Nickel in PDB 7tsj: Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris

Enzymatic activity of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris

All present enzymatic activity of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris:
1.2.7.4;

Protein crystallography data

The structure of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris, PDB code: 7tsj was solved by A.Biester, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	46.72 / 2.10
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	113.892, 100.87, 65.384, 90, 124.88, 90
*R / R_free (%)*	16.7 / 20.6

Other elements in 7tsj:

The structure of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Iron	(Fe)	9 atoms
Xenon	(Xe)	12 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris (pdb code 7tsj). 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 Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris, PDB code: 7tsj:

Nickel binding site 1 out of 1 in 7tsj

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Nickel Binding Sites List in 7tsj

Nickel binding site 1 out of 1 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) 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 Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni703 b:52.5 occ:0.90	NI	A:CUV703	0.0	52.5	0.9
	NE2	A:HIS266	2.0	53.4	1.0
	SG	A:CYS519	2.6	53.9	1.0
	SG	A:CYS302	2.7	48.2	1.0
	FE2	A:CUV703	2.8	55.6	0.9
	CE1	A:HIS266	2.9	51.7	1.0
	NZ	A:LYS556	3.0	55.7	1.0
	FE1	A:CUV703	3.0	52.8	0.9
	CD2	A:HIS266	3.0	47.0	1.0
	CE	A:LYS556	3.3	52.5	1.0
	CB	A:CYS519	3.4	41.1	1.0
	CB	A:CYS302	3.7	47.2	1.0
	S4	A:CUV703	3.8	53.2	0.9
	ND1	A:HIS266	4.0	49.3	1.0
	CG	A:HIS266	4.1	49.1	1.0
	SG	A:CYS340	4.3	52.7	1.0
	SG	A:CYS301	4.4	55.4	1.0
	N	A:CYS519	4.6	38.8	1.0
	CA	A:CYS519	4.6	36.9	1.0
	CD	A:LYS556	4.8	43.0	1.0
	CA	A:CYS302	5.0	46.8	1.0

Reference:

A.Biester, S.Dementin, C.L.Drennan. Visualizing the Gas Channel of A Monofunctional Carbon Monoxide Dehydrogenase. J.Inorg.Biochem. V. 230 11774 2022.
ISSN: ISSN 0162-0134
PubMed: 35278753
DOI: 10.1016/J.JINORGBIO.2022.111774

Page generated: Fri Apr 7 19:17:57 2023

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