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Sodium 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:

Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7zs8

Go back to Sodium Binding Sites List in 7zs8
Sodium 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 Sodium with other atoms in the Na 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:Na404

b:26.0
occ:1.00
 OD1 A:ASN155 2.8 16.3 1.0
OG1 A:THR158 2.9 14.7 1.0
O A:HOH763 3.2 23.0 1.0
CB A:THR158 3.3 12.7 1.0
O A:HOH544 3.5 27.3 1.0
CG2 A:THR158 3.6 12.3 1.0
CE1 A:PHE145 3.6 19.2 1.0
CE A:LYS154 3.6 29.1 1.0
CG A:LYS154 3.6 16.6 1.0
CG A:ASN155 3.9 14.3 1.0
CA A:ASN155 4.0 13.7 1.0
O A:LYS154 4.0 13.4 1.0
CD1 A:PHE145 4.0 19.2 1.0
CD A:LYS154 4.2 24.0 1.0
C A:LYS154 4.3 14.3 1.0
CZ A:PHE145 4.3 15.5 1.0
N A:ASN155 4.3 13.6 1.0
CB A:ASN155 4.5 13.5 1.0
CA A:THR158 4.8 11.0 1.0
NZ A:LYS154 4.8 37.6 1.0
CB A:LYS154 4.8 18.1 1.0
CG A:PHE145 4.9 18.6 1.0
O A:HOH676 4.9 29.8 1.0
ND2 A:ASN155 5.0 15.3 1.0

Sodium binding site 2 out of 2 in 7zs8

Go back to Sodium Binding Sites List in 7zs8
Sodium 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 Sodium with other atoms in the Na 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:Na404

b:28.4
occ:1.00
 O B:HOH789 2.3 32.8 1.0
O B:HOH730 2.9 23.8 1.0
N B:GLU272 3.0 13.3 1.0
OE1 B:GLU272 3.1 25.9 1.0
N B:TRP271 3.3 13.4 1.0
CB B:GLU272 3.4 16.8 1.0
CG B:GLU272 3.6 20.1 1.0
O A:HOH601 3.6 29.3 1.0
CA B:GLU272 3.8 14.9 1.0
CD B:GLU272 3.8 24.2 1.0
C B:TRP271 3.9 12.7 1.0
CA B:TRP271 3.9 12.7 1.0
CG1 B:VAL270 3.9 16.2 1.0
CB B:TRP271 4.1 12.1 1.0
C B:VAL270 4.2 12.3 1.0
CG B:LYS275 4.2 23.7 1.0
CA B:VAL270 4.4 13.5 1.0
CB B:LYS275 4.4 17.1 1.0
O B:HOH792 4.5 29.1 1.0
O B:GLU272 4.6 15.0 1.0
SD A:MET324 4.6 25.7 1.0
NZ B:LYS275 4.7 38.0 1.0
C B:GLU272 4.7 13.3 1.0
CB B:VAL270 4.8 15.7 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: Wed Oct 9 10:18:49 2024

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