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Cobalt in PDB 6jvc: Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan

Enzymatic activity of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan

All present enzymatic activity of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan, PDB code: 6jvc was solved by J.K.Stanfield, A.Matsumoto, C.Kasai, H.Sugimoto, Y.Shiro, Y.Watanabe, O.Shoji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.87 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.898, 148.247, 63.219, 90.00, 98.02, 90.00
R / Rfree (%) 18.6 / 22

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan (pdb code 6jvc). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan, PDB code: 6jvc:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 6jvc

Go back to Cobalt Binding Sites List in 6jvc
Cobalt binding site 1 out of 4 in the Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co512

b:18.4
occ:0.47
 CO A:COH512 0.0 18.4 0.5
CO A:COH512 0.0 18.6 0.5
ND A:COH512 1.9 17.5 0.5
NA A:COH512 1.9 17.4 0.5
NC A:COH512 1.9 19.4 0.5
NB A:COH512 1.9 19.9 0.5
NA A:COH512 2.0 18.7 0.5
NB A:COH512 2.0 18.4 0.5
ND A:COH512 2.0 18.6 0.5
NC A:COH512 2.0 19.1 0.5
O A:DMS513 2.2 36.4 1.0
SG A:CYS400 2.3 20.7 1.0
C4C A:COH512 2.9 19.8 0.5
C1D A:COH512 3.0 18.8 0.5
C4A A:COH512 3.0 18.4 0.5
C4D A:COH512 3.0 18.3 0.5
C1C A:COH512 3.0 19.0 0.5
C1A A:COH512 3.0 18.1 0.5
C4B A:COH512 3.0 19.6 0.5
C1A A:COH512 3.0 18.5 0.5
C1B A:COH512 3.0 20.1 0.5
C4B A:COH512 3.0 18.9 0.5
C4A A:COH512 3.0 19.0 0.5
C4C A:COH512 3.0 18.5 0.5
C1D A:COH512 3.0 18.8 0.5
C1B A:COH512 3.0 17.5 0.5
C4D A:COH512 3.0 18.4 0.5
C1C A:COH512 3.1 19.9 0.5
CB A:CYS400 3.3 18.8 1.0
CHD A:COH512 3.4 18.3 0.5
CHB A:COH512 3.4 17.6 0.5
CHA A:COH512 3.4 17.8 0.5
CHB A:COH512 3.4 19.1 0.5
CHD A:COH512 3.4 18.7 0.5
CHA A:COH512 3.4 17.8 0.5
CHC A:COH512 3.4 18.7 0.5
CHC A:COH512 3.4 19.4 0.5
S A:DMS513 3.6 61.1 1.0
CA A:CYS400 4.0 16.1 1.0
C1 A:DMS513 4.2 53.2 1.0
C3C A:COH512 4.2 19.9 0.5
C3A A:COH512 4.3 18.2 0.5
C2D A:COH512 4.3 18.5 0.5
C3B A:COH512 4.3 20.0 0.5
C3D A:COH512 4.3 18.1 0.5
C2C A:COH512 4.3 19.5 0.5
C2A A:COH512 4.3 17.9 0.5
C3A A:COH512 4.3 18.8 0.5
C3B A:COH512 4.3 19.2 0.5
C2D A:COH512 4.3 18.7 0.5
C2A A:COH512 4.3 18.3 0.5
C2B A:COH512 4.3 20.0 0.5
C3C A:COH512 4.3 20.3 0.5
C3D A:COH512 4.4 18.4 0.5
C2B A:COH512 4.4 18.4 0.5
C2C A:COH512 4.4 20.7 0.5
C2 A:DMS513 4.5 51.9 1.0
CB A:ALA264 4.7 25.7 0.5
C A:CYS400 4.8 17.9 1.0
N A:GLY402 4.9 19.2 1.0
CB A:ALA264 4.9 29.2 0.5
N A:ILE401 4.9 17.2 1.0

Cobalt binding site 2 out of 4 in 6jvc

Go back to Cobalt Binding Sites List in 6jvc
Cobalt binding site 2 out of 4 in the Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co512

