Iron in PDB 3nc3: CYP134A1 Structure with A Closed Substrate Binding Loop

The structure of CYP134A1 Structure with A Closed Substrate Binding Loop, PDB code: 3nc3 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)	47.74 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.800, 105.400, 143.900, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.3

The structure of CYP134A1 Structure with A Closed Substrate Binding Loop also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Iron atom in the CYP134A1 Structure with A Closed Substrate Binding Loop (pdb code 3nc3). 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 Structure with A Closed Substrate Binding Loop, PDB code: 3nc3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe406 b:29.1 occ:1.00 FE A:HEM406 0.0 29.1 1.0 NA A:HEM406 2.0 25.7 1.0 NC A:HEM406 2.0 23.8 1.0 ND A:HEM406 2.1 26.7 1.0 NB A:HEM406 2.1 24.2 1.0 SG A:CYS353 2.3 42.7 1.0 O A:HOH428 2.5 43.5 1.0 C4A A:HEM406 3.0 27.7 1.0 C4C A:HEM406 3.0 24.4 1.0 C1A A:HEM406 3.0 26.9 1.0 C1B A:HEM406 3.0 25.1 1.0 C1D A:HEM406 3.0 26.5 1.0 C4D A:HEM406 3.1 28.2 1.0 C1C A:HEM406 3.1 23.6 1.0 C4B A:HEM406 3.1 25.6 1.0 CB A:CYS353 3.3 45.1 1.0 CHB A:HEM406 3.4 25.9 1.0 CHD A:HEM406 3.4 25.1 1.0 CHA A:HEM406 3.4 27.5 1.0 CHC A:HEM406 3.5 25.1 1.0 CA A:CYS353 4.1 49.3 1.0 C3A A:HEM406 4.2 27.8 1.0 C2A A:HEM406 4.2 27.7 1.0 C3C A:HEM406 4.2 22.7 1.0 C2D A:HEM406 4.3 27.1 1.0 C2C A:HEM406 4.3 22.6 1.0 C2B A:HEM406 4.3 25.8 1.0 C3D A:HEM406 4.3 28.5 1.0 C3B A:HEM406 4.3 25.9 1.0 O A:ALA233 4.4 35.0 1.0 C A:CYS353 4.7 50.6 1.0 N A:VAL354 4.7 52.1 1.0 CB A:ALA233 4.7 38.7 1.0 N A:GLY355 4.8 48.2 1.0 C A:ALA233 4.9 35.9 1.0

Iron binding site 2 out of 2 in the CYP134A1 Structure with A Closed Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CYP134A1 Structure with A Closed Substrate Binding Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe406 b:26.1 occ:1.00 FE B:HEM406 0.0 26.1 1.0 NA B:HEM406 2.0 24.6 1.0 NB B:HEM406 2.0 22.3 1.0 NC B:HEM406 2.0 22.2 1.0 ND B:HEM406 2.1 25.0 1.0 O B:HOH431 2.1 45.9 1.0 SG B:CYS353 2.3 32.8 1.0 C4A B:HEM406 3.0 26.8 1.0 C1B B:HEM406 3.0 24.0 1.0 C4C B:HEM406 3.0 22.7 1.0 C1C B:HEM406 3.1 23.0 1.0 C1A B:HEM406 3.1 27.0 1.0 C4B B:HEM406 3.1 24.6 1.0 C1D B:HEM406 3.1 25.3 1.0 C4D B:HEM406 3.1 27.0 1.0 CB B:CYS353 3.2 33.7 1.0 CHB B:HEM406 3.4 25.8 1.0 CHD B:HEM406 3.4 23.2 1.0 CHA B:HEM406 3.4 27.6 1.0 CHC B:HEM406 3.5 24.8 1.0 CA B:CYS353 3.9 36.0 1.0 C3A B:HEM406 4.2 26.7 1.0 C3C B:HEM406 4.2 22.3 1.0 C2A B:HEM406 4.3 27.4 1.0 C2C B:HEM406 4.3 22.0 1.0 C2B B:HEM406 4.3 24.9 1.0 C3B B:HEM406 4.3 25.4 1.0 C2D B:HEM406 4.3 25.2 1.0 C3D B:HEM406 4.4 27.0 1.0 O B:ALA233 4.5 31.5 1.0 C B:CYS353 4.5 36.3 1.0 N B:GLY355 4.7 34.0 1.0 N B:VAL354 4.7 37.4 1.0 O2 B:GOL407 4.7 63.4 1.0 CB B:ALA233 4.9 33.5 1.0

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