.9 1.0
CE1 M:HIS582 3.1 6.8 1.0
CD2 M:HIS582 3.2 7.0 1.0
C M:CYS528 3.3 7.0 1.0
OE2 M:GLU57 3.4 7.4 1.0
N M:CYS528 3.8 6.8 1.0
CA M:CYS528 4.0 6.8 1.0
OE2 M:GLU347 4.1 8.0 1.0
OE1 M:GLN527 4.2 9.5 1.0
OE1 M:GLU347 4.2 7.9 1.0
NZ M:LYS399 4.2 8.0 1.0
O M:HOH1052 4.3 7.2 1.0
O M:HOH797 4.3 7.8 1.0
ND1 M:HIS582 4.3 6.9 1.0
CB M:CYS528 4.3 7.2 1.0
CG M:HIS582 4.4 6.5 1.0
N M:VAL529 4.4 7.0 1.0
CG M:GLU57 4.4 7.3 1.0
CD M:LYS399 4.5 7.7 1.0
CD M:GLU347 4.6 7.5 1.0
CE M:LYS399 4.6 7.6 1.0
CA M:VAL529 4.7 7.0 1.0
C M:GLN527 4.9 7.2 1.0

Reference:

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Wed Aug 13 06:11:25 2025

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