Sodium in PDB 7oqr: Crystal Structure of Trypanosoma Cruzi Peroxidase

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi Peroxidase:
1.11.1.11;

The structure of Crystal Structure of Trypanosoma Cruzi Peroxidase, PDB code: 7oqr was solved by S.L.Freeman, H.Kwon, V.Skafar, A.J.Fielding, A.Martinez, L.Piacenza, R.Radi, E.L.Raven, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 1.76
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.594, 71.594, 254.581, 90, 90, 120
R / Rfree (%)	11.8 / 15.9

The structure of Crystal Structure of Trypanosoma Cruzi Peroxidase also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Trypanosoma Cruzi Peroxidase (pdb code 7oqr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Trypanosoma Cruzi Peroxidase, PDB code: 7oqr:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Trypanosoma Cruzi Peroxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Trypanosoma Cruzi Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:36.4 occ:1.00 O A:HOH568 2.7 31.6 1.0 O A:ASP236 2.7 23.3 1.0 O A:THR218 2.8 23.3 1.0 O A:GLY239 2.9 22.7 1.0 OG1 A:THR218 3.0 24.6 1.0 OG A:SER243 3.1 24.6 1.0 OG1 A:THR234 3.2 22.5 1.0 C A:THR218 3.6 21.9 1.0 OD1 A:ASP241 3.6 25.8 1.0 C A:GLY239 3.7 23.0 1.0 C A:ASP236 3.7 19.4 1.0 O A:HOH628 3.9 31.1 1.0 CB A:THR218 4.0 22.8 1.0 CB A:THR234 4.0 24.7 1.0 CA A:THR218 4.0 21.7 1.0 CA A:GLY239 4.1 26.1 1.0 CB A:ASP236 4.1 21.7 1.0 CG2 A:THR234 4.2 23.3 1.0 N A:GLY239 4.3 23.8 1.0 CG A:ASP241 4.4 26.2 1.0 CG2 A:THR218 4.4 23.7 1.0 CA A:ASP236 4.4 19.8 1.0 CB A:SER243 4.4 26.0 1.0 N A:CYS219 4.5 21.6 1.0 N A:PHE240 4.6 22.4 1.0 OD2 A:ASP236 4.7 21.6 1.0 N A:LYS237 4.7 20.2 1.0 OD2 A:ASP241 4.7 27.0 1.0 CG A:ASP236 4.7 22.2 1.0 CA A:LYS237 4.8 19.9 1.0 N A:ASP241 4.8 22.0 1.0 N A:ASP236 4.8 21.5 1.0 CA A:CYS219 4.9 22.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Cruzi Peroxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Trypanosoma Cruzi Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:35.8 occ:1.00 OE2 A:GLU117 2.7 22.4 1.0 OG A:SER111 2.8 21.5 1.0 OE2 A:GLU94 2.9 21.3 1.0 O A:GLU94 3.0 21.5 1.0 OG A:SER97 3.0 22.1 1.0 O A:SER106 3.1 20.2 1.0 CD A:GLU94 3.2 21.6 1.0 OE1 A:GLU94 3.4 20.3 1.0 OE1 A:GLU117 3.4 20.4 1.0 CD A:GLU117 3.4 22.8 1.0 O A:GLY105 3.5 24.2 1.0 C A:SER106 3.8 22.1 1.0 C A:GLU94 3.9 21.3 1.0 CB A:SER97 3.9 23.3 1.0 CA A:PRO107 4.0 22.4 1.0 O A:HOH513 4.0 27.4 1.0 CA A:GLU94 4.1 18.9 1.0 CB A:SER111 4.1 23.2 1.0 N A:PRO107 4.3 21.2 1.0 CG A:GLU94 4.3 19.7 1.0 N A:MET112 4.4 19.5 1.0 O A:HOH587 4.4 22.8 1.0 N A:SER111 4.5 22.3 1.0 O A:HIS93 4.6 20.7 1.0 N A:ASN108 4.7 21.3 1.0 C A:PRO107 4.7 22.2 1.0 CA A:SER111 4.7 23.3 1.0 C A:GLY105 4.7 23.2 1.0 CB A:SER106 4.7 27.4 1.0 OG A:SER109 4.8 25.1 1.0 C A:SER111 4.8 23.3 1.0 CB A:GLU94 4.8 18.8 1.0 CG A:GLU117 4.8 22.8 1.0 CA A:SER106 4.8 23.