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Nickel in PDB 1h2a: Single Crystals of Hydrogenase From Desulfovibrio Vulgaris

Enzymatic activity of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris

All present enzymatic activity of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris:
1.18.99.1;

Protein crystallography data

The structure of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris, PDB code: 1h2a was solved by Y.Higuchi, N.Yasuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.500, 126.500, 66.510, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.8

Other elements in 1h2a:

The structure of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris 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 Single Crystals of Hydrogenase From Desulfovibrio Vulgaris (pdb code 1h2a). 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 Single Crystals of Hydrogenase From Desulfovibrio Vulgaris, PDB code: 1h2a:

Nickel binding site 1 out of 1 in 1h2a

Go back to Nickel Binding Sites List in 1h2a
Nickel binding site 1 out of 1 in the Single Crystals of Hydrogenase From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Single Crystals of Hydrogenase From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni1004

b:18.1
occ:1.00
NI L:NFE1004 0.0 18.1 1.0
S4 L:NFE1004 2.2 19.3 1.0
SG L:CYS81 2.2 16.6 1.0
SG L:CYS546 2.3 21.0 1.0
SG L:CYS549 2.4 15.2 1.0
SG L:CYS84 2.4 11.9 1.0
FE L:NFE1004 2.6 13.1 1.0
CB L:CYS81 2.9 15.6 1.0
CB L:CYS549 3.6 18.1 1.0
CB L:CYS84 3.6 17.5 1.0
CB L:CYS546 3.6 16.0 1.0
N L:CYS84 3.9 17.6 1.0
S3 L:NFE1004 4.0 12.6 1.0
C2 L:NFE1004 4.1 14.9 1.0
C1 L:NFE1004 4.1 13.4 1.0
CA L:CYS84 4.3 15.9 1.0
CA L:CYS81 4.4 13.0 1.0
CA L:CYS549 4.6 16.7 1.0
CB L:VAL83 4.6 9.8 1.0
N L:CYS549 4.7 20.7 1.0
N L:VAL83 4.8 7.3 1.0
O L:CYS84 4.9 20.1 1.0
C L:CYS84 4.9 19.1 1.0
C L:VAL83 4.9 13.7 1.0
CA L:CYS546 5.0 16.3 1.0
C L:CYS81 5.0 17.0 1.0

Reference:

Y.Higuchi, T.Yagi, N.Yasuoka. Unusual Ligand Structure in Ni-Fe Active Center and An Additional Mg Site in Hydrogenase Revealed By High Resolution X-Ray Structure Analysis. Structure V. 5 1671 1997.
ISSN: ISSN 0969-2126
PubMed: 9438867
DOI: 10.1016/S0969-2126(97)00313-4
Page generated: Thu Oct 29 06:14:09 2020
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