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Iron in PDB 7d1f: Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine

Enzymatic activity of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine

All present enzymatic activity of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine, PDB code: 7d1f was solved by J.K.Stanfield, H.Sugimoto, O.Shoji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.23 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.474, 127.338, 147.759, 90, 90, 90
R / Rfree (%) 14.3 / 17.4

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine (pdb code 7d1f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine, PDB code: 7d1f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7d1f

Go back to Iron Binding Sites List in 7d1f
Iron binding site 1 out of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:15.0
occ:0.70
 FE A:HEM501 0.0 15.0 0.7
FE A:HEM501 0.0 14.2 0.3
ND A:HEM501 1.9 14.1 0.3
ND A:HEM501 1.9 13.2 0.7
NA A:HEM501 2.0 12.8 0.3
NA A:HEM501 2.0 14.4 0.7
NC A:HEM501 2.0 13.1 0.3
NC A:HEM501 2.1 14.9 0.7
NB A:HEM501 2.1 14.3 0.7
NB A:HEM501 2.1 13.5 0.3
N A:NME503 2.2 14.1 0.7
N A:NME503 2.2 16.5 0.3
SG A:CYS400 2.3 14.9 1.0
C1D A:HEM501 2.9 14.1 0.3
C4D A:HEM501 2.9 13.8 0.3
C1D A:HEM501 3.0 13.3 0.7
C4D A:HEM501 3.0 13.5 0.7
C4C A:HEM501 3.0 13.5 0.3
C4C A:HEM501 3.0 15.0 0.7
C1A A:HEM501 3.0 13.2 0.3
C4B A:HEM501 3.0 15.1 0.7
C1B A:HEM501 3.0 14.8 0.7
C1A A:HEM501 3.0 13.7 0.7
C4B A:HEM501 3.1 13.0 0.3
C1B A:HEM501 3.1 12.9 0.3
C4A A:HEM501 3.1 14.6 0.7
C4A A:HEM501 3.1 12.8 0.3
C1C A:HEM501 3.1 13.1 0.3
C1C A:HEM501 3.1 14.7 0.7
C A:NME503 3.2 16.6 0.3
C A:NME503 3.3 18.0 0.7
CB A:CYS400 3.3 14.4 1.0
CHD A:HEM501 3.3 14.2 0.3
CHD A:HEM501 3.4 15.4 0.7
CHA A:HEM501 3.4 13.6 0.3
CHB A:HEM501 3.4 14.8 0.7
CHA A:HEM501 3.4 13.5 0.7
CHC A:HEM501 3.5 15.7 0.7
CHC A:HEM501 3.5 13.7 0.3
CHB A:HEM501 3.5 13.6 0.3
CA A:CYS400 4.0 14.4 1.0
C2D A:HEM501 4.2 14.2 0.3
C3C A:HEM501 4.2 13.6 0.3
C3D A:HEM501 4.2 14.7 0.3
C2D A:HEM501 4.2 14.3 0.7
C2A A:HEM501 4.2 13.8 0.3
C3D A:HEM501 4.2 14.7 0.7
C2C A:HEM501 4.3 12.5 0.3
C3A A:HEM501 4.3 13.6 0.3
C3C A:HEM501 4.3 16.3 0.7
C2C A:HEM501 4.3 16.6 0.7
C3A A:HEM501 4.3 14.2 0.7
C2A A:HEM501 4.3 14.9 0.7
C2B A:HEM501 4.3 15.1 0.7
C2B A:HEM501 4.3 12.7 0.3
C3B A:HEM501 4.3 14.8 0.7
C3B A:HEM501 4.3 13.0 0.3
C A:CYS400 4.8 14.9 1.0
N A:GLY402 4.8 14.8 1.0
N A:ILE401 5.0 14.0 1.0
CB A:ALA264 5.0 19.9 1.0

