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Nickel in PDB 1wuj: Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuj 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 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.162, 125.924, 66.441, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 16.2

Other elements in 1wuj:

The structure of Three-Dimensional Structure of the Ni-B 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 Three-Dimensional Structure of the Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1wuj). 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 Ni-B State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuj:

Nickel binding site 1 out of 1 in 1wuj

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

b:11.8
occ:0.90
 NI L:NFO1004 0.0 11.8 0.9
O4 L:NFO1004 1.7 12.5 0.6
SG L:CSO546 2.1 14.1 0.9
SG L:CYS81 2.2 13.1 1.0
SG L:CYS84 2.4 11.7 1.0
SG L:CYS549 2.5 10.3 0.9
FE L:NFO1004 2.7 10.1 1.0
OD L:CSO546 2.7 24.2 0.9
CB L:CYS81 3.1 12.3 1.0
CB L:CSO546 3.3 10.6 1.0
CB L:CYS84 3.5 11.2 1.0
CB L:CYS549 3.7 10.2 1.0
N L:CYS84 3.7 9.1 1.0
C1 L:NFO1004 3.9 8.3 1.0
C2 L:NFO1004 4.0 9.4 0.9
CA L:CYS84 4.1 9.2 1.0
C3 L:NFO1004 4.3 8.3 1.0
NH1 L:ARG479 4.4 10.9 1.0
CB L:VAL83 4.5 9.3 1.0
CA L:CYS81 4.5 9.5 1.0
CA L:CSO546 4.6 9.0 1.0
CA L:CYS549 4.7 9.5 1.0
CD L:ARG479 4.7 9.8 1.0
CZ L:ARG479 4.7 8.2 1.0
N L:CYS549 4.7 10.1 1.0
O1 L:NFO1004 4.7 13.8 1.0
NE L:ARG479 4.8 9.1 1.0
C L:VAL83 4.8 8.1 1.0
C L:CYS84 4.9 8.9 1.0
N2 L:NFO1004 4.9 9.5 0.9
N L:VAL83 5.0 8.9 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: Wed Oct 9 16:30:59 2024

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