Sodium in PDB 4ief: Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains

All present enzymatic activity of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains:
3.4.22.37;

The structure of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief was solved by I.De Diego, F.T.Veillard, T.Guevara, B.Potempa, M.Sztukowska, 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)	33.67 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.420, 133.140, 109.830, 90.00, 90.52, 90.00
R / Rfree (%)	18.9 / 22.5

The structure of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Barium	(Ba)	4 atoms
Chlorine	(Cl)	1 atom
Calcium	(Ca)	14 atoms

The binding sites of Sodium atom in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains (pdb code 4ief). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range: probe atom residue distance (Å) B Occ F:Na706 b:38.3 occ:1.00 O H:HOH911 2.2 26.8 1.0 OD1 H:ASP258 2.4 34.4 1.0 O F:HOH810 3.0 28.1 1.0 OE1 F:GLU254 3.3 83.0 1.0 CG H:ASP258 3.4 31.7 1.0 OE2 F:GLU254 3.5 85.3 1.0 CD F:GLU254 3.6 82.5 1.0 OD2 H:ASP258 3.7 33.8 1.0 O H:ASP614 4.0 37.3 1.0 MG H:MG705 4.1 50.4 1.0 CG H:GLU254 4.3 47.5 1.0 CD H:GLU254 4.4 77.8 1.0 OE2 H:GLU254 4.4 73.6 1.0 NA F:NA708 4.4 42.9 1.0 O H:GLU254 4.6 33.3 1.0 CB H:ASP258 4.7 28.5 1.0 CG F:GLU254 4.9 48.2 1.0 CA H:GLY615 4.9 33.9 1.0 OE1 H:GLU254 4.9 86.1 1.0 O H:GLY615 4.9 38.8 1.0 C H:GLY615 5.0 39.1 1.0

Sodium binding site 2 out of 3 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range: probe atom residue distance (Å) B Occ F:Na707 b:63.5 occ:1.00 O H:HOH922 2.4 67.6 1.0 O F:HOH829 2.5 46.4 1.0 O H:HOH921 2.5 66.0 1.0 O F:HOH929 2.6 32.7 1.0 OD1 H:ASP255 2.6 51.0 1.0 OD2 H:ASP255 2.9 58.4 1.0 CG F:ASP616 3.1 58.7 1.0 CB F:ASP616 3.1 40.1 1.0 CG H:ASP255 3.1 49.4 1.0 OD1 F:ASP616 3.3 61.1 1.0 OD2 F:ASP616 3.6 67.1 1.0 OD2 F:ASP613 4.0 44.3 1.0 O F:ASP613 4.2 34.2 1.0 CA F:ASP616 4.6 36.3 1.0 CB H:ASP255 4.6 31.4 1.0 CG F:ASP613 4.7 39.5 1.0

Sodium binding site 3 out of 3 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range: probe atom residue distance (Å) B Occ F:Na708 b:42.9 occ:1.00 OD1 F:ASP258 2.2 44.3 1.0 OE1 H:GLU254 3.0 86.1 1.0 CG F:ASP258 3.2 41.5 1.0 O F:HOH810 3.2 28.1 1.0 OE2 H:GLU254 3.4 73.6 1.0 CD H:GLU254 3.4 77.8 1.0 OD2 F:ASP258 3.4 47.0 1.0 MG H:MG705 3.9 50.4 1.0 CG F:GLU254 4.0 48.2 1.0 CD F:GLU254 4.2 82.5 1.0 OE2 F:GLU254 4.4 85.3 1.0 NA F:NA706 4.4 38.3 1.0 O F:ASP614 4.5 37.3 1.0 O F:GLU254 4.6 32.1 1.0 CB F:ASP258 4.6 31.1 1.0 CG H:GLU254 4.7 47.5 1.0 OE1 F:GLU254 4.8 83.0 1.0 CA F:ASP258 5.0 28.0 1.0

I.De Diego, F.T.Veillard, T.Guevara, B.Potempa, M.Sztukowska, J.Potempa, F.X.Gomis-Ruth. Porphyromonas Gingivalis Virulence Factor Gingipain Rgpb Shows A Unique Zymogenic Mechanism For Cysteine Peptidases. J.Biol.Chem. V. 288 14287 2013.
ISSN: ISSN 0021-9258
PubMed: 23558682
DOI: 10.1074/JBC.M112.444927