Nickel in PDB 8x9e: Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration

Enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration

All present enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration, PDB code: 8x9e was solved by H.H.Lee, Y.Heo, H.J.Yoon, S.M.Kim, S.Y.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.22 / 2.50
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	112.083, 75.088, 71.14, 90, 111.39, 90
*R / R_free (%)*	17.7 / 22.7

Other elements in 8x9e:

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration also contains other interesting chemical elements:

Iron

(Fe)

11 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration (pdb code 8x9e). 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 Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration, PDB code: 8x9e:

Nickel binding site 1 out of 1 in 8x9e

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Nickel Binding Sites List in 8x9e

Nickel binding site 1 out of 1 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni703 b:43.6 occ:0.70	NI	A:XCC703	0.0	43.6	0.7
	O	A:HOH906	1.9	36.1	1.0
	S1	A:XCC703	2.2	57.9	0.7
	S4	A:XCC703	2.4	40.5	0.7
	FE2	A:XCC703	2.6	48.4	0.7
	SG	A:CYS526	2.7	38.0	1.0
	FE3	A:XCC703	2.8	46.1	0.7
	CB	A:CYS526	3.2	35.5	1.0
	FE4	A:XCC703	3.6	49.7	0.7
	NZ	A:LYS563	3.8	40.5	1.0
	FE1	A:XCC703	4.0	43.1	0.6
	S3	A:XCC703	4.1	43.8	0.7
	NE2	A:HIS261	4.3	42.1	1.0
	CA	A:CYS526	4.5	33.0	1.0
	CE	A:LYS563	4.6	37.4	1.0
	CA	A:GLY445	4.6	32.6	1.0
	C	A:GLY445	4.6	34.1	1.0
	SG	A:CYS446	4.7	35.8	1.0
	SG	A:CYS295	4.8	40.2	1.0
	S2	A:XCC703	4.8	44.8	0.7
	O	A:GLY445	4.8	34.0	1.0
	CB	A:LYS563	4.8	31.4	1.0

Reference:

S.M.Kim, S.H.Kang, J.Lee, Y.Heo, E.G.Poloniataki, J.Kang, H.J.Yoon, S.Y.Kong, Y.Yun, H.Kim, J.Ryu, H.H.Lee, Y.H.Kim. Identifying A Key Spot For Electron Mediator-Interaction to Tailor Co Dehydrogenase'S Affinity Nat Commun V. 15 2732 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-46909-1

Page generated: Mon Aug 18 22:20:40 2025

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