Calcium in PDB 4rbm: Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains

All present enzymatic activity of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains:
3.4.22.47;

The structure of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains, PDB code: 4rbm was solved by I.De Diego, F.Veillard, M.N.Sztukowska, T.Guevara, B.Potempa, A.Pomowski, J.A.Huntington, 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)	44.41 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.640, 58.810, 135.500, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.2

The structure of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Calcium atom in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains (pdb code 4rbm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains, PDB code: 4rbm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:11.5 occ:1.00 O A:PHE482 2.3 12.0 1.0 OE2 A:GLU491 2.4 13.9 1.0 O A:HOH853 2.5 12.1 1.0 O A:HOH850 2.5 11.6 1.0 O A:HOH816 2.5 12.8 1.0 OD1 A:ASP313 2.5 12.1 1.0 OD2 A:ASP313 2.6 12.2 1.0 OE1 A:GLU491 2.6 11.9 1.0 CD A:GLU491 2.9 14.9 1.0 CG A:ASP313 2.9 12.2 1.0 C A:PHE482 3.4 11.4 1.0 CA A:PHE482 4.1 8.8 1.0 CB A:PHE482 4.4 9.2 1.0 N A:ASP483 4.4 8.7 1.0 CG A:GLU491 4.4 9.5 1.0 NH2 A:ARG495 4.4 9.8 1.0 CB A:ASP313 4.4 9.4 1.0 O A:HOH909 4.5 23.9 1.0 CA A:ASP483 4.5 9.5 1.0 OG A:SER350 4.6 11.4 1.0 O A:HOH856 4.6 11.8 1.0 O A:HOH1241 4.6 40.0 1.0 OG1 A:THR314 4.6 13.8 1.0 O A:TYR484 4.6 13.6 1.0 O A:HOH1102 4.7 28.3 1.0 CA A:PRO487 4.7 10.2 1.0 N A:TYR484 4.9 11.7 1.0 C A:ASP483 5.0 13.3 1.0 O A:GLN486 5.0 15.8 1.0

Calcium binding site 2 out of 2 in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:14.2 occ:1.00 OD1 A:ASP337 2.3 14.8 1.0 O A:PHE341 2.3 14.7 1.0 OE1 A:GLU343 2.3 15.4 1.0 OD1 A:ASP339 2.3 14.1 1.0 O A:HOH874 2.4 17.1 1.0 O A:HOH836 2.4 12.6 1.0 OE2 A:GLU343 2.6 14.2 1.0 CD A:GLU343 2.8 17.5 1.0 CG A:ASP337 3.3 16.9 1.0 CG A:ASP339 3.4 16.3 1.0 C A:PHE341 3.5 15.5 1.0 OD2 A:ASP339 3.7 16.9 1.0 OD2 A:ASP337 3.8 21.3 1.0 CA A:PHE341 4.2 11.1 1.0 N A:PHE341 4.2 12.0 1.0 O A:HOH1178 4.2 22.9 1.0 CB A:PHE341 4.2 11.9 1.0 CG A:GLU343 4.3 14.6 1.0 N A:ASP337 4.3 15.2 1.0 O A:ASP339 4.4 17.2 1.0 C A:PRO342 4.4 13.7 1.0 O A:ASP337 4.5 19.7 1.0 N A:PRO342 4.6 12.1 1.0 CB A:ASP337 4.6 17.6 1.0 O A:PRO342 4.6 10.8 1.0 N A:ASP339 4.6 14.1 1.0 N A:GLU343 4.6 9.2 1.0 C A:ASP339 4.6 17.4 1.0 C A:ASP337 4.6 19.4 1.0 N A:VAL336 4.6 11.8 1.0 CB A:ASP339 4.6 13.5 1.0 O A:HOH1179 4.7 38.3 1.0 CA A:ASP337 4.7 15.5 1.0 O A:HOH1328 4.7 41.1 1.0 CA A:PRO342 4.7 11.2 1.0 CA A:ALA335 4.8 12.8 1.0 CA A:ASP339 4.9 12.5 1.0

I.De Diego, F.Veillard, M.Sztukowska, T.Guevara, B.Potempa, A.Pomowski, J.A.Huntington, J.Potempa, F.X.Gomis-Ruth. Structure and Mechanism of Cysteine Peptidase Kgp, A Major Virulence Factor of Porphyromonas Gingivalis in Periodontitis. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25266723
DOI: 10.1074/JBC.M114.602052