Atomistry » Nickel » PDB 1t6u-1xmk » 1wuj
Atomistry »
  Nickel »
    PDB 1t6u-1xmk »
      1wuj »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy