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Calcium in PDB 1zzh: Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus

Enzymatic activity of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus

All present enzymatic activity of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus:
1.11.1.5;

Protein crystallography data

The structure of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus, PDB code: 1zzh was solved by L.De Smet, S.N.Savvides, E.Van Horen, G.Pettigrew, J.J.Vanbeeumen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.630, 132.470, 163.940, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 27.8

Other elements in 1zzh:

The structure of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus (pdb code 1zzh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus, PDB code: 1zzh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1zzh

Go back to Calcium Binding Sites List in 1zzh
Calcium binding site 1 out of 4 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:46.1
occ:1.00
 O A:HOH1030 2.2 23.1 1.0
O A:PRO261 2.3 31.5 1.0
O A:HOH1029 2.3 31.3 1.0
OD1 A:ASN82 2.4 44.3 1.0
O A:THR259 2.4 32.9 1.0
CG A:ASN82 3.4 41.5 1.0
C A:PRO261 3.5 30.8 1.0
C A:THR259 3.6 33.7 1.0
ND2 A:ASN82 3.9 40.9 1.0
O1A A:HEC803 4.0 52.0 1.0
CA A:TYR262 4.0 33.0 1.0
CD2 A:TYR262 4.2 37.7 1.0
CB A:THR259 4.2 37.0 1.0
N A:TYR262 4.2 31.6 1.0
OG1 A:THR259 4.2 42.5 1.0
O2A A:HEC803 4.3 53.1 1.0
C A:ALA260 4.3 30.2 1.0
N A:PRO261 4.4 29.9 1.0
O A:ALA83 4.5 49.1 1.0
CA A:ALA260 4.5 32.1 1.0
N A:ALA260 4.5 32.3 1.0
CA A:THR259 4.5 35.2 1.0
CA A:PRO261 4.6 30.1 1.0
CGA A:HEC803 4.6 50.1 1.0
CB A:ASN82 4.6 41.2 1.0
O A:ALA260 4.7 30.9 1.0
CE2 A:TYR262 4.8 38.4 1.0
C A:TYR262 4.8 32.8 1.0
CG A:TYR262 4.9 36.8 1.0
CB A:TYR262 4.9 34.2 1.0
CG1 A:VAL65 5.0 44.3 1.0
N A:PHE263 5.0 32.9 1.0
CD A:PRO261 5.0 29.6 1.0

Calcium binding site 2 out of 4 in 1zzh

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Calcium binding site 2 out of 4 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:40.1
occ:1.00
 OD1 B:ASN82 2.2 43.9 1.0
O B:THR259 2.4 28.4 1.0
O B:PRO261 2.5 30.2 1.0
CG B:ASN82 3.4 42.2 1.0
C B:THR259 3.6 27.8 1.0
C B:PRO261 3.8 29.8 1.0
O B:HOH1010 3.8 26.1 1.0
ND2 B:ASN82 3.9 41.1 1.0
CB B:THR259 4.1 31.3 1.0
O B:ALA83 4.1 43.1 1.0
O B:HOH1032 4.1 26.7 1.0
OG1 B:THR259 4.2 34.9 1.0
O1A B:HEC402 4.3 47.7 1.0
O2A B:HEC402 4.3 53.2 1.0
CA B:TYR262 4.4 32.5 1.0
C B:ALA260 4.5 27.9 1.0
CD2 B:TYR262 4.5 32.1 1.0
CA B:THR259 4.5 29.1 1.0
N B:PRO261 4.5 28.9 1.0
N B:TYR262 4.5 31.2 1.0
CB B:ASN82 4.6 40.8 1.0
N B:ALA260 4.6 27.5 1.0
CA B:ALA260 4.7 28.1 1.0
CG1 B:VAL65 4.7 43.4 1.0
CGA B:HEC402 4.8 49.9 1.0
O B:ALA260 4.8 27.8 1.0
CA B:PRO261 4.8 28.8 1.0
CG2 B:VAL65 5.0 31.6 1.0
CE2 B:TYR262 5.0 33.7 1.0

