Calcium 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:

Iron

(Fe)

8 atoms

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

Calcium binding site 1 out of 4 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:13.1 occ:1.00 OD1 A:ASN88 2.4 14.5 1.0 O A:PRO262 2.4 12.9 1.0 O A:HOH1001 2.4 12.3 1.0 O A:HOH1058 2.5 10.5 1.0 O A:THR260 2.5 12.3 1.0 O A:HOH1018 2.5 15.2 1.0 O A:HOH1056 2.6 13.6 1.0 CG A:ASN88 3.4 13.8 1.0 C A:PRO262 3.6 13.2 1.0 C A:THR260 3.7 12.1 1.0 ND2 A:ASN88 3.8 13.2 1.0 O A:HOH1179 4.0 20.5 1.0 C A:TYR261 4.2 11.8 1.0 O A:SER89 4.2 13.6 0.5 N A:PRO262 4.3 11.9 1.0 CA A:TYR263 4.3 14.1 1.0 O A:TYR261 4.3 11.2 1.0 N A:TYR263 4.4 14.1 1.0 O A:SER89 4.4 13.5 0.5 CB A:THR260 4.4 11.7 1.0 O A:HOH1002 4.5 14.2 1.0 O A:HOH1279 4.5 15.1 1.0 O2A A:HEM501 4.5 13.0 1.0 CA A:TYR261 4.5 12.5 1.0 N A:TYR261 4.6 12.4 1.0 CA A:PRO262 4.6 12.4 1.0 OG1 A:THR260 4.6 14.2 1.0 O1A A:HEM501 4.6 10.9 1.0 CA A:THR260 4.6 12.2 1.0 O A:HOH1044 4.6 14.1 1.0 CB A:ASN88 4.7 14.3 1.0 CD1 A:TYR263 4.7 13.9 1.0 CD A:PRO262 4.8 11.7 1.0 O A:PHE264 4.9 15.3 1.0 C A:TYR263 5.0 15.0 1.0 CGA A:HEM501 5.0 10.9 1.0

Calcium binding site 2 out of 4 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:11.2 occ:1.00 OD1 B:ASN88 2.3 15.6 1.0 O B:HOH1075 2.3 15.7 1.0 O B:PRO262 2.4 14.4 1.0 O B:HOH1086 2.4 15.4 1.0 O B:THR260 2.4 15.4 1.0 O B:HOH1059 2.5 17.2 1.0 O B:HOH1072 2.6 17.6 1.0 CG B:ASN88 3.4 15.4 1.0 C B:PRO262 3.6 14.7 1.0 C B:THR260 3.7 14.9 1.0 ND2 B:ASN88 3.9 19.1 1.0 O B:HOH1064 4.0 21.7 1.0 C B:TYR261 4.2 14.2 1.0 CA B:TYR263 4.3 15.8 1.0 N B:PRO262 4.3 14.3 1.0 O B:TYR261 4.4 14.0 1.0 O B:SER89 4.4 14.9 1.0 O B:HOH1055 4.4 15.0 1.0 N B:TYR263 4.4 15.3 1.0 O2A B:HEM502 4.5 8.7 1.0 CB B:THR260 4.5 14.9 1.0 O B:HOH1041 4.5 14.5 1.0 N B:TYR261 4.5 14.9 1.0 CA B:TYR261 4.6 15.1 1.0 CB B:ASN88 4.6 16.2 1.0 O1A B:HEM502 4.6 7.9 1.0 CA B:PRO262 4.6 14.4 1.0 CA B:THR260 4.6 15.0 1.0 O B:HOH1024 4.7 17.1 1.0 CD1 B:TYR263 4.7 15.2 1.0 OG1 B:THR260 4.8 16.4 1.0 O B:PHE264 4.9 17.8 1.0 CD B:PRO262 4.9 14.2 1.0 CGA B:HEM502 5.0 8.6 1.0 C B:TYR263 5.0 16.6 1.0

Calcium binding site 3 out of 4 in the Cytochrome C Peroxidase Bccp of Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:11.1 occ:1.00 O C:PRO262 2.3 12.1 1.0 O C:THR260 2.3 11.5 1.0 O C:HOH1007 2.4 14.4 1.0 OD1 C:ASN88 2.5 15.3 1.0 O C:HOH1003 2.5 11.8 1.0 O C:HOH1088 2.5 18.6 1.0 O C:HOH1018 2.7 14.2 1.0 CG C:ASN88 3.4 15.3 1.0 C C:PRO262 3.5 13.3 1.0 C C:THR260 3.6 12.5 1.0 ND2 C:ASN88 3.8 14.5 1.0 O C:HOH1073 4.1 17.1 1.0 C C:TYR261 4.1 11.6 1.0 CA C:TYR263 4.3 15.0 1.0 O C:TYR261 4.3 12.0 1.0 O C:HOH1015 4.3 14.4 1.0 N C:PRO262 4.3 11.9 1.0 N C:TYR263 4.3 14.4 1.0 CB C:THR260 4.3 12.0 1.0 N C:TYR261 4.4 12.2 1.0 O C:SER89 4.4 15.2 1.0 CA C:TYR261 4.5 12.1 1.0 OG1 C:THR260 4.5 12.5 1.0 O1A C:HEM503 4.5 11.2 1.0 O C:HOH1030 4.5 16.5 1.0 O2A C:HEM503 4.5 8.8 1.0 CA C:THR260 4.5 12.3 1.0 O C:HOH1061 4.6 19.0 1.0 CA C:PRO262 4.6 12.4 1.0 CB C:ASN88 4.7 15.0 1.0 CD1 C:TYR263 4.7 16.2 1.0 CGA C:HEM503 4.9 10.1 1.0 O C:PHE264 5.0 16.3 1.0 C C:TYR263 5.0 15.7 1.0 CD C:PRO262 5.0 11.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cytochrome C Peroxidase Bccp of Shewanella Oneidensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca604 b:13.3 occ:1.00 O D:PRO262 2.3 13.9 1.0 O D:HOH1041 2.3 12.2 1.0 O D:HOH1113 2.3 14.1 1.0 OD1 D:ASN88 2.3 14.5 1.0 O D:THR260 2.3 12.8 1.0 O D:HOH1037 2.4 15.1 1.0 O D:HOH1068 2.6 15.9 1.0 CG D:ASN88 3.3 14.3 1.0 C D:PRO262 3.5 14.5 1.0 C D:THR260 3.6 14.0 1.0 ND2 D:ASN88 3.7 13.8 1.0 O D:HOH1162 3.9 19.4 1.0 C D:TYR261 4.1 13.8 1.0 N D:PRO262 4.2 14.3 1.0 CA D:TYR263 4.3 15.5 1.0 N D:TYR263 4.4 14.8 1.0 O D:TYR261 4.4 13.6 1.0 O D:SER89 4.4 17.4 1.0 CB D:THR260 4.4 14.4 1.0 O D:HOH1062 4.4 17.4 1.0 N D:TYR261 4.4 13.7 1.0 O2A D:HEM504 4.5 13.5 1.0 CA D:TYR261 4.5 14.5 1.0 CA D:PRO262 4.5 14.4 1.0 OG1 D:THR260 4.5 13.4 1.0 CA D:THR260 4.6 13.6 1.0 O D:HOH1071 4.6 18.4 1.0 CB D:ASN88 4.6 15.7 1.0 O D:HOH1011 4.6 12.4 1.0 CD D:PRO262 4.7 13.5 1.0 O1A D:HEM504 4.7 10.8 1.0 CD1 D:TYR263 4.8 17.6 1.0 O D:PHE264 4.9 17.6 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