Iron in PDB 3o5c: Cytochrome C Peroxidase Bccp of Shewanella Oneidensis

The structure of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis, PDB code: 3o5c was solved by J.Seidel, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.50 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.840, 81.220, 85.920, 113.96, 102.10, 90.01
R / Rfree (%)	19.8 / 25.7

The structure of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Iron atom in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis (pdb code 3o5c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis, PDB code: 3o5c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.7 occ:1.00 FE A:HEM401 0.0 12.7 1.0 NA A:HEM401 2.0 13.0 1.0 NB A:HEM401 2.0 12.6 1.0 ND A:HEM401 2.1 13.4 1.0 NC A:HEM401 2.1 14.1 1.0 NE2 A:HIS64 2.1 14.5 1.0 O A:HOH1172 2.4 28.5 1.0 C4B A:HEM401 3.0 13.2 1.0 C1A A:HEM401 3.0 11.8 1.0 C1B A:HEM401 3.0 12.5 1.0 C4D A:HEM401 3.0 9.5 1.0 C4A A:HEM401 3.0 12.1 1.0 C1D A:HEM401 3.1 12.2 1.0 C1C A:HEM401 3.1 12.0 1.0 CE1 A:HIS64 3.1 15.3 1.0 CD2 A:HIS64 3.1 14.9 1.0 C4C A:HEM401 3.1 12.3 1.0 CHB A:HEM401 3.4 14.1 1.0 CHA A:HEM401 3.4 10.8 1.0 CHC A:HEM401 3.4 12.1 1.0 CHD A:HEM401 3.4 12.4 1.0 OE1 A:GLN113 3.9 14.7 1.0 ND1 A:HIS64 4.2 12.1 1.0 CG A:HIS64 4.2 13.4 1.0 C3B A:HEM401 4.2 11.5 1.0 C2B A:HEM401 4.2 14.3 1.0 C3D A:HEM401 4.2 11.2 1.0 C3A A:HEM401 4.2 13.4 1.0 C2A A:HEM401 4.2 11.8 1.0 C2D A:HEM401 4.3 10.5 1.0 C2C A:HEM401 4.3 11.3 1.0 C3C A:HEM401 4.3 12.1 1.0 O A:HOH1146 4.4 41.2 1.0 CG A:PRO117 4.7 15.8 1.0 CB A:PRO117 4.8 15.3 1.0 CD A:GLN113 4.9 16.3 1.0

Iron binding site 2 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:10.2 occ:1.00 FE A:HEM501 0.0 10.2 1.0 NC A:HEM501 2.0 10.6 1.0 ND A:HEM501 2.1 10.1 1.0 NA A:HEM501 2.1 10.0 1.0 NB A:HEM501 2.1 8.6 1.0 NE2 A:HIS208 2.1 16.9 1.0 SD A:MET279 2.4 22.5 1.0 C1D A:HEM501 3.0 10.5 1.0 C4D A:HEM501 3.1 10.8 1.0 C4C A:HEM501 3.1 10.9 1.0 CD2 A:HIS208 3.1 19.1 1.0 C1B A:HEM501 3.1 8.8 1.0 C1C A:HEM501 3.1 11.0 1.0 C1A A:HEM501 3.1 10.4 1.0 C4A A:HEM501 3.1 9.9 1.0 C4B A:HEM501 3.1 10.2 1.0 CE1 A:HIS208 3.1 17.2 1.0 CHD A:HEM501 3.4 11.8 1.0 CHB A:HEM501 3.4 8.4 1.0 CHA A:HEM501 3.4 10.6 1.0 CHC A:HEM501 3.5 11.6 1.0 CG A:MET279 3.5 22.2 1.0 CE A:MET279 3.5 23.1 1.0 ND1 A:HIS208 4.2 18.5 1.0 CG A:HIS208 4.2 19.2 1.0 C3D A:HEM501 4.3 9.3 1.0 C2D A:HEM501 4.3 10.8 1.0 C3C A:HEM501 4.3 11.0 1.0 C2B A:HEM501 4.3 8.2 1.0 C2C A:HEM501 4.3 11.0 1.0 C2A A:HEM501 4.3 10.2 1.0 C3B A:HEM501 4.3 8.9 1.0 C3A A:HEM501 4.3 10.0 1.0 CB A:MET279 4.3 22.9 1.0

