Sodium in PDB 6i0x: Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine.

The structure of Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine., PDB code: 6i0x was solved by F.X.Gomis-Ruth, T.Goulas, M.Sola, J.Potempa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.08 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.840, 71.870, 104.720, 90.00, 95.86, 90.00
R / Rfree (%)	18 / 19.3

The binding sites of Sodium atom in the Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine. (pdb code 6i0x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine., PDB code: 6i0x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:14.2 occ:1.00 O A:PHE148 2.3 13.1 1.0 O A:HOH832 2.3 15.4 1.0 O A:ASP158 2.4 16.1 1.0 OD1 A:ASP158 2.4 16.6 1.0 O A:HOH804 2.5 24.3 1.0 OD1 A:ASP147 2.5 17.2 1.0 C A:ASP158 3.4 16.4 1.0 CG A:ASP158 3.5 17.7 1.0 CG A:ASP147 3.5 19.6 1.0 C A:PHE148 3.5 14.7 1.0 CA A:ASP158 3.7 13.2 1.0 OD2 A:ASP147 3.8 20.4 1.0 N A:PHE148 4.0 14.2 1.0 N A:TYR150 4.1 13.8 1.0 CG A:PRO161 4.1 16.9 1.0 CB A:ASP158 4.1 14.5 1.0 CD A:PRO161 4.2 14.5 1.0 OD2 A:ASP158 4.4 20.8 1.0 CA A:PHE148 4.4 13.2 1.0 N A:ILE149 4.4 13.5 1.0 CA A:ILE149 4.5 13.6 1.0 O A:HOH739 4.5 13.5 0.5 N A:GLU159 4.6 13.7 1.0 CB A:TYR150 4.6 12.9 1.0 O A:HOH861 4.7 30.2 1.0 C A:ILE149 4.7 14.4 1.0 O A:TYR131 4.8 12.4 1.0 CB A:ASP147 4.8 14.0 1.0 CD1 A:PHE148 4.9 16.4 1.0 CD1 A:PHE45 4.9 21.8 1.0 CA A:TYR150 5.0 11.7 1.0 C A:ASP147 5.0 15.6 1.0

Sodium binding site 2 out of 3 in the Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:32.5 occ:1.00 O A:HOH680 2.2 35.7 1.0 O A:HOH869 2.3 22.1 1.0 O A:HOH651 2.5 19.6 1.0 O A:ASP124 2.6 15.8 1.0 C A:ASP124 3.4 15.1 1.0 CA A:ASP124 3.5 12.5 1.0 NH2 A:ARG70 3.9 15.8 1.0 O A:THR123 4.1 15.2 1.0 CB A:ASP124 4.2 14.1 1.0 OD1 A:ASP124 4.6 17.7 1.0 N A:SER125 4.6 12.5 1.0 N A:ASP124 4.6 12.3 1.0 O A:HOH997 4.7 31.9 1.0 C A:THR123 4.8 15.8 1.0 CG A:ASP124 5.0 16.7 1.0

Sodium binding site 3 out of 3 in the Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Porphyromonas Gingivalis Peptidylarginine Deminase (Ppad) Mutant G231N/E232T/N235D in Complex with Cl-Amidine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:18.4 occ:1.00 O B:PHE148 2.3 18.9 1.0 O B:HOH832 2.4 16.7 1.0 OD1 B:ASP158 2.4 20.0 1.0 O B:ASP158 2.4 18.7 1.0 OD1 B:ASP147 2.5 22.8 1.0 O B:HOH744 2.5 22.6 1.0 C B:ASP158 3.4 19.4 1.0 CG B:ASP147 3.4 23.9 1.0 CG B:ASP158 3.5 22.1 1.0 C B:PHE148 3.5 20.1 1.0 OD2 B:ASP147 3.7 29.7 1.0 CA B:ASP158 3.8 16.6 1.0 N B:PHE148 3.9 18.2 1.0 N B:TYR150 4.1 17.6 1.0 CG B:PRO161 4.1 22.3 1.0 CB B:ASP158 4.2 17.3 1.0 CD B:PRO161 4.2 19.1 1.0 O B:HOH963 4.3 34.0 1.0 OD2 B:ASP158 4.4 26.8 1.0 CA B:PHE148 4.4 17.0 1.0 N B:ILE149 4.5 18.1 1.0 CA B:ILE149 4.5 18.8 1.0 O B:HOH849 4.6 28.5 1.0 N B:GLU159 4.6 17.1 1.0 CB B:TYR150 4.7 17.9 1.0 C B:ILE149 4.8 19.4 1.0 CB B:ASP147 4.8 17.8 1.0 O B:TYR131 4.8 17.7 1.0 CD1 B:PHE45 4.9 29.5 1.0 CD1 B:PHE148 4.9 18.9 1.0 C B:ASP147 5.0 18.8 1.0 CA B:TYR150 5.0 17.1 1.0

G.Bereta, T.Goulas, M.Madej, E.Bielecka, M.Sola, J.Potempa, F.Xavier Gomis-Ruth. Structure, Function, and Inhibition of A Genomic/Clinical Variant of Porphyromonas Gingivalis Peptidylarginine Deiminase. Protein Sci. V. 28 478 2019.
ISSN: ESSN 1469-896X
PubMed: 30638292
DOI: 10.1002/PRO.3571