b:18.6
occ:0.53
 CO A:COH512 0.0 18.6 0.5
CO A:COH512 0.0 18.4 0.5
NC A:COH512 1.9 19.4 0.5
ND A:COH512 1.9 17.5 0.5
NA A:COH512 1.9 17.4 0.5
NB A:COH512 1.9 19.9 0.5
NB A:COH512 1.9 18.4 0.5
NC A:COH512 2.0 19.1 0.5
NA A:COH512 2.0 18.7 0.5
ND A:COH512 2.0 18.6 0.5
O A:DMS513 2.1 36.4 1.0
SG A:CYS400 2.4 20.7 1.0
C4C A:COH512 2.9 19.8 0.5
C1D A:COH512 3.0 18.8 0.5
C4A A:COH512 3.0 18.4 0.5
C1C A:COH512 3.0 19.0 0.5
C4B A:COH512 3.0 19.6 0.5
C4B A:COH512 3.0 18.9 0.5
C1B A:COH512 3.0 20.1 0.5
C4D A:COH512 3.0 18.3 0.5
C1A A:COH512 3.0 18.1 0.5
C4C A:COH512 3.0 18.5 0.5
C4A A:COH512 3.0 19.0 0.5
C1B A:COH512 3.0 17.5 0.5
C1A A:COH512 3.0 18.5 0.5
C1D A:COH512 3.0 18.8 0.5
C1C A:COH512 3.0 19.9 0.5
C4D A:COH512 3.0 18.4 0.5
CB A:CYS400 3.4 18.8 1.0
CHD A:COH512 3.4 18.3 0.5
CHB A:COH512 3.4 17.6 0.5
CHC A:COH512 3.4 18.7 0.5
CHB A:COH512 3.4 19.1 0.5
CHC A:COH512 3.4 19.4 0.5
CHD A:COH512 3.4 18.7 0.5
CHA A:COH512 3.4 17.8 0.5
CHA A:COH512 3.4 17.8 0.5
S A:DMS513 3.6 61.1 1.0
CA A:CYS400 4.0 16.1 1.0
C1 A:DMS513 4.2 53.2 1.0
C3C A:COH512 4.2 19.9 0.5
C3B A:COH512 4.3 20.0 0.5
C2C A:COH512 4.3 19.5 0.5
C3A A:COH512 4.3 18.2 0.5
C2D A:COH512 4.3 18.5 0.5
C3B A:COH512 4.3 19.2 0.5
C3D A:COH512 4.3 18.1 0.5
C2A A:COH512 4.3 17.9 0.5
C3A A:COH512 4.3 18.8 0.5
C2B A:COH512 4.3 20.0 0.5
C3C A:COH512 4.3 20.3 0.5
C2D A:COH512 4.3 18.7 0.5
C2A A:COH512 4.3 18.3 0.5
C2B A:COH512 4.4 18.4 0.5
C3D A:COH512 4.4 18.4 0.5
C2C A:COH512 4.4 20.7 0.5
C2 A:DMS513 4.5 51.9 1.0
CB A:ALA264 4.7 25.7 0.5
C A:CYS400 4.8 17.9 1.0
CB A:ALA264 4.8 29.2 0.5
N A:GLY402 4.9 19.2 1.0
N A:ILE401 5.0 17.2 1.0

Cobalt binding site 3 out of 4 in 6jvc

Go back to Cobalt Binding Sites List in 6jvc
Cobalt binding site 3 out of 4 in the Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co514

b:18.6
occ:0.48
 CO C:COH514 0.0 18.6 0.5
CO C:COH514 0.0 18.2 0.5
ND C:COH514 1.9 17.6 0.5
NA C:COH514 1.9 17.9 0.5
NC C:COH514 1.9 19.4 0.5
NC C:COH514 1.9 17.6 0.5
NB C:COH514 2.0 18.9 0.5
ND C:COH514 2.0 18.5 0.5
NA C:COH514 2.0 18.2 0.5
NB C:COH514 2.0 17.9 0.5
O C:DMS515 2.2 33.9 1.0
SG C:CYS400 2.3 19.5 1.0
C4C C:COH514 3.0 17.0 0.5
C1D C:COH514 3.0 17.2 0.5
C4C C:COH514 3.0 19.1 0.5
C4B C:COH514 3.0 18.7 0.5
C4A C:COH514 3.0 17.5 0.5
C4D C:COH514 3.0 17.6 0.5
C1C C:COH514 3.0 19.3 0.5
C1D C:COH514 3.0 18.2 0.5
C1A C:COH514 3.0 17.8 0.5
C4A C:COH514 3.0 17.8 0.5
C1B C:COH514 3.0 17.3 0.5
C1A C:COH514 3.0 17.7 0.5
C4B C:COH514 3.0 17.5 0.5
C1C C:COH514 3.0 17.0 0.5
C4D C:COH514 3.0 18.1 0.5
C1B C:COH514 3.1 18.3 0.5
CB C:CYS400 3.3 17.6 1.0
CHD C:COH514 3.4 16.3 0.5
CHB C:COH514 3.4 16.5 0.5
CHC C:COH514 3.4 17.6 0.5
CHD C:COH514 3.4 18.7 0.5
CHC C:COH514 3.4 18.1 0.5
CHA C:COH514 3.4 17.4 0.5
CHB C:COH514 3.4 18.3 0.5
CHA C:COH514 3.4 17.8 0.5
S C:DMS515 3.6 63.3 1.0
CA C:CYS400 4.0 17.1 1.0
C3C C:COH514 4.3 19.5 0.5
C3B C:COH514 4.3 19.1 0.5
C2D C:COH514 4.3 17.4 0.5
C3A C:COH514 4.3 17.7 0.5
C3D C:COH514 4.3 18.0 0.5
C2A C:COH514 4.3 18.0 0.5
C3C C:COH514 4.3 18.3 0.5
C2C C:COH514 4.3 19.9 0.5
C2D C:COH514 4.3 17.3 0.5
C3B C:COH514 4.3 18.2 0.5
C2A C:COH514 4.3 17.6 0.5
C3A C:COH514 4.3 16.9 0.5
C3D C:COH514 4.4 18.0 0.5
C2B C:COH514 4.4 18.7 0.5
C2C C:COH514 4.4 17.6 0.5
C2B C:COH514 4.4 18.1 0.5
C2 C:DMS515 4.4 55.5 1.0
C1 C:DMS515 4.6 58.6 1.0
CB C:ALA264 4.8 25.5 0.5
C C:CYS400 4.8 16.9 1.0
N C:GLY402 4.8 17.0 1.0
CB C:ALA264 4.8 26.7 0.5
N C:ILE401 4.9 19.1 1.0

