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Iron in PDB 3nc6: CYP134A1 1-Phenylimidazole Bound Structure

Protein crystallography data

The structure of CYP134A1 1-Phenylimidazole Bound Structure, PDB code: 3nc6 was solved by M.J.Cryle, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.84 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.950, 106.900, 142.930, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 27.8

Other elements in 3nc6:

The structure of CYP134A1 1-Phenylimidazole Bound Structure also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the CYP134A1 1-Phenylimidazole Bound Structure (pdb code 3nc6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the CYP134A1 1-Phenylimidazole Bound Structure, PDB code: 3nc6:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3nc6

Go back to Iron Binding Sites List in 3nc6
Iron binding site 1 out of 2 in the CYP134A1 1-Phenylimidazole Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CYP134A1 1-Phenylimidazole Bound Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe406

b:24.9
occ:1.00
FE A:HEM406 0.0 24.9 1.0
ND A:HEM406 2.0 21.6 1.0
NA A:HEM406 2.1 19.2 1.0
NC A:HEM406 2.1 18.6 1.0
NB A:HEM406 2.1 19.6 1.0
SG A:CYS353 2.5 58.8 1.0
C4D A:HEM406 3.0 24.2 1.0
C1A A:HEM406 3.0 19.9 1.0
C1D A:HEM406 3.1 22.7 1.0
C1C A:HEM406 3.1 19.3 1.0
C4C A:HEM406 3.1 19.1 1.0
C4B A:HEM406 3.1 19.7 1.0
C4A A:HEM406 3.1 19.4 1.0
C1B A:HEM406 3.1 19.6 1.0
CB A:CYS353 3.2 58.6 1.0
CHA A:HEM406 3.4 21.8 1.0
CHD A:HEM406 3.4 20.6 1.0
CHC A:HEM406 3.4 18.5 1.0
CHB A:HEM406 3.5 18.3 1.0
N3 A:PIW407 3.9 63.8 1.0
CA A:CYS353 4.1 62.9 1.0
O A:ALA233 4.2 47.5 1.0
C2A A:HEM406 4.3 21.3 1.0
C3D A:HEM406 4.3 27.2 1.0
C2C A:HEM406 4.3 19.6 1.0
C2D A:HEM406 4.3 25.3 1.0
C3C A:HEM406 4.3 19.8 1.0
C3A A:HEM406 4.3 19.9 1.0
C3B A:HEM406 4.3 20.4 1.0
C2B A:HEM406 4.3 20.0 1.0
C4 A:PIW407 4.5 63.8 1.0
CB A:ALA233 4.6 51.7 1.0
C A:CYS353 4.8 65.2 1.0
C A:ALA233 4.8 47.9 1.0
C2 A:PIW407 4.9 64.7 1.0

Iron binding site 2 out of 2 in 3nc6

Go back to Iron Binding Sites List in 3nc6
Iron binding site 2 out of 2 in the CYP134A1 1-Phenylimidazole Bound Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CYP134A1 1-Phenylimidazole Bound Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe406

b:21.6
occ:1.00
FE B:HEM406 0.0 21.6 1.0
NB B:HEM406 2.0 18.5 1.0
ND B:HEM406 2.0 18.9 1.0
NA B:HEM406 2.0 17.9 1.0
NC B:HEM406 2.0 17.0 1.0
SG B:CYS353 2.2 36.9 1.0
C4D B:HEM406 3.0 21.9 1.0
C1D B:HEM406 3.0 20.9 1.0
C1B B:HEM406 3.0 19.0 1.0
C4B B:HEM406 3.0 19.4 1.0
C1A B:HEM406 3.0 19.2 1.0
C4C B:HEM406 3.0 16.5 1.0
C4A B:HEM406 3.1 18.0 1.0
C1C B:HEM406 3.1 17.6 1.0
CB B:CYS353 3.2 36.9 1.0
CHA B:HEM406 3.4 20.7 1.0
CHD B:HEM406 3.4 18.3 1.0
CHB B:HEM406 3.4 17.9 1.0
CHC B:HEM406 3.4 18.3 1.0
N3 B:PIW407 4.1 47.0 1.0
CA B:CYS353 4.2 39.3 1.0
C2B B:HEM406 4.2 19.1 1.0
C2D B:HEM406 4.2 22.8 1.0
C3B B:HEM406 4.2 20.2 1.0
C3D B:HEM406 4.2 25.6 1.0
C3C B:HEM406 4.3 16.6 1.0
C2A B:HEM406 4.3 19.1 1.0
C2C B:HEM406 4.3 16.7 1.0
C3A B:HEM406 4.3 17.6 1.0
CB B:ALA233 4.6 40.8 1.0
O B:ALA233 4.7 39.9 1.0
C4 B:PIW407 4.9 46.3 1.0
C B:CYS353 4.9 40.2 1.0

Reference:

M.J.Cryle, S.G.Bell, I.Schlichting. Structural and Biochemical Characterization of the Cytochrome P450 Cypx (CYP134A1) From Bacillus Subtilis: A Cyclo-L-Leucyl-L-Leucyl Dipeptide Oxidase. Biochemistry V. 49 7282 2010.
ISSN: ISSN 0006-2960
PubMed: 20690619
DOI: 10.1021/BI100910Y
Page generated: Sun Dec 13 15:14:04 2020

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