Iron binding site 3 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:11.8 occ:1.00 FE B:HEM402 0.0 11.8 1.0 NC B:HEM402 2.0 10.9 1.0 NB B:HEM402 2.0 10.9 1.0 ND B:HEM402 2.0 9.7 1.0 NA B:HEM402 2.1 11.5 1.0 NE2 B:HIS64 2.1 15.8 1.0 O B:HOH1225 2.8 28.2 1.0 C4B B:HEM402 3.0 12.8 1.0 C1C B:HEM402 3.0 11.5 1.0 C4C B:HEM402 3.0 11.6 1.0 C4D B:HEM402 3.0 11.6 1.0 C1D B:HEM402 3.1 12.5 1.0 CE1 B:HIS64 3.1 14.9 1.0 C1B B:HEM402 3.1 11.7 1.0 C1A B:HEM402 3.1 12.6 1.0 CD2 B:HIS64 3.1 15.9 1.0 C4A B:HEM402 3.1 10.8 1.0 CHC B:HEM402 3.3 12.6 1.0 CHA B:HEM402 3.4 12.4 1.0 CHD B:HEM402 3.4 11.2 1.0 CHB B:HEM402 3.5 12.2 1.0 NE2 B:GLN113 3.9 13.0 1.0 ND1 B:HIS64 4.2 14.6 1.0 C3B B:HEM402 4.2 11.3 1.0 C2C B:HEM402 4.2 11.3 1.0 C3C B:HEM402 4.2 12.8 1.0 CG B:HIS64 4.2 14.1 1.0 C2B B:HEM402 4.2 11.4 1.0 C3D B:HEM402 4.3 12.7 1.0 C2D B:HEM402 4.3 13.6 1.0 C2A B:HEM402 4.3 11.0 1.0 C3A B:HEM402 4.3 13.1 1.0 CG B:PRO117 4.4 16.2 1.0 CB B:PRO117 4.8 15.0 1.0 CD B:GLN113 5.0 14.9 1.0

Iron binding site 4 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:11.7 occ:1.00 FE B:HEM502 0.0 11.7 1.0 NB B:HEM502 2.0 11.8 1.0 NA B:HEM502 2.0 11.3 1.0 NC B:HEM502 2.1 11.1 1.0 ND B:HEM502 2.1 11.1 1.0 NE2 B:HIS208 2.1 14.2 1.0 SD B:MET279 2.3 21.0 1.0 C4B B:HEM502 3.0 12.5 1.0 C1B B:HEM502 3.0 11.6 1.0 C1A B:HEM502 3.0 10.8 1.0 C4D B:HEM502 3.1 10.0 1.0 C4A B:HEM502 3.1 11.2 1.0 C1C B:HEM502 3.1 11.1 1.0 C4C B:HEM502 3.1 10.7 1.0 C1D B:HEM502 3.1 11.1 1.0 CE1 B:HIS208 3.1 12.8 1.0 CD2 B:HIS208 3.1 14.2 1.0 CHA B:HEM502 3.4 9.2 1.0 CHB B:HEM502 3.4 11.3 1.0 CHC B:HEM502 3.4 12.1 1.0 CHD B:HEM502 3.5 10.1 1.0 CE B:MET279 3.5 21.9 1.0 CG B:MET279 3.5 18.1 1.0 ND1 B:HIS208 4.2 13.0 1.0 C3B B:HEM502 4.2 12.0 1.0 C2B B:HEM502 4.2 11.4 1.0 CG B:HIS208 4.3 16.8 1.0 C2A B:HEM502 4.3 9.4 1.0 C3D B:HEM502 4.3 11.5 1.0 C3A B:HEM502 4.3 10.9 1.0 C2C B:HEM502 4.3 11.6 1.0 C3C B:HEM502 4.3 11.3 1.0 C2D B:HEM502 4.3 10.3 1.0 CB B:MET279 4.3 19.2 1.0 CG B:GLN283 5.0 20.0 1.0

