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Magnesium in PDB 1ubo: Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1ubo was solved by H.Ogata, Y.Mizoguchi, N.Mizuno, K.Miki, S.Adachi, N.Yasuoka, T.Yagi, O.Yamauchi, S.Hirota, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.000, 125.980, 66.570, 90.00, 90.00, 90.00
R / Rfree (%) 13.4 / 13.7

Other elements in 1ubo:

The structure of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F 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 the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1ubo). 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 the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1ubo:

Magnesium binding site 1 out of 1 in 1ubo

Go back to Magnesium Binding Sites List in 1ubo
Magnesium binding site 1 out of 1 in the Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


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 the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1005

b:8.0
occ:1.00
 O L:HOH3001 2.1 9.3 1.0
O L:HOH3002 2.1 8.8 1.0
O L:HOH3003 2.1 9.0 1.0
OE2 L:GLU62 2.1 9.2 1.0
NE2 L:HIS552 2.1 8.5 1.0
O L:LEU498 2.2 8.4 1.0
CE1 L:HIS552 3.1 9.6 1.0
CD L:GLU62 3.1 8.6 1.0
CD2 L:HIS552 3.2 8.8 1.0
C L:LEU498 3.3 8.1 1.0
OE1 L:GLU62 3.4 8.9 1.0
N L:LEU498 3.7 8.7 1.0
CA L:LEU498 3.9 7.8 1.0
OE1 L:GLN497 4.1 9.7 1.0
OE1 L:GLU337 4.1 10.2 1.0
OE2 L:GLU337 4.2 9.7 1.0
NZ L:LYS374 4.2 8.6 1.0
CB L:LEU498 4.2 9.8 1.0
ND1 L:HIS552 4.2 8.8 1.0
O L:HOH3050 4.3 8.9 1.0
O L:HOH3056 4.3 8.9 1.0
CG L:HIS552 4.3 8.4 1.0
N L:VAL499 4.4 7.8 1.0
CG L:GLU62 4.4 8.5 1.0
CD L:GLU337 4.5 9.9 1.0
CD L:LYS374 4.6 8.6 1.0
CA L:VAL499 4.7 7.7 1.0
CE L:LYS374 4.7 8.6 1.0
C L:GLN497 4.7 7.9 1.0

Reference:

H.Ogata, Y.Mizoguchi, N.Mizuno, K.Miki, S.Adachi, N.Yasuoka, T.Yagi, O.Yamauchi, S.Hirota, Y.Higuchi. Structural Studies of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulfovibrio Vulgaris Miyazaki F: Suggestion For the Initial Activation Site For Dihydrogen J.Am.Chem.Soc. V. 124 11628 2002.
ISSN: ISSN 0002-7863
PubMed: 12296727
DOI: 10.1021/JA012645K
Page generated: Sun Aug 10 05:05:04 2025

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