Cobalt in PDB 9fy4: Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III))

Enzymatic activity of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III))

All present enzymatic activity of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)):
1.14.14.18;

Protein crystallography data

The structure of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)), PDB code: 9fy4 was solved by R.J.Labidi, B.Faivre, P.Carpentier, J.Perard, P.Gotico, Y.Li, M.Atta, M.Fontecave, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.61 / 2.84
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	41.681, 63.525, 76.12, 90, 97.37, 90
*R / R_free (%)*	23.4 / 30.6

Other elements in 9fy4:

The structure of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)) (pdb code 9fy4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)), PDB code: 9fy4:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 9fy4

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Cobalt Binding Sites List in 9fy4

Cobalt binding site 1 out of 3 in the Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III))

Mono view

Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Co301 b:99.5 occ:1.00	NE2	A:GLN206	4.2	50.9	1.0
	CB	A:PRO104	4.5	45.3	1.0
	OD1	A:ASP210	4.7	48.4	1.0
	OD2	A:ASP210	4.9	50.0	1.0

Cobalt binding site 2 out of 3 in 9fy4

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Cobalt Binding Sites List in 9fy4

Cobalt binding site 2 out of 3 in the Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III))

Mono view

Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Co302 b:65.2 occ:1.00	CO	A:COH302	0.0	65.2	1.0
	NA	A:COH302	1.9	65.2	1.0
	NB	A:COH302	1.9	65.2	1.0
	ND	A:COH302	1.9	65.2	1.0
	NC	A:COH302	1.9	65.2	1.0
	O	A:HOH403	2.1	36.4	1.0
	NE2	A:HIS20	2.5	62.3	1.0
	C1A	A:COH302	2.9	65.2	1.0
	C4B	A:COH302	2.9	65.3	1.0
	C4D	A:COH302	2.9	65.2	1.0
	C1C	A:COH302	2.9	65.2	1.0
	C4A	A:COH302	2.9	65.2	1.0
	C1B	A:COH302	2.9	65.2	1.0
	C1D	A:COH302	2.9	65.2	1.0
	C4C	A:COH302	3.0	65.2	1.0
	CHA	A:COH302	3.2	65.2	1.0
	CHC	A:COH302	3.2	65.2	1.0
	CHB	A:COH302	3.3	65.2	1.0
	CHD	A:COH302	3.3	65.2	1.0
	CD2	A:HIS20	3.3	61.2	1.0
	CE1	A:HIS20	3.5	62.4	1.0
	C3B	A:COH302	4.2	65.3	1.0
	C2A	A:COH302	4.2	65.1	1.0
	C3C	A:COH302	4.2	65.2	1.0
	C3A	A:COH302	4.2	65.1	1.0
	C3D	A:COH302	4.3	65.3	1.0
	C2D	A:COH302	4.3	65.2	1.0
	C2C	A:COH302	4.3	65.2	1.0
	C2B	A:COH302	4.3	65.2	1.0
	CG	A:HIS20	4.5	60.1	1.0
	ND1	A:HIS20	4.6	62.0	1.0
	CA	A:GLY135	4.9	40.0	1.0

Cobalt binding site 3 out of 3 in 9fy4

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Cobalt Binding Sites List in 9fy4

Cobalt binding site 3 out of 3 in the Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III))

Mono view

Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Heme-Oxygenase Mutant I143K From Corynebacterium Diphtheriae Complexed with Cobalt-Porphyrine (Humo-Co(III)) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
H:Co901 b:52.1 occ:1.00	CO	H:COH901	0.0	52.1	1.0
	NB	H:COH901	1.9	52.1	1.0
	NA	H:COH901	1.9	52.1	1.0
	ND	H:COH901	1.9	52.2	1.0
	NC	H:COH901	1.9	52.2	1.0
	O	H:HOH1001	2.1	61.3	1.0
	NE2	H:HIS20	2.3	55.4	1.0
	C4B	H:COH901	3.0	52.2	1.0
	C4A	H:COH901	3.0	52.0	1.0
	C4D	H:COH901	3.0	52.2	1.0
	C4C	H:COH901	3.0	52.2	1.0
	C1A	H:COH901	3.0	52.0	1.0
	C1D	H:COH901	3.0	52.3	1.0
	C1C	H:COH901	3.0	52.2	1.0
	C1B	H:COH901	3.0	52.1	1.0
	CD2	H:HIS20	3.2	54.3	1.0
	CE1	H:HIS20	3.4	55.5	1.0
	CHC	H:COH901	3.4	52.2	1.0
	CHA	H:COH901	3.4	52.1	1.0
	CHB	H:COH901	3.4	52.1	1.0
	CHD	H:COH901	3.4	52.3	1.0
	C3B	H:COH901	4.3	52.2	1.0
	C3C	H:COH901	4.3	52.2	1.0
	C3A	H:COH901	4.3	52.0	1.0
	C3D	H:COH901	4.3	52.3	1.0
	C2D	H:COH901	4.3	52.3	1.0
	C2A	H:COH901	4.3	52.0	1.0
	C2C	H:COH901	4.3	52.2	1.0
	C2B	H:COH901	4.3	52.2	1.0
	CG	H:HIS20	4.4	53.2	1.0
	ND1	H:HIS20	4.4	55.0	1.0
	O	H:HOH1043	4.7	41.9	1.0
	CA	H:GLY135	5.0	35.1	1.0
	OG	H:SER138	5.0	42.6	1.0

Reference:

R.J.Labidi, B.Faivre, P.Carpentier, J.Perard, P.Gotico, Y.Li, M.Atta, M.Fontecave. Light-Activated Artificial Co 2 -Reductase: Structure and Activity. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 39352411
DOI: 10.1021/JACS.4C08927

Page generated: Thu Oct 31 18:22:59 2024

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