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Nickel in PDB 1ubk: 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: 1ubk 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 / 1.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.600, 125.260, 66.420, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 14.9

Other elements in 1ubk:

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:

Magnesium (Mg) 1 atom
Iron (Fe) 12 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1ubk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1ubk:

Nickel binding site 1 out of 1 in 1ubk

Go back to Nickel Binding Sites List in 1ubk
Nickel 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 Nickel with other atoms in the Ni 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:Ni1004

b:11.5
occ:1.00
 NI L:FNE1004 0.0 11.5 1.0
C L:CMO1006 1.8 13.1 1.0
SG L:CYS81 2.3 11.1 1.0
SG L:CYS84 2.3 10.5 1.0
SG L:CYS549 2.3 10.5 1.0
SG L:CYS546 2.4 14.6 1.0
FE L:FNE1004 2.6 10.1 1.0
O L:CMO1006 2.8 17.5 1.0
CB L:CYS81 3.2 10.8 1.0
CB L:CYS546 3.3 11.5 1.0
CB L:CYS84 3.4 10.7 1.0
CB L:CYS549 3.4 9.7 1.0
C1 L:FNE1004 3.6 10.6 1.0
N L:CYS84 3.7 10.6 1.0
C2 L:FNE1004 3.8 10.2 1.0
CA L:CYS84 4.1 10.3 1.0
C3 L:FNE1004 4.2 9.4 1.0
O1 L:FNE1004 4.5 12.9 1.0
CA L:CYS549 4.5 10.2 1.0
N L:CYS549 4.5 10.2 1.0
CA L:CYS81 4.6 9.6 1.0
NH1 L:ARG479 4.7 11.0 1.0
CB L:VAL83 4.7 10.4 1.0
CD L:ARG479 4.7 10.7 1.0
CA L:CYS546 4.7 11.6 1.0
O2 L:FNE1004 4.8 11.8 1.0
C L:VAL83 4.9 10.1 1.0
NE L:ARG479 4.9 10.4 1.0
C L:CYS84 4.9 9.9 1.0
CZ L:ARG479 4.9 10.0 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: Wed Oct 9 16:28:06 2024

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