Nickel in PDB 7xdp: Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition)

Enzymatic activity of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition)

All present enzymatic activity of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition):
1.2.7.4;

Protein crystallography data

The structure of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition), PDB code: 7xdp was solved by Y.Y.Heo, S.M.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	33.23 / 1.84
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	111.934, 74.969, 71.323, 90, 111.29, 90
*R / R_free (%)*	14.8 / 19.3

Other elements in 7xdp:

The structure of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) (pdb code 7xdp). 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition), PDB code: 7xdp:

Nickel binding site 1 out of 1 in 7xdp

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Nickel Binding Sites List in 7xdp

Nickel binding site 1 out of 1 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition)

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni703 b:63.1 occ:1.00	NI1	A:NFS703	0.0	63.1	1.0
	SG	A:CYS526	2.0	50.3	1.0
	S3	A:NFS703	2.2	54.4	1.0
	S2	A:NFS703	2.3	56.0	1.0
	S5	A:NFS703	2.4	46.5	1.0
	O	A:HOH1198	2.6	33.9	1.0
	FE1	A:NFS703	2.8	50.2	1.0
	FE3	A:NFS703	2.9	72.5	1.0
	CB	A:CYS526	3.4	25.2	1.0
	FE4	A:NFS703	3.6	56.7	1.0
	FE2	A:NFS703	4.1	57.1	1.0
	S1	A:NFS703	4.2	58.3	1.0
	NZ	A:LYS563	4.2	26.6	1.0
	NE2	A:HIS261	4.3	28.1	1.0
	SG	A:CYS446	4.4	24.4	1.0
	O	A:HOH997	4.5	19.5	1.0
	SG	A:CYS295	4.6	24.5	1.0
	CA	A:GLY445	4.6	19.4	1.0
	C	A:GLY445	4.6	20.0	1.0
	CA	A:CYS526	4.7	17.3	1.0
	CE	A:LYS563	4.7	24.6	1.0
	O	A:GLY445	4.8	17.9	1.0
	O	A:HOH1188	4.9	32.4	1.0
	N	A:CYS446	5.0	24.5	1.0
	S4	A:NFS703	5.0	47.6	1.0

Reference:

S.M.Kim, J.H.Lee, S.H.Kang, Y.Y.Heo, H.J.Yoon, J.S.Hahn, H.H.Lee, Y.H.Kim. O2-Tolerant Co Dehydrogenase Via Tunnel Redesign For the Removal of Co From Industrial Flue Gas Nat Catal V. 5 807 2022.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00834-Y

Page generated: Thu Oct 10 09:29:30 2024

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