Atomistry » Cobalt » PDB 6ega-6kfl » 6jvc
Atomistry »
  Cobalt »
    PDB 6ega-6kfl »
      6jvc »

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: Tue Jul 30 18:42:49 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy