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

Nickel in PDB 1ubh: Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1ubh was solved by H.Ogata, Y.Mizoguchi, N.Mizuno, K.Miki, S.Adachi, N.Yasuoka, T.Yagi, O.Yamauchi, S.Hirota, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.065, 126.206, 66.679, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.8

Other elements in 1ubh:

The structure of Three-Dimensional Structure of the Carbon Monoxide Complex 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 Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1ubh). 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 Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1ubh:

Nickel binding site 1 out of 1 in 1ubh

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

b:12.2
occ:1.00
 NI L:FNE1004 0.0 12.2 1.0
C L:CMO1006 1.7 14.2 0.8
SG L:CYS81 2.3 12.4 1.0
SG L:CYS546 2.3 15.7 1.0
SG L:CYS84 2.3 11.0 1.0
SG L:CYS549 2.3 11.0 1.0
FE L:FNE1004 2.6 10.5 1.0
O L:CMO1006 2.7 16.4 0.8
CB L:CYS81 3.1 13.6 1.0
CB L:CYS546 3.3 11.8 1.0
CB L:CYS84 3.4 10.4 1.0
CB L:CYS549 3.4 9.5 1.0
C1 L:FNE1004 3.7 10.7 1.0
N L:CYS84 3.7 11.4 1.0
C2 L:FNE1004 3.8 10.0 1.0
CA L:CYS84 4.1 9.9 1.0
C3 L:FNE1004 4.2 9.2 1.0
CA L:CYS549 4.5 9.8 1.0
CA L:CYS81 4.5 10.4 1.0
N L:CYS549 4.5 9.5 1.0
O1 L:FNE1004 4.6 13.1 1.0
NH1 L:ARG479 4.7 13.6 1.0
CB L:VAL83 4.7 11.0 1.0
CA L:CYS546 4.7 11.0 1.0
CD L:ARG479 4.7 10.6 1.0
O2 L:FNE1004 4.8 12.2 1.0
C L:VAL83 4.9 10.8 1.0
C L:CYS84 4.9 9.1 1.0
NE L:ARG479 4.9 10.6 1.0
CZ L:ARG479 5.0 10.5 1.0

Reference:

H.Ogata, Y.Mizoguchi, N.Mizuno, K.Miki, S.Adachi, N.Yasuoka, T.Yagi, O.Yamauchi, S.Hirota, Y.Higuchi. Structural Studies of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulfovibrio Vulgaris Miyazaki F: Suggestion For the Initial Activation Site For Dihydrogen J.Am.Chem.Soc. V. 124 11628 2002.
ISSN: ISSN 0002-7863
PubMed: 12296727
DOI: 10.1021/JA012645K
Page generated: Wed Oct 9 16:28:06 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy