Sodium in PDB 3g0t: Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution

The structure of Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution, PDB code: 3g0t was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.40 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	220.440, 54.970, 81.154, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 17.1

The structure of Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution (pdb code 3g0t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution, PDB code: 3g0t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution


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 Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na437 b:17.1 occ:1.00 O A:GLU237 2.2 10.2 1.0 O A:HOH861 2.2 15.2 1.0 O A:HOH851 2.3 13.2 1.0 O A:LEU239 2.4 9.9 1.0 O A:HIS234 2.5 11.5 1.0 C A:GLU237 3.4 11.3 1.0 C A:LEU239 3.5 10.0 1.0 C A:HIS234 3.6 12.6 1.0 N A:HIS234 3.9 12.5 1.0 O A:TYR232 4.0 14.7 1.0 C A:PRO238 4.0 12.1 1.0 CD1 A:TYR240 4.1 13.4 1.0 CA A:HIS234 4.1 13.2 1.0 O A:HOH650 4.1 11.3 1.0 N A:LEU239 4.1 11.1 1.0 C A:TYR232 4.2 12.6 1.0 CA A:PRO238 4.2 10.8 1.0 N A:GLU237 4.2 11.0 1.0 N A:TYR240 4.2 9.3 1.0 N A:PRO238 4.3 11.3 1.0 CA A:TYR240 4.3 10.1 1.0 CE1 A:TYR240 4.4 10.5 1.0 CA A:GLU237 4.4 12.7 1.0 CA A:LEU239 4.4 10.6 1.0 O A:PRO238 4.4 13.1 1.0 CG A:GLU237 4.4 16.7 1.0 CB A:HIS234 4.4 15.1 1.0 CA A:TYR232 4.4 10.6 1.0 O A:LEU96 4.6 11.6 1.0 CG A:TYR240 4.6 8.3 1.0 O A:ASP231 4.6 10.4 1.0 N A:SER233 4.7 12.7 1.0 N A:PRO235 4.7 12.3 1.0 N A:GLY236 4.9 12.0 1.0 C A:SER233 4.9 13.0 1.0 CA A:PRO235 4.9 10.8 1.0 C A:PRO235 5.0 11.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution


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 Putative Aspartate Aminotransferase (NP_905498.1) From Porphyromonas Gingivalis W83 at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na437 b:20.4 occ:1.00 O B:HOH977 2.2 15.6 1.0 O B:GLU237 2.3 7.8 1.0 O B:HOH978 2.3 11.3 1.0 O B:LEU239 2.4 9.8 1.0 O B:HIS234 2.4 12.9 1.0 C B:LEU239 3.5 9.2 1.0 C B:GLU237 3.5 8.5 1.0 C B:HIS234 3.5 11.6 1.0 N B:HIS234 3.9 12.7 1.0 C B:PRO238 4.0 9.9 1.0 O B:HOH602 4.0 12.2 1.0 O B:TYR232 4.0 12.6 1.0 N B:LEU239 4.1 10.3 1.0 CA B:HIS234 4.1 13.0 1.0 CD1 B:TYR240 4.1 13.3 1.0 C B:TYR232 4.2 12.7 1.0 CA B:PRO238 4.2 8.7 1.0 CE1 B:TYR240 4.3 12.6 1.0 O B:PRO238 4.3 8.9 1.0 N B:GLU237 4.3 8.9 1.0 N B:TYR240 4.3 10.0 1.0 CA B:LEU239 4.3 9.8 1.0 N B:PRO238 4.3 8.9 1.0 CB B:HIS234 4.4 13.2 1.0 CA B:TYR240 4.5 11.0 1.0 CA B:TYR232 4.5 12.6 1.0 O B:LEU96 4.5 9.0 1.0 CA B:GLU237 4.5 9.4 1.0 CG B:GLU237 4.5 9.6 1.0 O B:ASP231 4.6 12.3 1.0 N B:PRO235 4.6 11.1 1.0 N B:SER233 4.7 11.6 1.0 CG B:TYR240 4.7 10.9 1.0 C B:SER233 4.9 12.5 1.0 CA B:PRO235 4.9 9.7 1.0 CZ B:TYR240 5.0 11.8 1.0

N.M.Fleischman, D.Das, A.Kumar, Q.Xu, H.J.Chiu, L.Jaroszewski, M.W.Knuth, H.E.Klock, M.D.Miller, M.A.Elsliger, A.Godzik, S.A.Lesley, A.M.Deacon, I.A.Wilson, M.D.Toney. Molecular Characterization of Novel Pyridoxal-5'-Phosphate-Dependent Enzymes From the Human Microbiome. Protein Sci. V. 23 1060 2014.
ISSN: ISSN 0961-8368
PubMed: 24888348
DOI: 10.1002/PRO.2493