Cobalt binding site 4 out of 4 in 6jvc

Go back to Cobalt Binding Sites List in 6jvc
Cobalt binding site 4 out of 4 in the Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co514

b:18.2
occ:0.52
 CO C:COH514 0.0 18.2 0.5
CO C:COH514 0.0 18.6 0.5
NC C:COH514 1.9 19.4 0.5
NB C:COH514 1.9 18.9 0.5
ND C:COH514 1.9 17.6 0.5
ND C:COH514 1.9 18.5 0.5
NA C:COH514 1.9 17.9 0.5
NA C:COH514 2.0 18.2 0.5
NC C:COH514 2.0 17.6 0.5
NB C:COH514 2.0 17.9 0.5
O C:DMS515 2.2 33.9 1.0
SG C:CYS400 2.3 19.5 1.0
C4C C:COH514 3.0 19.1 0.5
C4B C:COH514 3.0 18.7 0.5
C1D C:COH514 3.0 18.2 0.5
C1C C:COH514 3.0 19.3 0.5
C4C C:COH514 3.0 17.0 0.5
C1D C:COH514 3.0 17.2 0.5
C4A C:COH514 3.0 17.8 0.5
C4A C:COH514 3.0 17.5 0.5
C4D C:COH514 3.0 17.6 0.5
C1A C:COH514 3.0 17.8 0.5
C1A C:COH514 3.0 17.7 0.5
C4D C:COH514 3.0 18.1 0.5
C1B C:COH514 3.0 18.3 0.5
C4B C:COH514 3.0 17.5 0.5
C1C C:COH514 3.0 17.0 0.5
C1B C:COH514 3.0 17.3 0.5
CB C:CYS400 3.3 17.6 1.0
CHC C:COH514 3.4 17.6 0.5
CHD C:COH514 3.4 16.3 0.5
CHD C:COH514 3.4 18.7 0.5
CHB C:COH514 3.4 16.5 0.5
CHC C:COH514 3.4 18.1 0.5
CHB C:COH514 3.4 18.3 0.5
CHA C:COH514 3.4 17.4 0.5
CHA C:COH514 3.5 17.8 0.5
S C:DMS515 3.6 63.3 1.0
CA C:CYS400 4.0 17.1 1.0
C3C C:COH514 4.2 19.5 0.5
C3B C:COH514 4.3 19.1 0.5
C2C C:COH514 4.3 19.9 0.5
C2D C:COH514 4.3 17.4 0.5
C3A C:COH514 4.3 17.7 0.5
C2D C:COH514 4.3 17.3 0.5
C3C C:COH514 4.3 18.3 0.5
C3D C:COH514 4.3 18.0 0.5
C2A C:COH514 4.3 18.0 0.5
C3A C:COH514 4.3 16.9 0.5
C2A C:COH514 4.3 17.6 0.5
C2B C:COH514 4.3 18.7 0.5
C3D C:COH514 4.3 18.0 0.5
C3B C:COH514 4.3 18.2 0.5
C2C C:COH514 4.4 17.6 0.5
C2B C:COH514 4.4 18.1 0.5
C2 C:DMS515 4.4 55.5 1.0
C1 C:DMS515 4.6 58.6 1.0
CB C:ALA264 4.8 25.5 0.5
C C:CYS400 4.8 16.9 1.0
N C:GLY402 4.8 17.0 1.0
CB C:ALA264 4.9 26.7 0.5
N C:ILE401 5.0 19.1 1.0

Reference:

O.Shoji, J.K.Stanfield. Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan at 1.75 Angstrom Resolution To Be Published.
Page generated: Sun Jul 13 21:03:37 2025

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