Atomistry » Nickel » PDB 1fwc-1j6p » 1h2r
Atomistry »
  Nickel »
    PDB 1fwc-1j6p »
      1h2r »

Nickel in PDB 1h2r: Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution

Enzymatic activity of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution

All present enzymatic activity of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution:
1.12.2.1;

Protein crystallography data

The structure of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution, PDB code: 1h2r was solved by Y.Higuchi, H.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.440, 126.860, 66.680, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.4

Other elements in 1h2r:

The structure of Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution 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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution (pdb code 1h2r). 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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution, PDB code: 1h2r:

Nickel binding site 1 out of 1 in 1h2r

Go back to Nickel Binding Sites List in 1h2r
Nickel binding site 1 out of 1 in the Three-Dimensional Structure of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution


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 Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F in the Reduced Form at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni1004

b:16.2
occ:1.00
 NI L:NFE1004 0.0 16.2 1.0
SG L:CYS546 2.2 18.8 1.0
SG L:CYS81 2.3 15.4 1.0
SG L:CYS84 2.3 14.4 1.0
SG L:CYS549 2.4 12.6 1.0
FE L:NFE1004 2.6 10.8 1.0
CB L:CYS81 3.1 13.0 1.0
CB L:CYS84 3.4 13.6 1.0
CB L:CYS546 3.4 14.1 1.0
CB L:CYS549 3.6 11.9 1.0
N L:CYS84 3.8 13.2 1.0
C2 L:NFE1004 3.9 14.1 1.0
S3 L:NFE1004 4.0 19.7 1.0
C1 L:NFE1004 4.2 14.9 1.0
CA L:CYS84 4.2 13.1 1.0
CA L:CYS81 4.6 11.5 1.0
CA L:CYS549 4.7 11.9 1.0
CB L:VAL83 4.7 10.7 1.0
NH1 L:ARG479 4.7 10.7 1.0
CA L:CYS546 4.8 12.3 1.0
N L:CYS549 4.8 12.2 1.0
O2 L:NFE1004 4.8 12.6 1.0
CD L:ARG479 4.8 10.8 1.0
C L:VAL83 4.9 12.2 1.0
C L:CYS84 4.9 13.1 1.0
CZ L:ARG479 4.9 11.7 1.0
NE L:ARG479 5.0 10.5 1.0
O L:HOH3070 5.0 93.1 1.0
O L:CYS84 5.0 11.7 1.0

Reference:

Y.Higuchi, H.Ogata, K.Miki, N.Yasuoka, T.Yagi. Removal of the Bridging Ligand Atom at the Ni-Fe Active Site of [Nife] Hydrogenase Upon Reduction with H2, As Revealed By X-Ray Structure Analysis at 1.4 A Resolution. Structure Fold.Des. V. 7 549 1999.
ISSN: ISSN 0969-2126
PubMed: 10378274
DOI: 10.1016/S0969-2126(99)80071-9
Page generated: Wed Oct 9 14:54:44 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