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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 Dec 16 01:12:02 2020

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