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Calcium in PDB 7zs8: Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution

Enzymatic activity of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution

All present enzymatic activity of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution:
1.11.1.5;

Protein crystallography data

The structure of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution, PDB code: 7zs8 was solved by A.L.Carvalho, M.J.Romao, S.Pauleta, C.Nobrega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.95 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.842, 89.144, 89.731, 90, 90, 90
R / Rfree (%) 19.6 / 22.1

Other elements in 7zs8:

The structure of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution (pdb code 7zs8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution, PDB code: 7zs8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7zs8

Go back to Calcium Binding Sites List in 7zs8
Calcium binding site 1 out of 2 in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.8
occ:1.00
 OD1 A:ASN83 2.3 13.0 1.0
O A:PRO263 2.3 15.3 1.0
O A:HOH605 2.4 11.0 1.0
O A:THR261 2.4 13.2 1.0
O A:HOH539 2.4 13.0 1.0
O A:HOH535 2.4 13.1 1.0
O A:HOH644 2.5 13.0 1.0
CG A:ASN83 3.4 13.4 1.0
C A:PRO263 3.6 15.6 1.0
C A:THR261 3.6 13.7 1.0
ND2 A:ASN83 3.8 14.2 1.0
C A:TYR262 4.2 13.6 1.0
CB A:THR261 4.3 13.8 1.0
N A:PRO263 4.3 13.2 1.0
CA A:TYR264 4.4 14.0 1.0
N A:TYR264 4.4 15.4 1.0
O A:SER84 4.4 12.5 1.0
OG1 A:THR261 4.4 13.6 1.0
N A:TYR262 4.5 12.7 1.0
O A:TYR262 4.5 13.3 1.0
CA A:TYR262 4.5 12.6 1.0
O2A A:HEC402 4.5 13.0 1.0
CA A:THR261 4.6 12.5 1.0
O A:HOH691 4.6 12.9 1.0
O1A A:HEC402 4.6 15.0 1.0
CA A:PRO263 4.6 14.1 1.0
O A:HOH566 4.6 14.7 1.0
CB A:ASN83 4.7 13.8 1.0
CD1 A:TYR264 4.7 14.7 1.0
CD A:PRO263 4.9 13.3 1.0
O A:HOH626 5.0 22.3 1.0
CGA A:HEC402 5.0 12.2 1.0

Calcium binding site 2 out of 2 in 7zs8

Go back to Calcium Binding Sites List in 7zs8
Calcium binding site 2 out of 2 in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:10.4
occ:1.00
 OD1 B:ASN83 2.3 11.2 1.0
O B:THR261 2.4 10.1 1.0
O B:HOH625 2.4 10.8 1.0
O B:HOH619 2.4 11.8 1.0
O B:PRO263 2.4 11.1 1.0
O B:HOH537 2.4 10.9 1.0
O B:HOH667 2.5 10.2 1.0
CG B:ASN83 3.4 9.9 1.0
C B:PRO263 3.6 9.4 1.0
C B:THR261 3.6 9.9 1.0
ND2 B:ASN83 3.8 11.1 1.0
C B:TYR262 4.2 10.7 1.0
CB B:THR261 4.3 9.4 1.0
N B:PRO263 4.3 10.2 1.0
CA B:TYR264 4.4 11.0 1.0
OG1 B:THR261 4.4 9.2 1.0
N B:TYR264 4.4 10.7 1.0
O B:SER84 4.4 11.0 1.0
O B:TYR262 4.5 10.4 1.0
N B:TYR262 4.5 11.4 1.0
CA B:TYR262 4.5 11.2 1.0
O B:HOH706 4.5 10.9 1.0
CA B:THR261 4.5 9.8 1.0
O2A B:HEC402 4.6 12.3 1.0
O B:HOH642 4.6 10.9 1.0
CA B:PRO263 4.6 10.8 1.0
CB B:ASN83 4.6 10.6 1.0
O1A B:HEC402 4.7 10.8 1.0
CD1 B:TYR264 4.7 10.3 1.0
O B:HOH586 4.8 21.4 1.0
CD B:PRO263 4.9 12.1 1.0

Reference:

C.S.Nobrega, A.L.Carvalho, M.J.Romao, S.R.Pauleta. Structural Characterization of Neisseria Gonorrhoeae Bacterial Peroxidase - Insights Into the Catalytic Cycle of Bacterial Peroxidases Int J Mol Sci 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24076246
Page generated: Fri Jul 19 06:37:09 2024

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