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Magnesium in PDB 1h2r: Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution

Enzymatic activity of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution

All present enzymatic activity of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution, PDB code: 1h2r was solved by Y.Higuchi, H.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.440, 126.860, 66.680, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.4

Other elements in 1h2r:

The structure of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Iron (Fe) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution (pdb code 1h2r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution, PDB code: 1h2r:

Magnesium binding site 1 out of 1 in 1h2r

Go back to Magnesium Binding Sites List in 1h2r
Magnesium binding site 1 out of 1 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1005

b:8.9
occ:1.00
 O L:HOH3001 2.1 10.6 1.0
O L:HOH3002 2.1 9.9 1.0
O L:HOH3003 2.1 11.0 1.0
NE2 L:HIS552 2.2 9.8 1.0
OE2 L:GLU62 2.2 10.0 1.0
O L:LEU498 2.2 9.9 1.0
CE1 L:HIS552 3.1 9.6 1.0
CD L:GLU62 3.2 11.5 1.0
CD2 L:HIS552 3.3 9.6 1.0
C L:LEU498 3.4 9.7 1.0
OE1 L:GLU62 3.5 11.3 1.0
N L:LEU498 3.7 11.2 1.0
O L:HOH3210 3.8 69.0 1.0
CA L:LEU498 4.0 10.6 1.0
OE1 L:GLU337 4.1 12.3 1.0
OE1 L:GLN497 4.1 12.2 1.0
OE2 L:GLU337 4.2 12.2 1.0
NZ L:LYS374 4.2 8.4 1.0
ND1 L:HIS552 4.3 11.5 1.0
O L:HOH3004 4.3 9.5 1.0
CB L:LEU498 4.3 10.2 1.0
O L:HOH3005 4.4 10.3 1.0
CG L:HIS552 4.4 9.9 1.0
N L:VAL499 4.5 9.8 1.0
CG L:GLU62 4.5 9.7 1.0
CD L:LYS374 4.6 10.0 1.0
CD L:GLU337 4.6 12.0 1.0
O L:HOH3066 4.7 95.4 1.0
C L:GLN497 4.8 10.4 1.0
CE L:LYS374 4.8 9.1 1.0
CA L:VAL499 4.8 9.7 1.0

Reference:

Y.Higuchi, H.Ogata, K.Miki, N.Yasuoka, T.Yagi. Removal of the Bridging Ligand Atom at the Ni-Fe Active Site of [Nife] Hydrogenase Upon Reduction with H2, As Revealed By X-Ray Structure Analysis at 1.4 A Resolution. Structure Fold.Des. V. 7 549 1999.
ISSN: ISSN 0969-2126
PubMed: 10378274
DOI: 10.1016/S0969-2126(99)80071-9
Page generated: Tue Aug 13 03:52:41 2024

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