Iron in PDB 1rz5: Di-Haem Cytochrome C Peroxidase, Form Out

All present enzymatic activity of Di-Haem Cytochrome C Peroxidase, Form Out:
1.11.1.5;

The structure of Di-Haem Cytochrome C Peroxidase, Form Out, PDB code: 1rz5 was solved by J.M.Dias, T.Alves, C.Bonifacio, A.S.Pereira, D.Bourgeois, I.Moura, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	150.553, 150.553, 155.349, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 20.9

The structure of Di-Haem Cytochrome C Peroxidase, Form Out also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Di-Haem Cytochrome C Peroxidase, Form Out (pdb code 1rz5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Di-Haem Cytochrome C Peroxidase, Form Out, PDB code: 1rz5:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Di-Haem Cytochrome C Peroxidase, Form Out


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Di-Haem Cytochrome C Peroxidase, Form Out within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:27.7 occ:1.00 FE A:HEM401 0.0 27.7 1.0 ND A:HEM401 2.0 27.9 1.0 NC A:HEM401 2.0 25.5 1.0 NA A:HEM401 2.0 28.0 1.0 NB A:HEM401 2.0 27.8 1.0 NE2 A:HIS55 2.0 27.5 1.0 O A:HOH563 2.6 56.2 1.0 C1B A:HEM401 3.0 27.8 1.0 C4C A:HEM401 3.0 26.8 1.0 C4A A:HEM401 3.0 29.6 1.0 C1D A:HEM401 3.0 27.7 1.0 C4D A:HEM401 3.0 28.1 1.0 C1C A:HEM401 3.0 25.2 1.0 CD2 A:HIS55 3.0 25.0 1.0 CE1 A:HIS55 3.0 27.8 1.0 C1A A:HEM401 3.0 30.3 1.0 C4B A:HEM401 3.1 26.2 1.0 CHB A:HEM401 3.3 28.0 1.0 CHD A:HEM401 3.3 27.3 1.0 CHA A:HEM401 3.4 29.6 1.0 CHC A:HEM401 3.4 27.1 1.0 ND1 A:HIS55 4.1 24.2 1.0 CG A:HIS55 4.2 25.8 1.0 C3C A:HEM401 4.2 26.3 1.0 C2B A:HEM401 4.2 28.1 1.0 C3A A:HEM401 4.2 31.5 1.0 C3D A:HEM401 4.2 28.5 1.0 C2C A:HEM401 4.2 24.8 1.0 C2A A:HEM401 4.3 31.6 1.0 C2D A:HEM401 4.3 27.2 1.0 C3B A:HEM401 4.3 27.9 1.0 O A:HOH813 4.5 56.7 1.0 O A:PRO108 4.6 37.2 1.0 CA A:GLY112 4.8 41.2 1.0

Iron binding site 2 out of 2 in the Di-Haem Cytochrome C Peroxidase, Form Out


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Di-Haem Cytochrome C Peroxidase, Form Out within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:33.9 occ:1.00 FE A:HEM402 0.0 33.9 1.0 ND A:HEM402 2.0 29.7 1.0 NE2 A:HIS201 2.0 32.5 1.0 NB A:HEM402 2.0 34.3 1.0 NC A:HEM402 2.0 34.7 1.0 NA A:HEM402 2.0 33.0 1.0 SD A:MET275 2.3 40.4 1.0 CE1 A:HIS201 2.8 28.5 1.0 C1B A:HEM402 3.0 36.8 1.0 C1D A:HEM402 3.0 30.3 1.0 C4D A:HEM402 3.0 30.2 1.0 C4A A:HEM402 3.0 32.2 1.0 C1C A:HEM402 3.0 35.0 1.0 C4B A:HEM402 3.1 37.0 1.0 C1A A:HEM402 3.1 32.1 1.0 C4C A:HEM402 3.1 34.4 1.0 CD2 A:HIS201 3.1 31.6 1.0 CHB A:HEM402 3.3 34.2 1.0 CE A:MET275 3.3 44.1 1.0 CHA A:HEM402 3.4 31.8 1.0 CHD A:HEM402 3.4 32.5 1.0 CHC A:HEM402 3.4 35.8 1.0 CG A:MET275 3.7 46.0 1.0 ND1 A:HIS201 4.0 30.9 1.0 CG A:HIS201 4.2 31.2 1.0 C2B A:HEM402 4.2 37.3 1.0 C3B A:HEM402 4.3 37.2 1.0 C2D A:HEM402 4.3 30.6 1.0 C3A A:HEM402 4.3 33.4 1.0 C3D A:HEM402 4.3 29.0 1.0 C2A A:HEM402 4.3 33.2 1.0 C2C A:HEM402 4.3 36.7 1.0 CB A:MET275 4.3 49.9 1.0 C3C A:HEM402 4.3 35.5 1.0

J.M.Dias, T.Alves, C.Bonifacio, A.S.Pereira, J.Trincao, D.Bourgeois, I.Moura, M.J.Romao. Structural Basis For the Mechanism of Ca(2+) Activation of the Di-Heme Cytochrome C Peroxidase From Pseudomonas Nautica 617. Structure V. 12 961 2004.
ISSN: ISSN 0969-2126
PubMed: 15274917
DOI: 10.1016/J.STR.2004.03.025