Iron binding site 5 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:12.2 occ:1.00 FE C:HEM403 0.0 12.2 1.0 NB C:HEM403 2.0 11.4 1.0 ND C:HEM403 2.0 11.3 1.0 NA C:HEM403 2.0 10.3 1.0 NC C:HEM403 2.1 13.0 1.0 NE2 C:HIS64 2.2 13.3 1.0 O C:HOH1135 2.7 22.1 1.0 C4B C:HEM403 3.0 10.3 1.0 C1B C:HEM403 3.0 9.5 1.0 C4D C:HEM403 3.0 11.5 1.0 CD2 C:HIS64 3.1 14.7 1.0 C1A C:HEM403 3.1 10.3 1.0 C1D C:HEM403 3.1 11.8 1.0 C4A C:HEM403 3.1 8.8 1.0 C1C C:HEM403 3.1 11.3 1.0 C4C C:HEM403 3.1 12.1 1.0 CE1 C:HIS64 3.2 15.3 1.0 CHC C:HEM403 3.4 9.8 1.0 CHA C:HEM403 3.4 11.4 1.0 CHB C:HEM403 3.4 10.7 1.0 CHD C:HEM403 3.4 11.8 1.0 OE1 C:GLN113 4.0 15.7 1.0 C3B C:HEM403 4.1 9.0 1.0 C2B C:HEM403 4.2 8.8 1.0 CG C:HIS64 4.2 13.1 1.0 ND1 C:HIS64 4.3 13.1 1.0 C3D C:HEM403 4.3 10.2 1.0 C2A C:HEM403 4.3 9.4 1.0 C2D C:HEM403 4.3 11.1 1.0 C3A C:HEM403 4.3 8.5 1.0 C3C C:HEM403 4.3 11.1 1.0 C2C C:HEM403 4.3 9.5 1.0 CG C:PRO117 4.5 16.8 1.0 CB C:PRO117 4.8 16.3 1.0 CD C:GLN113 4.9 16.2 1.0 OG C:SER89 4.9 14.6 0.5

Iron binding site 6 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:10.4 occ:1.00 FE C:HEM503 0.0 10.4 1.0 NB C:HEM503 2.0 7.2 1.0 NA C:HEM503 2.0 7.8 1.0 ND C:HEM503 2.1 8.4 1.0 NC C:HEM503 2.1 9.8 1.0 NE2 C:HIS208 2.1 21.5 1.0 SD C:MET279 2.4 24.4 1.0 C1B C:HEM503 3.0 5.7 1.0 C1D C:HEM503 3.0 8.4 1.0 C4A C:HEM503 3.0 7.6 1.0 CD2 C:HIS208 3.0 21.9 1.0 C4C C:HEM503 3.0 9.1 1.0 C1A C:HEM503 3.1 8.0 1.0 C4B C:HEM503 3.1 8.8 1.0 C4D C:HEM503 3.1 7.9 1.0 C1C C:HEM503 3.1 10.1 1.0 CE1 C:HIS208 3.2 21.4 1.0 CHD C:HEM503 3.4 9.5 1.0 CHB C:HEM503 3.4 7.0 1.0 CHA C:HEM503 3.4 8.1 1.0 CHC C:HEM503 3.5 9.8 1.0 CG C:MET279 3.5 24.1 1.0 CE C:MET279 3.5 23.6 1.0 C2B C:HEM503 4.2 8.1 1.0 CG C:HIS208 4.2 22.0 1.0 C3B C:HEM503 4.2 8.7 1.0 ND1 C:HIS208 4.3 22.4 1.0 C3A C:HEM503 4.3 9.3 1.0 C2A C:HEM503 4.3 7.5 1.0 C2D C:HEM503 4.3 8.1 1.0 C3C C:HEM503 4.3 11.4 1.0 C3D C:HEM503 4.3 8.5 1.0 C2C C:HEM503 4.3 10.7 1.0 CB C:MET279 4.4 25.4 1.0

