Barium 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
Chlorine	(Cl)	1 atom
Calcium	(Ca)	14 atoms
Sodium	(Na)	3 atoms

The binding sites of Barium 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 Barium atom.
In total 4 binding sites of Barium where determined in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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 B:Ba701 b:55.1 occ:1.00 O B:HOH917 2.5 17.7 1.0 OD2 B:ASP521 2.5 42.5 1.0 OE1 B:GLU390 2.6 31.6 1.0 O B:HOH916 2.6 28.6 1.0 ND1 B:HIS395 2.8 29.4 1.0 OD1 B:ASP521 3.0 33.8 1.0 CG B:ASP521 3.1 35.8 1.0 CD B:GLU390 3.5 39.0 1.0 CG B:HIS395 3.6 27.7 1.0 CE1 B:HIS395 3.7 28.4 1.0 OE2 B:GLU390 3.7 40.9 1.0 CB B:HIS395 3.8 24.9 1.0 CA B:HIS395 3.9 24.4 1.0 O B:HOH915 4.2 22.8 1.0 O B:HIS395 4.3 26.5 1.0 OD2 B:ASP387 4.3 28.4 1.0 CB B:ASP521 4.6 28.3 1.0 C B:HIS395 4.6 27.9 1.0 O B:ASP387 4.6 28.9 1.0 O B:MET517 4.7 27.8 1.0 CD2 B:HIS395 4.8 29.2 1.0 NE2 B:HIS395 4.8 28.6 1.0 CG B:GLU390 4.8 32.1 1.0 CE B:MET517 4.9 25.4 1.0 ND2 B:ASN388 5.0 36.4 1.0 CB B:GLU390 5.0 28.8 1.0

Barium binding site 2 out of 4 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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 D:Ba701 b:63.2 occ:1.00 OD2 D:ASP521 2.6 32.4 1.0 OE1 D:GLU390 2.6 37.8 1.0 ND1 D:HIS395 2.9 33.0 1.0 OD1 D:ASP521 3.1 26.4 1.0 CG D:ASP521 3.2 27.7 1.0 CD D:GLU390 3.4 45.3 1.0 OE2 D:GLU390 3.6 35.8 1.0 CG D:HIS395 3.6 31.7 1.0 CE1 D:HIS395 3.8 31.9 1.0 CB D:HIS395 3.8 29.1 1.0 CA D:HIS395 3.8 28.4 1.0 O D:HOH804 4.0 27.2 1.0 O D:HIS395 4.2 28.1 1.0 OD2 D:ASP387 4.2 37.8 1.0 C D:HIS395 4.5 29.8 1.0 O C:HOH334 4.6 34.1 1.0 O D:ASP387 4.6 37.5 1.0 O D:MET517 4.6 28.6 1.0 CB D:ASP521 4.7 26.1 1.0 CG D:GLU390 4.7 41.1 1.0 CD2 D:HIS395 4.7 33.7 1.0 NE2 D:HIS395 4.8 32.6 1.0 CB D:GLU390 4.9 33.9 1.0 CE D:MET517 5.0 32.0 1.0

Barium binding site 3 out of 4 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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:Ba701 b:59.5 occ:1.00 OE1 F:GLU390 2.5 32.2 1.0 O F:HOH877 2.6 25.8 1.0 OD2 F:ASP521 2.6 40.3 1.0 O F:HOH876 2.6 25.6 1.0 ND1 F:HIS395 2.9 31.2 1.0 OD1 F:ASP521 3.1 25.5 1.0 CG F:ASP521 3.2 30.0 1.0 CD F:GLU390 3.4 43.5 1.0 OE2 F:GLU390 3.5 33.7 1.0 CG F:HIS395 3.6 29.9 1.0 CB F:HIS395 3.6 27.5 1.0 CA F:HIS395 3.8 27.5 1.0 CE1 F:HIS395 3.9 29.9 1.0 O F:HIS395 4.2 32.4 1.0 OD2 F:ASP387 4.2 31.6 1.0 O F:HOH913 4.3 31.5 1.0 C F:HIS395 4.5 31.8 1.0 O F:ASP387 4.6 31.4 1.0 CB F:ASP521 4.7 28.0 1.0 CE F:MET517 4.7 28.2 1.0 O F:MET517 4.7 28.0 1.0 ND2 F:ASN388 4.8 55.3 1.0 CG F:GLU390 4.8 37.2 1.0 CD2 F:HIS395 4.8 31.0 1.0 NE2 F:HIS395 4.9 30.1 1.0 CG2 F:ILE398 5.0 32.7 1.0

Barium binding site 4 out of 4 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range: probe atom residue distance (Å) B Occ H:Ba701 b:68.0 occ:1.00 OD2 H:ASP521 2.6 34.2 1.0 O H:HOH877 2.6 15.2 1.0 O H:HOH876 2.6 23.4 1.0 OE1 H:GLU390 2.7 59.0 1.0 ND1 H:HIS395 2.8 33.8 1.0 OD1 H:ASP521 3.1 34.8 1.0 CG H:ASP521 3.2 33.5 1.0 O H:HOH910 3.3 40.1 1.0 CD H:GLU390 3.4 56.5 1.0 CE1 H:HIS395 3.6 32.5 1.0 OE2 H:GLU390 3.7 52.4 1.0 CG H:HIS395 3.7 32.1 1.0 CB H:HIS395 4.0 29.2 1.0 CA H:HIS395 4.0 29.0 1.0 OD2 H:ASP387 4.2 48.7 1.0 O H:HOH815 4.2 35.7 1.0 O H:HIS395 4.4 27.8 1.0 O H:ASP387 4.6 36.9 1.0 O H:MET517 4.6 29.2 1.0 CG H:GLU390 4.6 42.5 1.0 NE2 H:HIS395 4.6 32.5 1.0 C H:HIS395 4.7 30.4 1.0 CB H:ASP521 4.7 27.9 1.0 CD2 H:HIS395 4.7 33.4 1.0 ND2 H:ASN388 4.8 53.5 1.0 CB H:GLU390 4.8 37.4 1.0 CE H:MET517 4.8 28.6 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