Calcium binding site 3 out of 4 in 1zzh

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Calcium binding site 3 out of 4 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:45.5
occ:1.00
 O C:THR259 2.2 29.0 1.0
OD1 C:ASN82 2.4 44.1 1.0
O C:PRO261 2.6 31.0 1.0
C C:THR259 3.4 27.4 1.0
CG C:ASN82 3.5 39.9 1.0
CB C:THR259 3.8 29.6 1.0
C C:PRO261 3.9 29.6 1.0
OG1 C:THR259 4.0 33.4 1.0
ND2 C:ASN82 4.0 40.2 1.0
O C:ALA83 4.1 42.5 1.0
O C:HOH1011 4.2 19.7 1.0
CA C:THR259 4.2 28.1 1.0
C C:ALA260 4.3 30.9 1.0
N C:ALA260 4.4 27.5 1.0
O2A C:HEC402 4.4 41.1 1.0
O1A C:HEC402 4.5 36.2 1.0
CD2 C:TYR262 4.5 27.7 1.0
N C:PRO261 4.5 31.2 1.0
CG1 C:VAL65 4.5 39.0 1.0
CA C:ALA260 4.5 30.2 1.0
O C:ALA260 4.6 30.1 1.0
CA C:TYR262 4.6 30.2 1.0
N C:TYR262 4.7 29.1 1.0
CG2 C:VAL65 4.7 29.9 1.0
CB C:ASN82 4.8 39.8 1.0
CA C:PRO261 4.9 29.1 1.0
CE2 C:TYR262 4.9 26.3 1.0
CGA C:HEC402 4.9 36.8 1.0

Calcium binding site 4 out of 4 in 1zzh

Go back to Calcium Binding Sites List in 1zzh
Calcium binding site 4 out of 4 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:53.5
occ:1.00
 O D:THR259 2.2 43.3 1.0
OD1 D:ASN82 2.2 47.5 1.0
O D:PRO261 2.4 40.3 1.0
CG D:ASN82 3.3 45.9 1.0
C D:THR259 3.4 40.7 1.0
C D:PRO261 3.7 38.6 1.0
ND2 D:ASN82 3.7 47.8 1.0
CB D:THR259 4.0 39.5 1.0
O D:ALA83 4.1 45.5 1.0
C D:ALA260 4.1 38.6 1.0
OG1 D:THR259 4.2 37.8 1.0
N D:PRO261 4.2 38.2 1.0
O D:ALA260 4.3 40.8 1.0
CA D:THR259 4.3 39.8 1.0
N D:ALA260 4.4 38.7 1.0
CG1 D:VAL65 4.4 42.7 1.0
CA D:ALA260 4.4 38.5 1.0
CA D:TYR262 4.5 37.3 1.0
N D:TYR262 4.6 38.5 1.0
CD2 D:TYR262 4.6 38.8 1.0
CB D:ASN82 4.6 44.6 1.0
CA D:PRO261 4.6 37.5 1.0
O1A D:HEC402 4.6 50.2 1.0
O2A D:HEC402 4.7 49.6 1.0
CD D:PRO261 4.8 36.3 1.0
CG2 D:VAL65 4.8 37.9 1.0

Reference:

L.De Smet, S.N.Savvides, E.Van Horen, G.Pettigrew, J.J.Van Beeumen. Structural and Mutagenesis Studies on the Cytochrome C Peroxidase From Rhodobacter Capsulatus Provide New Insights Into Structure-Function Relationships of Bacterial Di-Heme Peroxidases J.Biol.Chem. V. 281 4371 2006.
ISSN: ISSN 0021-9258
PubMed: 16314410
DOI: 10.1074/JBC.M509582200
Page generated: Sat Dec 12 03:30:30 2020

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