Sodium in PDB 4ytb: Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln.

The structure of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln., PDB code: 4ytb was solved by T.Goulas, D.Mizgalska, I.Garcia-Ferrer, T.Kantyka, T.Guevara, B.Szmigielski, A.Sroka, C.Millan, I.Uson, F.Veillard, B.Potempa, P.Mydel, M.Sola, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.15 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.534, 71.306, 105.664, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 14.9

The structure of Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln. (pdb code 4ytb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln., PDB code: 4ytb:

Sodium binding site 1 out of 1 in the Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln.


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 Porphyromonas Gingivalis Peptidylarginine Deiminase (Ppad) in Complex with Dipeptide Asp-Gln. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:11.6 occ:1.00 O A:PHE148 2.3 10.0 1.0 O A:HOH890 2.4 12.2 1.0 OD1 A:ASP158 2.4 11.7 1.0 O A:ASP158 2.4 11.1 1.0 OD1 A:ASP147 2.4 11.1 1.0 O A:HOH806 2.6 15.9 1.0 C A:ASP158 3.4 11.2 1.0 CG A:ASP147 3.5 11.8 1.0 CG A:ASP158 3.5 12.2 1.0 C A:PHE148 3.5 10.6 1.0 CA A:ASP158 3.7 11.1 1.0 OD2 A:ASP147 3.8 14.7 1.0 N A:PHE148 4.0 9.2 1.0 N A:TYR150 4.1 9.7 1.0 CB A:ASP158 4.1 12.1 1.0 CD A:PRO161 4.2 11.1 1.0 CG A:PRO161 4.3 12.2 1.0 OD2 A:ASP158 4.4 14.9 1.0 CA A:PHE148 4.4 8.9 1.0 CE1 A:PHE45 4.4 11.9 1.0 N A:ILE149 4.5 9.6 1.0 CA A:ILE149 4.5 9.6 1.0 N A:GLU159 4.6 11.0 1.0 O A:HOH773 4.6 33.5 1.0 CB A:TYR150 4.7 10.2 1.0 C A:ILE149 4.7 10.9 1.0 CD1 A:PHE45 4.8 13.0 1.0 CB A:ASP147 4.8 10.5 1.0 O A:TYR131 4.8 10.5 1.0 CD1 A:PHE148 4.9 9.1 1.0 CA A:TYR150 5.0 9.3 1.0 O A:ASP157 5.0 10.6 1.0

T.Goulas, D.Mizgalska, I.Garcia-Ferrer, T.Kantyka, T.Guevara, B.Szmigielski, A.Sroka, C.Millan, I.Uson, F.Veillard, B.Potempa, P.Mydel, M.Sola, J.Potempa, F.X.Gomis-Ruth. Structure and Mechanism of A Bacterial Host-Protein Citrullinating Virulence Factor, Porphyromonas Gingivalis Peptidylarginine Deiminase. Sci Rep V. 5 11969 2015.
ISSN: ESSN 2045-2322
PubMed: 26132828
DOI: 10.1038/SREP11969