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Iron in PDB 6jlv: Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan

Enzymatic activity of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan

All present enzymatic activity of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan, PDB code: 6jlv was solved by J.K.Stanfield, 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) 48.22 / 1.22
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.964, 148.732, 63.910, 90.00, 98.38, 90.00
R / Rfree (%) 13.4 / 15.6

Other elements in 6jlv:

The structure of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 6jlv

Go back to Iron Binding Sites List in 6jlv
Iron binding site 1 out of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:11.3
occ:0.47
FE A:HEM501 0.0 11.3 0.5
FE A:HEM501 0.0 12.1 0.5
ND A:HEM501 1.9 11.1 0.5
ND A:HEM501 2.0 11.1 0.5
NA A:HEM501 2.0 11.4 0.5
NA A:HEM501 2.1 10.3 0.5
NB A:HEM501 2.1 11.8 0.5
NC A:HEM501 2.1 11.3 0.5
NC A:HEM501 2.1 11.1 0.5
NB A:HEM501 2.1 11.0 0.5
O A:HOH684 2.2 18.8 1.0
SG A:CYS400 2.3 12.4 1.0
C1D A:HEM501 2.9 11.7 0.5
C4D A:HEM501 3.0 10.9 0.5
C1D A:HEM501 3.0 11.2 0.5
C4B A:HEM501 3.0 12.3 0.5
C4D A:HEM501 3.0 11.1 0.5
C4C A:HEM501 3.0 11.3 0.5
C1B A:HEM501 3.0 11.8 0.5
C4B A:HEM501 3.0 10.9 0.5
C4C A:HEM501 3.0 12.0 0.5
C1A A:HEM501 3.1 10.9 0.5
C1B A:HEM501 3.1 11.1 0.5
C4A A:HEM501 3.1 11.7 0.5
C1A A:HEM501 3.1 10.4 0.5
C1C A:HEM501 3.1 11.4 0.5
C1C A:HEM501 3.1 11.5 0.5
C4A A:HEM501 3.1 10.2 0.5
CB A:CYS400 3.3 11.4 1.0
CHD A:HEM501 3.4 11.4 0.5
CHD A:HEM501 3.4 11.4 0.5
CHB A:HEM501 3.4 11.8 0.5
CHA A:HEM501 3.4 10.4 0.5
CHC A:HEM501 3.4 11.8 0.5
CHA A:HEM501 3.5 10.8 0.5
CHC A:HEM501 3.5 11.1 0.5
CHB A:HEM501 3.5 10.4 0.5
CA A:CYS400 4.0 10.8 1.0
O A:ALA264 4.2 17.5 1.0
C2D A:HEM501 4.2 11.3 0.5
C3D A:HEM501 4.2 11.4 0.5
C3C A:HEM501 4.3 11.5 0.5
C2C A:HEM501 4.3 11.2 0.5
C3C A:HEM501 4.3 12.2 0.5
C2B A:HEM501 4.3 12.1 0.5
C2C A:HEM501 4.3 12.0 0.5
C2A A:HEM501 4.3 10.7 0.5
C3A A:HEM501 4.3 11.5 0.5
C2D A:HEM501 4.3 11.4 0.5
C3B A:HEM501 4.3 12.5 0.5
C3A A:HEM501 4.3 10.5 0.5
C2B A:HEM501 4.3 10.9 0.5
C2A A:HEM501 4.3 10.3 0.5
C3D A:HEM501 4.3 11.0 0.5
C3B A:HEM501 4.3 11.0 0.5
CB A:ALA264 4.5 18.8 1.0
N A:GLY402 4.7 11.3 1.0
C A:CYS400 4.8 10.7 1.0
C A:ALA264 4.8 17.2 1.0
N A:ILE401 4.9 10.8 1.0