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Trypanosoma Cruzi Peroxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Trypanosoma Cruzi Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na409 b:41.2 occ:1.00 OG B:SER243 2.6 31.9 1.0 O B:HOH540 2.7 31.6 1.0 O B:THR218 2.7 22.3 1.0 OG1 B:THR218 2.7 26.4 1.0 O B:ASP236 2.8 21.3 1.0 O B:GLY239 3.0 24.5 1.0 OG1 B:THR234 3.2 19.9 1.0 OD1 B:ASP241 3.5 25.3 1.0 C B:THR218 3.6 22.8 1.0 C B:ASP236 3.8 20.6 1.0 C B:GLY239 3.8 23.2 1.0 CB B:SER243 3.9 26.6 1.0 CB B:THR218 3.9 23.2 1.0 CB B:THR234 4.0 22.5 1.0 CA B:THR218 4.0 22.8 1.0 O2 B:SO4404 4.1 22.8 0.5 CB B:ASP236 4.2 25.9 1.0 CG2 B:THR234 4.3 24.2 1.0 CG B:ASP241 4.3 31.4 1.0 CA B:GLY239 4.4 20.1 1.0 CA B:ASP236 4.4 21.4 1.0 N B:GLY239 4.6 20.8 1.0 OD2 B:ASP241 4.6 31.6 1.0 N B:PHE240 4.6 21.8 1.0 N B:CYS219 4.7 21.7 1.0 CG2 B:THR218 4.7 25.4 1.0 N B:LYS237 4.7 22.3 1.0 N B:ASP241 4.7 23.6 1.0 N B:ASP236 4.7 23.6 1.0 OD2 B:ASP236 4.8 25.4 1.0 CG B:ASP236 4.8 21.7 1.0 CA B:LYS237 4.9 24.1 1.0 CA B:SER243 5.0 22.1 1.0 CA B:PHE240 5.0 22.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Cruzi Peroxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Trypanosoma Cruzi Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na410 b:30.4 occ:1.00 OG B:SER111 2.7 22.3 1.0 OG B:SER97 2.8 24.8 1.0 OE2 B:GLU117 2.8 18.7 1.0 O B:GLU94 2.9 20.4 1.0 OE2 B:GLU94 2.9 17.7 1.0 O B:SER106 3.1 22.3 1.0 CD B:GLU94 3.3 19.5 1.0 OE1 B:GLU94 3.5 19.3 1.0 O B:GLY105 3.5 26.3 1.0 OE1 B:GLU117 3.5 21.7 1.0 CD B:GLU117 3.5 18.8 1.0 CB B:SER97 3.7 23.5 1.0 C B:SER106 3.8 24.4 1.0 O B:HOH594 3.9 22.2 1.0 CA B:PRO107 3.9 22.9 1.0 C B:GLU94 3.9 18.6 1.0 CB B:SER111 4.1 22.0 1.0 CA B:GLU94 4.2 19.8 1.0 N B:PRO107 4.2 23.6 1.0 CG B:GLU94 4.4 19.6 1.0 C B:PRO107 4.5 23.2 1.0 O B:HOH524 4.5 21.6 1.0 N B:ASN108 4.6 21.7 1.0 OG B:SER109 4.6 24.0 1.0 N B:SER111 4.6 21.1 1.0 N B:MET112 4.6 22.1 1.0 O B:HIS93 4.7 22.9 1.0 C B:GLY105 4.7 21.7 1.0 CA B:SER111 4.7 18.6 1.0 CA B:SER106 4.9 22.9 1.0 C B:SER111 4.9 19.1 1.0 CB B:GLU94 4.9 21.0 1.0 CB B:SER106 5.0 28.0 1.0 CA B:SER97 5.0 22.0 1.0

S.L.Freeman, V.Skafar, H.Kwon, A.J.Fielding, P.C.E.Moody, A.Martinez, F.M.Issoglio, L.Inchausti, P.Smircich, A.Zeida, L.Piacenza, R.Radi, E.L.Raven. Crystal Structure of Trypanosoma Cruzi Heme Peroxidase and Characterization of Its Substrate Specificity and Compound I Intermediate. J.Biol.Chem. V. 298 02204 2022.
ISSN: ESSN 1083-351X
PubMed: 35772495
DOI: 10.1016/J.JBC.2022.102204