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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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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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