Iron binding site 2 out of 4 in 6jlv

Go back to Iron Binding Sites List in 6jlv
Iron binding site 2 out of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.1
occ:0.53
FE A:HEM501 0.0 12.1 0.5
FE A:HEM501 0.0 11.3 0.5
ND A:HEM501 1.9 11.1 0.5
ND A:HEM501 2.0 11.1 0.5
NA A:HEM501 2.0 10.3 0.5
NA A:HEM501 2.0 11.4 0.5
NC A:HEM501 2.0 11.3 0.5
NB A:HEM501 2.1 11.0 0.5
NB A:HEM501 2.1 11.8 0.5
NC A:HEM501 2.1 11.1 0.5
O A:HOH684 2.2 18.8 1.0
SG A:CYS400 2.3 12.4 1.0
C1D A:HEM501 3.0 11.2 0.5
C1D A:HEM501 3.0 11.7 0.5
C4D A:HEM501 3.0 10.9 0.5
C4D A:HEM501 3.0 11.1 0.5
C4C A:HEM501 3.0 12.0 0.5
C4B A:HEM501 3.0 10.9 0.5
C4B A:HEM501 3.0 12.3 0.5
C1B A:HEM501 3.1 11.1 0.5
C1A A:HEM501 3.1 10.4 0.5
C4C A:HEM501 3.1 11.3 0.5
C4A A:HEM501 3.1 10.2 0.5
C1A A:HEM501 3.1 10.9 0.5
C1B A:HEM501 3.1 11.8 0.5
C1C A:HEM501 3.1 11.5 0.5
C4A A:HEM501 3.1 11.7 0.5
C1C A:HEM501 3.1 11.4 0.5
CB A:CYS400 3.3 11.4 1.0
CHD A:HEM501 3.4 11.4 0.5
CHD A:HEM501 3.4 11.4 0.5
CHA A:HEM501 3.4 10.4 0.5
CHA A:HEM501 3.4 10.8 0.5
CHB A:HEM501 3.4 10.4 0.5
CHC A:HEM501 3.5 11.8 0.5
CHB A:HEM501 3.5 11.8 0.5
CHC A:HEM501 3.5 11.1 0.5
CA A:CYS400 4.0 10.8 1.0
O A:ALA264 4.2 17.5 1.0
C3C A:HEM501 4.2 12.2 0.5
C2D A:HEM501 4.2 11.3 0.5
C3D A:HEM501 4.3 11.4 0.5
C2D A:HEM501 4.3 11.4 0.5
C3A A:HEM501 4.3 10.5 0.5
C2C A:HEM501 4.3 12.0 0.5
C2A A:HEM501 4.3 10.3 0.5
C2B A:HEM501 4.3 10.9 0.5
C3D A:HEM501 4.3 11.0 0.5
C2C A:HEM501 4.3 11.2 0.5
C3C A:HEM501 4.3 11.5 0.5
C2A A:HEM501 4.3 10.7 0.5
C3A A:HEM501 4.3 11.5 0.5
C3B A:HEM501 4.3 11.0 0.5
C2B A:HEM501 4.3 12.1 0.5
C3B A:HEM501 4.3 12.5 0.5
CB A:ALA264 4.5 18.8 1.0
N A:GLY402 4.8 11.3 1.0
C A:CYS400 4.8 10.7 1.0
C A:ALA264 4.8 17.2 1.0
N A:ILE401 4.9 10.8 1.0

Iron binding site 3 out of 4 in 6jlv

Go back to Iron Binding Sites List in 6jlv
Iron binding site 3 out of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.4
occ:0.41
FE B:HEM501 0.0 11.4 0.4
FE B:HEM501 0.0 11.5 0.6
ND B:HEM501 1.9 10.7 0.4
ND B:HEM501 1.9 10.8 0.6
NA B:HEM501 2.0 10.3 0.6
NA B:HEM501 2.0 10.8 0.4
NC B:HEM501 2.0 10.4 0.4
NB B:HEM501 2.0 11.2 0.6
NB B:HEM501 2.1 10.8 0.4
NC B:HEM501 2.1 11.2 0.6
O B:HOH624 2.2 19.2 1.0
SG B:CYS400 2.3 12.2 1.0
C1D B:HEM501 2.9 10.7 0.4
C4D B:HEM501 3.0 10.5 0.4
C4D B:HEM501 3.0 11.0 0.6
C1D B:HEM501 3.0 10.8 0.6
C4C B:HEM501 3.0 10.7 0.4
C4B B:HEM501 3.0 11.5 0.6
C4B B:HEM501 3.0 11.0 0.4
C1B B:HEM501 3.0 11.0 0.6
C1A B:HEM501 3.0 10.9 0.4
C4A B:HEM501 3.1 10.4 0.6
C1A B:HEM501 3.1 9.9 0.6
C1B B:HEM501 3.1 11.1 0.4
C4C B:HEM501 3.1 11.8 0.6
C4A B:HEM501 3.1 11.1 0.4
C1C B:HEM501 3.1 10.6 0.4
C1C B:HEM501 3.1 11.8 0.6
CB B:CYS400 3.3 10.8 1.0
CHD B:HEM501 3.4 10.8 0.4
CHA B:HEM501 3.4 10.7 0.4
CHB B:HEM501 3.4 10.8 0.6
CHA B:HEM501 3.4 10.6 0.6
CHD B:HEM501 3.4 11.7 0.6
CHC B:HEM501 3.4 11.8 0.6
CHC B:HEM501 3.5 11.0 0.4
CHB B:HEM501 3.5 11.2 0.4
CA B:CYS400 4.0 10.8 1.0
O B:ALA264 4.2 18.6 1.0
C2D B:HEM501 4.2 10.8 0.4
C3D B:HEM501 4.2 10.9 0.4
C3C B:HEM501 4.2 11.2 0.4
C2C B:HEM501 4.2 10.8 0.4
C2A B:HEM501 4.3 10.9 0.4
C2A B:HEM501 4.3 10.5 0.6
C3D B:HEM501 4.3 11.0 0.6
C3A B:HEM501 4.3 10.4 0.6
C3A B:HEM501 4.3 11.5 0.4
C2B B:HEM501 4.3 11.5 0.6
C2D B:HEM501 4.3 10.5 0.6
C2C B:HEM501 4.3 12.2 0.6
C3B B:HEM501 4.3 11.9 0.6
C2B B:HEM501 4.3 11.2 0.4
C3C B:HEM501 4.3 12.3 0.6
C3B B:HEM501 4.3 11.4 0.4
CB B:ALA264 4.5 19.6 1.0
C B:CYS400 4.8 11.3 1.0
C B:ALA264 4.8 17.8 1.0
N B:GLY402 4.8 11.5 1.0
N B:ILE401 5.0 11.4 1.0

