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

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

All present enzymatic activity of Three-Dimensional Structure of the Ni-A 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-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wuh 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) 16.41 / 1.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.227, 126.261, 66.440, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 15.7

Other elements in 1wuh:

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

Nickel binding site 1 out of 1 in 1wuh

Go back to Nickel Binding Sites List in 1wuh
Nickel binding site 1 out of 1 in the Three-Dimensional 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 Three-Dimensional 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:13.5
occ:0.90
 NI L:NFC1004 0.0 13.5 0.9
O4 L:NFC1004 1.8 14.5 1.0
OD L:CSO84 1.8 14.9 0.7
O5 L:NFC1004 2.1 18.2 0.7
SG L:CSO546 2.1 16.9 0.9
OD L:CSO546 2.1 13.5 0.7
SG L:CYS81 2.2 14.3 0.9
SG L:CYS549 2.5 11.4 1.0
SG L:CSO84 2.6 11.7 1.0
FE L:NFC1004 2.9 10.2 1.0
CB L:CYS81 3.0 14.8 1.0
CB L:CSO546 3.2 14.6 1.0
CB L:CYS549 3.5 10.2 1.0
CB L:CSO84 3.6 11.4 1.0
N L:CSO84 3.8 10.2 1.0
C1 L:NFC1004 3.9 10.8 1.0
C2 L:NFC1004 4.1 9.9 1.0
CA L:CSO84 4.2 9.4 1.0
CA L:CYS81 4.4 10.1 1.0
N L:CYS549 4.5 9.7 1.0
CB L:VAL83 4.5 9.8 1.0
CA L:CYS549 4.5 10.3 1.0
C3 L:NFC1004 4.5 9.4 1.0
CA L:CSO546 4.6 10.4 1.0
NH1 L:ARG479 4.7 11.8 1.0
O1 L:NFC1004 4.8 12.2 1.0
C L:VAL83 4.8 10.0 1.0
CG L:GLU34 4.9 12.4 1.0
N L:VAL83 4.9 10.7 1.0
CD L:ARG479 4.9 9.6 1.0
CZ L:ARG479 4.9 9.1 1.0
C L:CYS81 4.9 8.6 1.0
NE L:ARG479 4.9 9.8 1.0
CA L:VAL83 5.0 9.2 1.0
C L:CSO84 5.0 9.6 1.0

Reference:

H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi. Structural Basis For the Activation Process of [Nife] Hydrogenase From D.Vulgaris Miyazaki F To Be Published.
Page generated: Mon Aug 18 18:02:42 2025

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