Iron binding site 2 out of 4 in 7d1f

Go back to Iron Binding Sites List in 7d1f
Iron binding site 2 out of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:14.2
occ:0.30
 FE A:HEM501 0.0 14.2 0.3
FE A:HEM501 0.0 15.0 0.7
ND A:HEM501 1.9 14.1 0.3
ND A:HEM501 1.9 13.2 0.7
NA A:HEM501 2.0 12.8 0.3
NA A:HEM501 2.0 14.4 0.7
NC A:HEM501 2.1 13.1 0.3
NC A:HEM501 2.1 14.9 0.7
NB A:HEM501 2.1 14.3 0.7
NB A:HEM501 2.1 13.5 0.3
N A:NME503 2.2 14.1 0.7
N A:NME503 2.2 16.5 0.3
SG A:CYS400 2.3 14.9 1.0
C1D A:HEM501 2.9 14.1 0.3
C4D A:HEM501 2.9 13.8 0.3
C1D A:HEM501 3.0 13.3 0.7
C4D A:HEM501 3.0 13.5 0.7
C4C A:HEM501 3.0 13.5 0.3
C1A A:HEM501 3.0 13.2 0.3
C4C A:HEM501 3.0 15.0 0.7
C1A A:HEM501 3.0 13.7 0.7
C1B A:HEM501 3.0 14.8 0.7
C4B A:HEM501 3.1 15.1 0.7
C4A A:HEM501 3.1 14.6 0.7
C4B A:HEM501 3.1 13.0 0.3
C1B A:HEM501 3.1 12.9 0.3
C4A A:HEM501 3.1 12.8 0.3
C1C A:HEM501 3.1 13.1 0.3
C1C A:HEM501 3.1 14.7 0.7
C A:NME503 3.2 16.6 0.3
C A:NME503 3.3 18.0 0.7
CHD A:HEM501 3.3 14.2 0.3
CB A:CYS400 3.4 14.4 1.0
CHD A:HEM501 3.4 15.4 0.7
CHA A:HEM501 3.4 13.6 0.3
CHA A:HEM501 3.4 13.5 0.7
CHB A:HEM501 3.4 14.8 0.7
CHC A:HEM501 3.5 15.7 0.7
CHB A:HEM501 3.5 13.6 0.3
CHC A:HEM501 3.5 13.7 0.3
CA A:CYS400 4.0 14.4 1.0
C2D A:HEM501 4.2 14.2 0.3
C3D A:HEM501 4.2 14.7 0.3
C3C A:HEM501 4.2 13.6 0.3
C2D A:HEM501 4.2 14.3 0.7
C2A A:HEM501 4.2 13.8 0.3
C3D A:HEM501 4.2 14.7 0.7
C3A A:HEM501 4.2 13.6 0.3
C3C A:HEM501 4.3 16.3 0.7
C2C A:HEM501 4.3 12.5 0.3
C3A A:HEM501 4.3 14.2 0.7
C2A A:HEM501 4.3 14.9 0.7
C2C A:HEM501 4.3 16.6 0.7
C2B A:HEM501 4.3 15.1 0.7
C2B A:HEM501 4.3 12.7 0.3
C3B A:HEM501 4.3 14.8 0.7
C3B A:HEM501 4.3 13.0 0.3
C A:CYS400 4.8 14.9 1.0
N A:GLY402 4.8 14.8 1.0
N A:ILE401 5.0 14.0 1.0
CB A:ALA264 5.0 19.9 1.0

Iron binding site 3 out of 4 in 7d1f

Go back to Iron Binding Sites List in 7d1f
Iron binding site 3 out of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.4
occ:0.50
 FE B:HEM501 0.0 13.4 0.5
FE B:HEM501 0.0 13.4 0.5
ND B:HEM501 1.9 13.1 0.5
ND B:HEM501 1.9 12.4 0.5
NA B:HEM501 2.0 12.6 0.5
NA B:HEM501 2.0 11.7 0.5
NC B:HEM501 2.0 12.8 0.5
NB B:HEM501 2.0 12.4 0.5
NC B:HEM501 2.1 13.1 0.5
NB B:HEM501 2.1 12.8 0.5
N B:NME503 2.1 15.0 0.5
N B:NME503 2.2 14.6 0.5
SG B:CYS400 2.3 13.7 1.0
C1D B:HEM501 2.9 13.7 0.5
C4D B:HEM501 3.0 11.8 0.5
C4D B:HEM501 3.0 12.6 0.5
C1D B:HEM501 3.0 12.3 0.5
C4C B:HEM501 3.0 13.9 0.5
C4B B:HEM501 3.0 12.9 0.5
C4C B:HEM501 3.0 14.4 0.5
C4B B:HEM501 3.0 13.8 0.5
C1A B:HEM501 3.0 12.1 0.5
C1A B:HEM501 3.0 11.2 0.5
C1B B:HEM501 3.0 12.7 0.5
C1B B:HEM501 3.1 13.7 0.5
C4A B:HEM501 3.1 12.6 0.5
C1C B:HEM501 3.1 13.6 0.5
C1C B:HEM501 3.1 13.9 0.5
C4A B:HEM501 3.1 10.9 0.5
C B:NME503 3.2 15.4 0.5
C B:NME503 3.2 15.5 0.5
CB B:CYS400 3.4 11.9 1.0
CHD B:HEM501 3.4 13.6 0.5
CHD B:HEM501 3.4 13.5 0.5
CHA B:HEM501 3.4 11.7 0.5
CHA B:HEM501 3.4 11.7 0.5
CHC B:HEM501 3.4 13.1 0.5
CHC B:HEM501 3.4 13.7 0.5
CHB B:HEM501 3.4 13.0 0.5
CHB B:HEM501 3.5 11.9 0.5
CA B:CYS400 4.1 12.1 1.0
C3C B:HEM501 4.2 14.9 0.5
C2D B:HEM501 4.2 13.8 0.5
C2A B:HEM501 4.2 12.6 0.5
C3D B:HEM501 4.2 13.3 0.5
C3A B:HEM501 4.2 12.8 0.5
C2D B:HEM501 4.2 12.4 0.5
C2C B:HEM501 4.2 14.0 0.5
C3C B:HEM501 4.2 14.3 0.5
C3D B:HEM501 4.2 12.5 0.5
C2C B:HEM501 4.3 14.7 0.5
C3B B:HEM501 4.3 13.3 0.5
C2B B:HEM501 4.3 13.2 0.5
C2A B:HEM501 4.3 11.5 0.5
C2B B:HEM501 4.3 13.4 0.5
C3A B:HEM501 4.3 11.2 0.5
C3B B:HEM501 4.3 14.5 0.5
N B:GLY402 4.8 14.2 1.0
C B:CYS400 4.9 13.2 1.0
CB B:ALA264 5.0 19.7 1.0

