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Nickel in PDB 1wuk: High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuk was solved by H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.291, 125.843, 66.440, 90.00, 90.00, 90.00
R / Rfree (%) 9.6 / 12.3

Other elements in 1wuk:

The structure of High Resolution Structure of the Oxidized State 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 High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1wuk). 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 High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuk:

Nickel binding site 1 out of 1 in 1wuk

Go back to Nickel Binding Sites List in 1wuk
Nickel binding site 1 out of 1 in the High Resolution Structure of the Oxidized State 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 High Resolution Structure of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni1004

b:6.5
occ:0.91
 NI L:NFO1004 0.0 6.5 0.9
O4 L:NFO1004 1.6 7.5 0.5
SG L:CSO546 2.1 9.0 0.9
SG L:CYS81 2.2 6.8 0.9
SG L:CYS84 2.3 6.0 1.0
SG L:CYS549 2.5 5.7 1.0
FE L:NFO1004 2.7 5.3 1.0
OD L:CSO546 2.9 9.5 0.7
CB L:CYS81 3.1 6.2 1.0
CB L:CSO546 3.3 7.0 1.0
CB L:CYS84 3.4 5.7 1.0
CB L:CYS549 3.6 6.0 1.0
N L:CYS84 3.7 5.4 1.0
C1 L:NFO1004 3.7 5.9 1.0
C2 L:NFO1004 3.9 5.5 1.0
CA L:CYS84 4.1 5.2 1.0
C3 L:NFO1004 4.2 5.6 1.0
NH1 L:ARG479 4.4 6.9 1.0
CA L:CYS81 4.5 5.6 1.0
CB L:VAL83 4.6 5.9 1.0
O1 L:NFO1004 4.6 6.8 0.9
CA L:CSO546 4.7 5.8 1.0
CZ L:ARG479 4.7 5.7 1.0
CA L:CYS549 4.7 5.7 1.0
CD L:ARG479 4.7 5.7 1.0
NE L:ARG479 4.7 5.6 1.0
N L:CYS549 4.7 5.9 1.0
C L:VAL83 4.8 5.6 1.0
N2 L:NFO1004 4.8 5.7 1.0
C L:CYS84 4.9 5.2 1.0

Reference:

H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi. Activation Process of [Nife] Hydrogenase Elucidated By High-Resolution X-Ray Analyses: Conversion of the Ready to the Unready State Structure V. 13 1635 2005.
ISSN: ISSN 0969-2126
PubMed: 16271886
DOI: 10.1016/J.STR.2005.07.018
Page generated: Mon Aug 18 18:02:47 2025

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