Iron binding site 4 out of 4 in 6jlv

Go back to Iron Binding Sites List in 6jlv
Iron binding site 4 out of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.5
occ:0.59
FE B:HEM501 0.0 11.5 0.6
FE B:HEM501 0.0 11.4 0.4
ND B:HEM501 1.9 10.8 0.6
ND B:HEM501 2.0 10.7 0.4
NA B:HEM501 2.0 10.8 0.4
NB B:HEM501 2.0 10.8 0.4
NA B:HEM501 2.1 10.3 0.6
NC B:HEM501 2.1 10.4 0.4
NC B:HEM501 2.1 11.2 0.6
NB B:HEM501 2.1 11.2 0.6
O B:HOH624 2.2 19.2 1.0
SG B:CYS400 2.3 12.2 1.0
C1D B:HEM501 3.0 10.8 0.6
C1D B:HEM501 3.0 10.7 0.4
C4D B:HEM501 3.0 11.0 0.6
C4B B:HEM501 3.0 11.0 0.4
C4D B:HEM501 3.0 10.5 0.4
C1B B:HEM501 3.0 11.1 0.4
C4B B:HEM501 3.0 11.5 0.6
C4C B:HEM501 3.0 11.8 0.6
C4C B:HEM501 3.0 10.7 0.4
C1A B:HEM501 3.0 10.9 0.4
C4A B:HEM501 3.1 11.1 0.4
C1C B:HEM501 3.1 11.8 0.6
C1B B:HEM501 3.1 11.0 0.6
C1C B:HEM501 3.1 10.6 0.4
C1A B:HEM501 3.1 9.9 0.6
C4A B:HEM501 3.1 10.4 0.6
CB B:CYS400 3.3 10.8 1.0
CHD B:HEM501 3.4 11.7 0.6
CHD B:HEM501 3.4 10.8 0.4
CHC B:HEM501 3.4 11.8 0.6
CHA B:HEM501 3.4 10.7 0.4
CHC B:HEM501 3.4 11.0 0.4
CHB B:HEM501 3.5 11.2 0.4
CHA B:HEM501 3.5 10.6 0.6
CHB B:HEM501 3.5 10.8 0.6
CA B:CYS400 4.0 10.8 1.0
O B:ALA264 4.1 18.6 1.0
C2A B:HEM501 4.2 10.9 0.4
C2B B:HEM501 4.2 11.2 0.4
C2C B:HEM501 4.2 12.2 0.6
C3A B:HEM501 4.2 11.5 0.4
C3C B:HEM501 4.2 12.3 0.6
C3C B:HEM501 4.3 11.2 0.4
C3D B:HEM501 4.3 11.0 0.6
C2C B:HEM501 4.3 10.8 0.4
C2D B:HEM501 4.3 10.8 0.4
C2D B:HEM501 4.3 10.5 0.6
C3B B:HEM501 4.3 11.4 0.4
C3D B:HEM501 4.3 10.9 0.4
C2B B:HEM501 4.3 11.5 0.6
C3B B:HEM501 4.3 11.9 0.6
C2A B:HEM501 4.3 10.5 0.6
C3A B:HEM501 4.3 10.4 0.6
CB B:ALA264 4.5 19.6 1.0
C B:ALA264 4.8 17.8 1.0
N B:GLY402 4.8 11.5 1.0
C B:CYS400 4.8 11.3 1.0
N B:ILE401 5.0 11.4 1.0

Reference:

O.Shoji, J.K.Stanfield. Structure of CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan at 1.22 Angstrom Resolution To Be Published.
Page generated: Tue Aug 6 23:23:52 2024

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