Iron binding site 4 out of 4 in 7d1f

Go back to Iron Binding Sites List in 7d1f
Iron binding site 4 out of 4 in the Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L- Phenylalanine in Complex with Methylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.4
occ:0.50
 FE B:HEM501 0.0 13.4 0.5
FE B:HEM501 0.0 13.4 0.5
ND B:HEM501 1.9 13.1 0.5
ND B:HEM501 1.9 12.4 0.5
NA B:HEM501 2.0 11.7 0.5
NA B:HEM501 2.0 12.6 0.5
NC B:HEM501 2.0 12.8 0.5
NB B:HEM501 2.0 12.4 0.5
NC B:HEM501 2.1 13.1 0.5
NB B:HEM501 2.1 12.8 0.5
N B:NME503 2.1 15.0 0.5
N B:NME503 2.2 14.6 0.5
SG B:CYS400 2.3 13.7 1.0
C4D B:HEM501 2.9 11.8 0.5
C1D B:HEM501 2.9 13.7 0.5
C1D B:HEM501 3.0 12.3 0.5
C4D B:HEM501 3.0 12.6 0.5
C4C B:HEM501 3.0 13.9 0.5
C4B B:HEM501 3.0 12.9 0.5
C1A B:HEM501 3.0 11.2 0.5
C1A B:HEM501 3.0 12.1 0.5
C1B B:HEM501 3.0 12.7 0.5
C4C B:HEM501 3.0 14.4 0.5
C4B B:HEM501 3.0 13.8 0.5
C4A B:HEM501 3.1 12.6 0.5
C1B B:HEM501 3.1 13.7 0.5
C1C B:HEM501 3.1 13.6 0.5
C4A B:HEM501 3.1 10.9 0.5
C1C B:HEM501 3.1 13.9 0.5
C B:NME503 3.2 15.4 0.5
C B:NME503 3.3 15.5 0.5
CB B:CYS400 3.4 11.9 1.0
CHD B:HEM501 3.4 13.5 0.5
CHA B:HEM501 3.4 11.7 0.5
CHA B:HEM501 3.4 11.7 0.5
CHD B:HEM501 3.4 13.6 0.5
CHC B:HEM501 3.5 13.1 0.5
CHC B:HEM501 3.5 13.7 0.5
CHB B:HEM501 3.5 13.0 0.5
CHB B:HEM501 3.5 11.9 0.5
CA B:CYS400 4.0 12.1 1.0
C3C B:HEM501 4.2 14.9 0.5
C2D B:HEM501 4.2 13.8 0.5
C2D B:HEM501 4.2 12.4 0.5
C3D B:HEM501 4.2 12.5 0.5
C2A B:HEM501 4.2 12.6 0.5
C3D B:HEM501 4.2 13.3 0.5
C3A B:HEM501 4.2 12.8 0.5
C2C B:HEM501 4.2 14.0 0.5
C2A B:HEM501 4.2 11.5 0.5
C2B B:HEM501 4.3 13.2 0.5
C3B B:HEM501 4.3 13.3 0.5
C3A B:HEM501 4.3 11.2 0.5
C3C B:HEM501 4.3 14.3 0.5
C2C B:HEM501 4.3 14.7 0.5
C2B B:HEM501 4.3 13.4 0.5
C3B B:HEM501 4.3 14.5 0.5
N B:GLY402 4.8 14.2 1.0
C B:CYS400 4.9 13.2 1.0
CB B:ALA264 5.0 19.7 1.0

Reference:

O.Shoji, J.K.Stanfield. Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine in Complex with Methylamine at 1.45 Angstrom Resolution To Be Published.
Page generated: Thu Aug 8 03:33:02 2024

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