Sodium in PDB 4pyq: Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine

All present enzymatic activity of Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine:
2.1.1.6;

The structure of Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine, PDB code: 4pyq was solved by A.Ehler, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.41 / 1.39
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	125.366, 125.366, 77.287, 90.00, 90.00, 120.00
R / Rfree (%)	13.2 / 16.1

The structure of Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine (pdb code 4pyq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine, PDB code: 4pyq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:13.9 occ:1.00 O A:SER229 2.3 14.9 1.0 O B:HOH401 2.4 15.5 1.0 O A:VAL226 2.5 18.0 1.0 O A:PHE232 2.5 11.9 1.0 O B:GLU242 2.5 14.5 1.0 O A:ARG227 2.5 13.6 1.0 HA A:ARG227 2.7 14.6 1.0 C A:ARG227 3.0 12.6 1.0 C B:GLU242 3.2 15.5 1.0 CA A:ARG227 3.3 12.2 1.0 HA B:GLU242 3.3 19.0 1.0 HB2 A:PHE232 3.3 16.9 1.0 C A:SER229 3.3 14.0 1.0 C A:VAL226 3.5 13.4 1.0 H A:PHE232 3.5 15.9 1.0 C A:PHE232 3.5 11.8 1.0 CA B:GLU242 3.8 15.8 1.0 H A:SER229 3.8 19.0 1.0 N A:SER229 3.8 15.8 1.0 N A:ARG227 3.9 13.3 1.0 HA B:TYR243 3.9 18.7 0.5 HA A:SER230 3.9 20.8 1.0 HA B:TYR243 3.9 20.1 0.5 N B:TYR243 4.0 15.1 1.0 N A:GLY228 4.0 12.2 1.0 HG A:CYS234 4.1 17.8 1.0 CB A:PHE232 4.1 14.1 1.0 O B:TYR243 4.1 13.7 1.0 CA A:SER229 4.1 15.9 1.0 CA A:PHE232 4.1 11.8 1.0 N A:PHE232 4.2 13.3 1.0 C A:GLY228 4.2 15.0 1.0 SG A:CYS234 4.3 14.8 1.0 N A:SER230 4.3 15.2 1.0 CA B:TYR243 4.3 15.6 0.5 HB3 B:GLU242 4.3 20.2 1.0 HA A:GLU233 4.3 15.3 1.0 CA B:TYR243 4.4 16.7 0.5 O B:LEU241 4.4 13.4 1.0 HB3 A:SER229 4.4 19.5 1.0 HB3 A:PHE232 4.4 16.9 1.0 CA A:SER230 4.5 17.3 1.0 CB A:ARG227 4.6 14.3 1.0 C B:TYR243 4.6 14.7 1.0 H A:GLY228 4.6 14.6 1.0 HB3 A:ARG227 4.6 17.2 1.0 H B:TYR243 4.6 18.1 0.5 HB2 A:CYS234 4.6 18.3 1.0 H B:TYR243 4.6 18.1 0.5 N A:GLU233 4.6 13.6 1.0 O A:GLY228 4.7 16.9 1.0 CB B:GLU242 4.7 16.9 1.0 CA A:GLY228 4.7 14.0 1.0 H A:ARG227 4.7 15.9 1.0 HA A:VAL226 4.8 15.1 1.0 CA A:VAL226 4.8 12.6 1.0 HD2 A:PHE232 4.8 15.7 1.0 C A:SER230 4.8 15.8 1.0 CB A:SER229 4.8 16.2 1.0 N B:GLU242 4.9 15.8 1.0 HG3 B:GLU242 4.9 20.9 1.0 H A:CYS234 4.9 13.7 1.0 HA2 A:GLY228 4.9 16.8 1.0 HA A:SER229 4.9 19.1 1.0 HG2 A:ARG227 5.0 15.5 1.0 CA A:GLU233 5.0 12.8 1.0

Sodium binding site 2 out of 2 in the Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Humanized Rat Apo-Comt in Complex with A Ureido-Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:14.4 occ:1.00 O B:SER229 2.3 15.6 1.0 O A:HOH489 2.4 13.5 1.0 O B:PHE232 2.4 13.3 1.0 O B:VAL226 2.4 15.0 1.0 O B:ARG227 2.4 14.6 1.0 O A:GLU242 2.6 14.0 1.0 HA B:ARG227 3.0 16.0 1.0 C B:ARG227 3.1 11.7 1.0 C A:GLU242 3.2 14.2 1.0 HA A:GLU242 3.2 19.2 1.0 HB2 B:PHE232 3.4 17.8 1.0 C B:SER229 3.5 15.8 1.0 CA B:ARG227 3.5 13.4 1.0 C B:VAL226 3.5 14.0 1.0 C B:PHE232 3.5 13.2 1.0 H B:PHE232 3.6 18.3 1.0 CA A:GLU242 3.7 16.0 1.0 N B:SER229 3.9 12.8 1.0 H B:SER229 3.9 15.3 1.0 N A:TYR243 4.0 15.3 1.0 N B:ARG227 4.0 13.9 1.0 HB3 B:SER229 4.1 16.2 1.0 HB3 A:GLU242 4.1 25.2 1.0 N B:GLY228 4.1 12.6 1.0 CB B:PHE232 4.1 14.8 1.0 C B:GLY228 4.1 14.3 1.0 CA B:PHE232 4.2 12.5 1.0 HA B:SER230 4.2 19.4 1.0 CA B:SER229 4.2 14.7 1.0 N B:PHE232 4.2 15.3 1.0 O A:TYR243 4.2 14.0 1.0 SG B:CYS234 4.3 15.0 1.0 HA A:TYR243 4.3 18.5 1.0 O A:LEU241 4.3 14.5 1.0 HA B:GLU233 4.4 16.3 1.0 CA A:TYR243 4.4 15.4 1.0 HB3 B:PHE232 4.5 17.8 1.0 C A:TYR243 4.5 14.2 1.0 N B:SER230 4.5 15.6 1.0 H A:TYR243 4.5 18.4 1.0 CB A:GLU242 4.5 21.0 1.0 O A:HOH488 4.5 20.4 1.0 O B:GLY228 4.6 16.1 1.0 HB2 B:CYS234 4.6 13.4 1.0 CA B:GLY228 4.6 12.3 1.0 N B:GLU233 4.7 14.1 1.0 CB B:SER229 4.7 13.5 1.0 HA B:VAL226 4.7 13.6 1.0 CA B:SER230 4.7 16.1 1.0 CA B:VAL226 4.8 11.3 1.0 H B:GLY228 4.8 15.2 1.0 HA2 B:GLY228 4.8 14.8 1.0 H B:CYS234 4.8 13.4 1.0 H B:ARG227 4.8 16.6 1.0 CB B:ARG227 4.9 14.9 1.0 N A:GLU242 4.9 14.6 1.0 HD2 B:PHE232 4.9 21.8 1.0 HB3 B:ARG227 4.9 17.9 1.0 CA B:GLU233 5.0 13.6 1.0 C B:SER230 5.0 16.6 1.0

A.Ehler, J.Benz, D.Schlatter, M.G.Rudolph. Mapping the Conformational Space Accessible to Catechol-O-Methyltransferase. Acta Crystallogr.,Sect.D V. 70 2163 2014.
ISSN: ISSN 0907-4449
PubMed: 25084335
DOI: 10.1107/S1399004714012917