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Nickel in PDB 4u9h: Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

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

All present enzymatic activity of Ultra 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 Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9h 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) 37.64 / 0.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.530, 97.950, 125.850, 90.00, 90.00, 90.00
R / Rfree (%) 9.6 / 10.6

Other elements in 4u9h:

The structure of Ultra 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 Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 4u9h). 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 Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9h:

Nickel binding site 1 out of 1 in 4u9h

Go back to Nickel Binding Sites List in 4u9h
Nickel binding site 1 out of 1 in the Ultra 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 Ultra 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:4.5
occ:1.00
 NI L:NWN601 0.0 4.5 1.0
H L:NWN601 1.6 3.3 1.0
SG L:CYS546 2.2 7.0 1.0
SG L:CYS84 2.2 4.3 1.0
SG L:CYS81 2.2 4.4 1.0
HG L:CYS546 2.3 1.6 1.0
SG L:CYS549 2.5 4.7 1.0
FE L:NWN601 2.6 4.2 1.0
H L:CYS84 2.9 7.1 1.0
CB L:CYS81 3.1 4.7 1.0
HB2 L:CYS81 3.1 5.2 1.0
HB3 L:CYS81 3.1 3.7 1.0
HB3 L:CYS84 3.3 4.9 1.0
HB2 L:CYS549 3.3 5.5 0.9
CB L:CYS546 3.3 5.0 1.0
CB L:CYS84 3.4 4.5 1.0
HB3 L:CYS546 3.4 5.7 1.0
HB2 L:CYS546 3.5 4.3 0.8
CB L:CYS549 3.6 4.8 1.0
C1 L:NWN601 3.6 4.5 1.0
N L:CYS84 3.7 4.4 1.0
C2 L:NWN601 3.7 4.4 1.0
HB L:VAL83 3.8 4.6 0.9
HD2 L:ARG479 3.9 4.7 1.0
CA L:CYS84 4.1 4.3 1.0
H L:CYS549 4.1 5.2 1.0
HH11 L:ARG479 4.1 3.0 0.9
HB2 L:CYS84 4.1 4.1 1.0
C3 L:NWN601 4.2 4.9 1.0
HB3 L:CYS549 4.2 6.1 1.0
NH1 L:ARG479 4.3 5.3 1.0
HG3 L:GLU34 4.3 6.2 0.9
HE2 L:HIS88 4.4 3.9 0.8
CA L:CYS81 4.5 4.3 1.0
H L:VAL83 4.5 3.9 1.0
N1 L:NWN601 4.6 5.2 1.0
CA L:CYS549 4.6 4.5 1.0
HH12 L:ARG479 4.6 6.0 0.8
CD L:ARG479 4.7 4.9 1.0
N L:CYS549 4.7 4.6 1.0
CZ L:ARG479 4.7 5.0 1.0
NE L:ARG479 4.7 4.9 1.0
CA L:CYS546 4.7 4.7 1.0
CB L:VAL83 4.7 4.9 1.0
N2 L:NWN601 4.7 4.8 1.0
HA L:CYS549 4.8 3.6 0.9
HA L:CYS546 4.8 6.7 1.0
HA L:CYS81 4.8 2.2 0.8
HB3 L:GLU34 4.8 5.3 1.0
C L:VAL83 4.8 4.3 1.0
HA L:CYS84 4.9 3.8 1.0
C L:CYS84 4.9 4.3 1.0
HD3 L:ARG479 4.9 5.1 1.0
HG12 L:VAL83 4.9 6.6 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: Wed Oct 9 19:11:00 2024

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