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Nickel in PDB 1wui: Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

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

Protein crystallography data

The structure of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wui 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 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.069, 125.966, 66.380, 90.00, 90.00, 90.00
R / Rfree (%) 9.8 / 13.4

Other elements in 1wui:

The structure of Ultra-High Resolution Structure of the Ni-A 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 Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1wui). 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 Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wui:

Nickel binding site 1 out of 1 in 1wui

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

b:11.2
occ:0.87
NI L:NFC1004 0.0 11.2 0.9
O4 L:NFC1004 1.7 12.9 1.0
OD L:CSO84 1.8 12.1 0.6
O5 L:NFC1004 2.0 17.3 0.6
SG L:CSO546 2.1 16.9 0.9
SG L:CYS81 2.2 11.6 0.9
OD L:CSO546 2.3 12.3 0.5
SG L:CYS549 2.5 8.0 1.0
SG L:CSO84 2.5 8.6 1.0
FE L:NFC1004 2.8 7.2 1.0
CB L:CYS81 3.0 10.4 1.0
CB L:CSO546 3.2 11.4 1.0
CB L:CYS549 3.5 7.8 1.0
CB L:CSO84 3.6 9.0 1.0
N L:CSO84 3.7 7.1 1.0
C1 L:NFC1004 3.9 8.0 1.0
C2 L:NFC1004 4.0 8.8 1.0
CA L:CSO84 4.2 6.8 1.0
C3 L:NFC1004 4.3 7.8 1.0
CA L:CYS81 4.5 7.9 1.0
CB L:VAL83 4.5 7.5 1.0
N L:CYS549 4.5 7.1 1.0
CA L:CYS549 4.6 7.4 1.0
CA L:CSO546 4.6 8.3 1.0
NH1 L:ARG479 4.6 9.7 1.0
O1 L:NFC1004 4.7 9.6 1.0
C L:VAL83 4.8 6.8 1.0
CD L:ARG479 4.9 7.1 1.0
NE L:ARG479 4.9 7.3 1.0
CZ L:ARG479 4.9 7.5 1.0
N L:VAL83 4.9 7.4 1.0
C L:CSO84 4.9 7.2 1.0
C L:CYS81 4.9 6.9 1.0
CG L:GLU34 5.0 8.7 1.0
CA L:VAL83 5.0 7.1 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 Dec 16 01:16:17 2020

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