Iron binding site 7 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe404 b:11.0 occ:1.00 FE D:HEM404 0.0 11.0 1.0 NB D:HEM404 2.0 11.2 1.0 NC D:HEM404 2.0 12.2 1.0 NE2 D:HIS64 2.1 15.0 1.0 NA D:HEM404 2.1 11.6 1.0 ND D:HEM404 2.1 10.1 1.0 O D:HOH1140 2.1 26.9 1.0 C4B D:HEM404 3.0 12.9 1.0 C1C D:HEM404 3.0 12.0 1.0 CD2 D:HIS64 3.0 14.0 1.0 C1B D:HEM404 3.1 11.6 1.0 C4D D:HEM404 3.1 11.6 1.0 CE1 D:HIS64 3.1 13.6 1.0 C1A D:HEM404 3.1 13.6 1.0 C1D D:HEM404 3.1 11.8 1.0 C4C D:HEM404 3.1 11.0 1.0 C4A D:HEM404 3.1 10.8 1.0 CHC D:HEM404 3.3 13.9 1.0 CHA D:HEM404 3.4 14.3 1.0 CHB D:HEM404 3.4 12.0 1.0 CHD D:HEM404 3.5 11.9 1.0 NE2 D:GLN113 3.9 19.2 1.0 O D:HOH1192 4.0 27.3 1.0 ND1 D:HIS64 4.2 12.5 1.0 CG D:HIS64 4.2 14.0 1.0 C3B D:HEM404 4.2 12.8 1.0 C2B D:HEM404 4.2 13.5 1.0 C2C D:HEM404 4.2 12.2 1.0 C3C D:HEM404 4.3 11.7 1.0 C3D D:HEM404 4.3 13.0 1.0 C2A D:HEM404 4.3 10.8 1.0 C3A D:HEM404 4.3 12.3 1.0 C2D D:HEM404 4.3 12.9 1.0 CG D:PRO117 4.7 15.4 1.0 CD D:GLN113 4.9 18.0 1.0 CB D:PRO117 4.9 14.4 1.0

Iron binding site 8 out of 8 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe504 b:11.0 occ:1.00 FE D:HEM504 0.0 11.0 1.0 NA D:HEM504 2.0 11.3 1.0 NC D:HEM504 2.0 10.8 1.0 NB D:HEM504 2.1 10.1 1.0 NE2 D:HIS208 2.1 20.6 1.0 ND D:HEM504 2.1 11.0 1.0 SD D:MET279 2.4 23.0 1.0 CE1 D:HIS208 3.0 22.1 1.0 C1A D:HEM504 3.0 10.5 1.0 C4D D:HEM504 3.0 12.2 1.0 C4B D:HEM504 3.0 10.3 1.0 C1C D:HEM504 3.1 10.4 1.0 C4C D:HEM504 3.1 11.8 1.0 C4A D:HEM504 3.1 10.3 1.0 C1B D:HEM504 3.1 9.5 1.0 C1D D:HEM504 3.1 12.5 1.0 CD2 D:HIS208 3.1 23.3 1.0 CHA D:HEM504 3.4 11.9 1.0 CG D:MET279 3.4 20.2 1.0 CHC D:HEM504 3.4 10.9 1.0 CHB D:HEM504 3.4 11.6 1.0 CHD D:HEM504 3.4 11.0 1.0 CE D:MET279 3.5 20.1 1.0 ND1 D:HIS208 4.1 21.5 1.0 C2A D:HEM504 4.2 10.1 1.0 CG D:HIS208 4.2 22.3 1.0 C3B D:HEM504 4.3 10.6 1.0 CB D:MET279 4.3 20.2 1.0 C3A D:HEM504 4.3 10.3 1.0 C2B D:HEM504 4.3 10.4 1.0 C3D D:HEM504 4.3 12.1 1.0 C3C D:HEM504 4.3 11.4 1.0 C2C D:HEM504 4.3 10.6 1.0 C2D D:HEM504 4.3 12.6 1.0 CG D:GLN283 5.0 22.0 1.0

B.Schutz, J.Seidel, G.Sturm, O.Einsle, J.Gescher. Investigation of the Electron Transport Chain to and the Catalytic Activity of the Diheme Cytochrome C Peroxidase Ccpa of Shewanella Oneidensis. Appl.Environ.Microbiol. V. 77 6172 2011.
ISSN: ISSN 0099-2240
PubMed: 21742904
DOI: 10.1128/AEM.00606-11