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Nickel in PDB 5y34: Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition

Enzymatic activity of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition

All present enzymatic activity of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition:
1.12.5.1;

Protein crystallography data

The structure of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition, PDB code: 5y34 was solved by Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.628, 116.943, 113.337, 90.00, 91.42, 90.00
R / Rfree (%) 13.1 / 15.8

Other elements in 5y34:

The structure of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 26 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition (pdb code 5y34). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition, PDB code: 5y34:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5y34

Go back to Nickel Binding Sites List in 5y34
Nickel binding site 1 out of 2 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:15.4
occ:1.00
O A:O603 1.7 14.5 1.0
SG A:CYS590 2.1 16.8 1.0
SG A:CYS76 2.2 15.5 1.0
SG A:CYS79 2.4 11.8 1.0
SG A:CYS593 2.6 11.7 1.0
FE A:FCO602 2.8 11.0 1.0
CB A:CYS76 3.1 13.5 1.0
CB A:CYS590 3.2 14.4 1.0
CB A:CYS79 3.5 12.7 1.0
N A:CYS79 3.6 12.1 1.0
CB A:CYS593 3.7 11.6 1.0
C2 A:FCO602 3.9 12.1 1.0
C1 A:FCO602 4.0 11.9 1.0
CA A:CYS79 4.1 12.6 1.0
NH1 A:ARG523 4.2 12.4 1.0
CB A:VAL78 4.4 13.3 1.0
CA A:CYS76 4.5 10.9 1.0
C3 A:FCO602 4.5 11.2 1.0
CZ A:ARG523 4.5 9.8 1.0
CA A:CYS590 4.6 11.1 1.0
N A:CYS593 4.6 9.9 1.0
NE A:ARG523 4.7 10.1 1.0
CA A:CYS593 4.7 10.0 1.0
C A:VAL78 4.7 11.6 1.0
CD A:ARG523 4.8 10.2 1.0
N2 A:FCO602 4.8 10.5 1.0
N A:VAL78 4.9 12.4 1.0
CA A:VAL78 4.9 11.8 1.0
N1 A:FCO602 4.9 11.1 1.0

Nickel binding site 2 out of 2 in 5y34

Go back to Nickel Binding Sites List in 5y34
Nickel binding site 2 out of 2 in the Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Membrane-Bound Respiratory [Nife]-Hydrogenase From Hydrogenovibrio Marinus in A Ferricyanide-Oxidized Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni702

b:17.4
occ:1.00
O C:O704 1.7 16.3 1.0
SG C:CYS590 2.1 19.1 1.0
SG C:CYS76 2.2 16.9 1.0
SG C:CYS79 2.5 13.4 1.0
SG C:CYS593 2.6 13.2 1.0
FE C:FCO703 2.8 12.7 1.0
CB C:CYS76 3.1 16.2 1.0
CB C:CYS590 3.2 15.6 1.0
CB C:CYS79 3.5 14.2 1.0
CB C:CYS593 3.7 12.8 1.0
N C:CYS79 3.7 14.5 1.0
C2 C:FCO703 4.0 13.0 1.0
C1 C:FCO703 4.0 13.6 1.0
CA C:CYS79 4.2 13.0 1.0
NH1 C:ARG523 4.2 14.1 1.0
CB C:VAL78 4.4 14.9 1.0
CA C:CYS76 4.5 12.7 1.0
CZ C:ARG523 4.5 11.6 1.0
C3 C:FCO703 4.5 12.3 1.0
CA C:CYS590 4.5 13.5 1.0
N C:CYS593 4.6 11.7 1.0
CA C:CYS593 4.6 11.5 1.0
NE C:ARG523 4.6 11.8 1.0
CD C:ARG523 4.7 13.0 1.0
C C:VAL78 4.8 13.4 1.0
N2 C:FCO703 4.9 12.1 1.0
N C:VAL78 4.9 14.1 1.0
CA C:VAL78 4.9 14.1 1.0
N1 C:FCO703 5.0 13.5 1.0

Reference:

Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi. Structural Basis For A [4FE-3S] Cluster in the Oxygen-Tolerant Membrane-Bound [Nife]-Hydrogenase Nature V. 479 253 2011.
ISSN: ESSN 1476-4687
PubMed: 22002607
DOI: 10.1038/NATURE10504
Page generated: Wed Dec 16 01:50:13 2020

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