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Nickel in PDB 4u9i: High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9i was solved by H.Ogata, K.Nishikawa, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 1.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.850, 99.690, 122.190, 90.00, 90.00, 90.00
R / Rfree (%) 11 / 13.2

Other elements in 4u9i:

The structure of High Resolution Structure of the Ni-R 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 High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 4u9i). 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 High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9i:

Nickel binding site 1 out of 1 in 4u9i

Go back to Nickel Binding Sites List in 4u9i
Nickel binding site 1 out of 1 in the High Resolution Structure of the Ni-R 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 High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni601

b:5.7
occ:1.00
 NI L:NWN601 0.0 5.7 1.0
H L:NWN601 1.6 3.0 1.0
SG L:CYS546 2.2 7.8 1.0
SG L:CYS84 2.2 5.4 1.0
SG L:CYS81 2.2 5.5 1.0
HG L:CYS546 2.3 1.6 1.0
SG L:CYS549 2.5 5.8 1.0
FE L:NWN601 2.6 5.3 1.0
H L:CYS84 2.9 7.2 1.0
CB L:CYS81 3.1 5.8 1.0
HB2 L:CYS81 3.1 6.0 1.0
HB3 L:CYS81 3.1 3.8 1.0
HB2 L:CYS549 3.2 1.3 1.0
HB3 L:CYS84 3.3 5.0 1.0
CB L:CYS546 3.3 5.5 1.0
HB3 L:CYS546 3.3 8.0 1.0
CB L:CYS84 3.3 6.4 1.0
HB2 L:CYS546 3.5 3.2 1.0
CB L:CYS549 3.6 5.9 1.0
C1 L:NWN601 3.6 5.8 1.0
N L:CYS84 3.7 5.8 1.0
C2 L:NWN601 3.7 5.7 1.0
HB L:VAL83 3.8 6.0 1.0
HD2 L:ARG479 3.9 8.7 1.0
CA L:CYS84 4.1 5.2 1.0
HH11 L:ARG479 4.1 13.8 1.0
H L:CYS549 4.1 5.4 1.0
HB2 L:CYS84 4.1 5.3 1.0
C3 L:NWN601 4.2 5.3 1.0
HB3 L:CYS549 4.2 5.4 1.0
HG3 L:GLU34 4.3 3.9 1.0
NH1 L:ARG479 4.3 6.4 1.0
HE2 L:HIS88 4.4 4.0 1.0
H L:VAL83 4.5 17.4 1.0
CA L:CYS81 4.5 5.2 1.0
N1 L:NWN601 4.5 6.3 1.0
CD L:ARG479 4.6 5.2 1.0
CA L:CYS549 4.6 5.1 1.0
HH12 L:ARG479 4.7 8.3 1.0
CZ L:ARG479 4.7 5.8 1.0
N L:CYS549 4.7 5.6 1.0
NE L:ARG479 4.7 5.3 1.0
CB L:VAL83 4.7 5.7 1.0
N2 L:NWN601 4.7 5.8 1.0
CA L:CYS546 4.7 5.5 1.0
HA L:CYS81 4.8 5.4 1.0
HA L:CYS549 4.8 5.2 1.0
HB3 L:GLU34 4.8 14.5 1.0
HA L:CYS546 4.8 2.3 1.0
HD3 L:ARG479 4.8 16.2 1.0
C L:VAL83 4.8 5.8 1.0
HA L:CYS84 4.9 0.0 1.0
C L:CYS84 4.9 5.2 1.0
HG12 L:VAL83 4.9 5.9 1.0

Reference:

H.Ogata, K.Nishikawa, W.Lubitz. Hydrogens Detected By Subatomic Resolution Protein Crystallography in A [Nife] Hydrogenase. Nature 2015.
ISSN: ESSN 1476-4687
PubMed: 25624102
DOI: 10.1038/NATURE14110
Page generated: Mon Aug 18 19:41:03 2025

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