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Nickel in PDB 7vxq: The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77

Enzymatic activity of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77

All present enzymatic activity of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77:
1.12.99.6;

Protein crystallography data

The structure of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77, PDB code: 7vxq was solved by K.Nishikawa, K.Higuchi, T.Imanishi, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.49 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.39, 122.32, 99.91, 90, 103.12, 90
R / Rfree (%) 16.1 / 19.3

Other elements in 7vxq:

The structure of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 (pdb code 7vxq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77, PDB code: 7vxq:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7vxq

Go back to Nickel Binding Sites List in 7vxq
Nickel binding site 1 out of 2 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni702

b:27.5
occ:1.00
NI A:NFU702 0.0 27.5 1.0
C A:CMO703 1.8 25.9 0.3
SG A:CYS546 2.3 30.3 1.0
SG A:CYS64 2.3 22.7 1.0
SG A:CYS61 2.3 28.4 1.0
SG A:CYS549 2.4 24.4 1.0
FE A:NFU702 2.6 25.3 1.0
O A:CMO703 2.9 26.4 0.3
CB A:CYS61 3.1 28.6 1.0
CB A:CYS546 3.3 26.2 1.0
CB A:CYS64 3.4 21.1 1.0
CB A:CYS549 3.5 23.6 1.0
C1 A:NFU702 3.7 23.8 1.0
N A:CYS64 3.8 26.7 1.0
C2 A:NFU702 3.8 21.5 1.0
CA A:CYS64 4.2 24.6 1.0
C3 A:NFU702 4.4 25.0 1.0
N A:CYS549 4.5 23.8 1.0
CA A:CYS549 4.5 24.2 1.0
CA A:CYS61 4.6 26.2 1.0
NH1 A:ARG479 4.6 24.6 1.0
N1 A:NFU702 4.6 24.7 1.0
CA A:CYS546 4.7 26.0 1.0
CD A:ARG479 4.7 23.1 1.0
CB A:VAL63 4.7 28.3 1.0
N2 A:NFU702 4.8 21.2 1.0
CZ A:ARG479 4.9 25.2 1.0
NE A:ARG479 4.9 25.0 1.0
C A:VAL63 4.9 27.1 1.0
C A:CYS64 4.9 27.9 1.0
OE2 A:GLU14 4.9 38.0 1.0
CG A:GLU14 5.0 31.3 1.0

Nickel binding site 2 out of 2 in 7vxq

Go back to Nickel Binding Sites List in 7vxq
Nickel binding site 2 out of 2 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni702

b:28.7
occ:1.00
NI C:NFU702 0.0 28.7 1.0
C C:CMO703 1.8 28.4 0.3
SG C:CYS61 2.2 32.9 1.0
SG C:CYS546 2.3 32.2 1.0
SG C:CYS64 2.3 26.4 1.0
SG C:CYS549 2.4 25.3 1.0
FE C:NFU702 2.7 25.3 1.0
O C:CMO703 2.9 26.9 0.3
CB C:CYS61 3.1 29.8 1.0
CB C:CYS546 3.3 27.8 1.0
CB C:CYS64 3.4 26.9 1.0
CB C:CYS549 3.4 25.2 1.0
C1 C:NFU702 3.7 24.4 1.0
N C:CYS64 3.8 29.6 1.0
C2 C:NFU702 3.9 25.0 1.0
CA C:CYS64 4.2 29.2 1.0
C3 C:NFU702 4.3 28.9 1.0
CA C:CYS549 4.5 25.3 1.0
NH1 C:ARG479 4.5 25.3 1.0
CA C:CYS61 4.5 25.3 1.0
N C:CYS549 4.5 24.4 1.0
N1 C:NFU702 4.6 27.1 1.0
CA C:CYS546 4.6 25.4 1.0
CD C:ARG479 4.7 23.1 1.0
CB C:VAL63 4.7 26.8 1.0
N2 C:NFU702 4.8 24.8 1.0
NE C:ARG479 4.9 25.2 1.0
CZ C:ARG479 4.9 27.5 1.0
C C:VAL63 4.9 26.8 1.0
C C:CYS64 4.9 25.7 1.0
OE2 C:GLU14 5.0 37.7 1.0

Reference:

T.Imanishi, K.Nishikawa, M.Taketa, K.Higuchi, H.Tai, S.Hirota, H.Hojo, T.Kawakami, K.Hataguchi, K.Matsumoto, H.Ogata, Y.Higuchi. Structural and Spectroscopic Characterization of Co Inhibition of [Nife]-Hydrogenase From Citrobacter Sp. S-77. Acta Crystallogr.,Sect.F V. 78 66 2022.
ISSN: ESSN 2053-230X
PubMed: 35102895
DOI: 10.1107/S2053230X22000188
Page generated: Thu Oct 10 09:27:58 2024

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