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Calcium in PDB 6i9a: Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36

Enzymatic activity of Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36

All present enzymatic activity of Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36:
3.4.22.47;

Protein crystallography data

The structure of Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36, PDB code: 6i9a was solved by F.X.Gomis-Ruth, T.Guevara, A.Rofdriguez-Banqueri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.19 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.670, 87.050, 129.210, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 14.8

Other elements in 6i9a:

The structure of Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36 also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36 (pdb code 6i9a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36, PDB code: 6i9a:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6i9a

Go back to Calcium Binding Sites List in 6i9a
Calcium binding site 1 out of 4 in the Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36


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) in Complex with Inhibitor Kyt-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:15.7
occ:1.00
 O A:PHE341 2.3 11.9 1.0
OD1 A:ASP337 2.3 18.1 1.0
OD1 A:ASP339 2.4 14.8 1.0
O A:HOH907 2.4 18.5 1.0
O A:HOH919 2.4 14.0 1.0
OE1 A:GLU343 2.5 15.2 1.0
OE2 A:GLU343 2.5 14.0 1.0
CD A:GLU343 2.8 13.5 1.0
CG A:ASP337 3.3 18.1 1.0
CG A:ASP339 3.4 16.2 1.0
C A:PHE341 3.5 11.3 1.0
OD2 A:ASP337 3.8 21.5 1.0
OD2 A:ASP339 3.8 19.9 1.0
N A:PHE341 4.1 11.9 1.0
CA A:PHE341 4.1 11.4 1.0
O A:HOH1142 4.2 16.1 0.5
CB A:PHE341 4.2 11.6 1.0
N A:ASP337 4.3 15.9 1.0
O A:HOH1142 4.3 20.6 0.5
CG A:GLU343 4.3 13.5 1.0
O A:ASP339 4.3 16.7 1.0
C A:PRO342 4.4 11.6 1.0
CB A:ASP337 4.5 16.5 1.0
N A:PRO342 4.5 11.4 1.0
C A:ASP339 4.6 15.4 1.0
N A:GLU343 4.6 11.6 1.0
O A:ASP337 4.6 16.3 1.0
N A:VAL336 4.6 12.9 1.0
N A:ASP339 4.6 16.8 1.0
O A:PRO342 4.6 13.2 1.0
C A:ASP337 4.6 16.8 1.0
CB A:ASP339 4.7 17.4 1.0
CA A:ASP337 4.7 15.9 1.0
CA A:PRO342 4.7 11.7 1.0
O A:HOH874 4.7 18.9 0.5
CA A:ALA335 4.8 14.1 1.0
CA A:ASP339 4.8 16.1 1.0

Calcium binding site 2 out of 4 in 6i9a

Go back to Calcium Binding Sites List in 6i9a
Calcium binding site 2 out of 4 in the Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36


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) in Complex with Inhibitor Kyt-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:10.3
occ:1.00
 O A:PHE482 2.4 10.1 1.0
O A:HOH1191 2.4 12.1 1.0
O A:HOH1136 2.4 12.9 1.0
O A:HOH1063 2.5 11.7 1.0
OE2 A:GLU491 2.5 10.7 1.0
OD1 A:ASP313 2.5 10.8 1.0
OD2 A:ASP313 2.5 11.1 1.0
OE1 A:GLU491 2.6 12.1 1.0
CG A:ASP313 2.9 10.4 1.0
CD A:GLU491 2.9 10.6 1.0
C A:PHE482 3.4 10.1 1.0
CA A:PHE482 4.1 10.2 1.0
O A:HOH1244 4.4 18.9 1.0
CB A:ASP313 4.4 10.9 1.0
N A:ASP483 4.4 10.3 1.0
CG A:GLU491 4.4 11.1 1.0
NH2 A:ARG495 4.4 11.1 1.0
CB A:PHE482 4.4 10.3 1.0
O A:HOH1335 4.5 18.8 1.0
O A:HOH1200 4.5 12.7 1.0
CA A:ASP483 4.5 10.5 1.0
OG A:SER350 4.6 10.8 1.0
OG1 A:THR314 4.6 13.3 1.0
O A:TYR484 4.7 12.1 1.0
CA A:PRO487 4.7 10.9 1.0
O A:HOH1420 4.9 36.9 1.0
N A:TYR484 5.0 11.1 1.0

Calcium binding site 3 out of 4 in 6i9a

Go back to Calcium Binding Sites List in 6i9a
Calcium binding site 3 out of 4 in the Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:10.6
occ:1.00
 O B:PHE341 2.3 11.3 1.0
OD1 B:ASP337 2.3 13.9 1.0
O B:HOH913 2.4 11.7 1.0
OD1 B:ASP339 2.4 11.9 1.0
OE2 B:GLU343 2.4 11.9 1.0
O B:HOH881 2.4 13.7 1.0
OE1 B:GLU343 2.5 11.2 1.0
CD B:GLU343 2.8 10.6 1.0
CG B:ASP339 3.4 12.0 1.0
CG B:ASP337 3.4 15.2 1.0
C B:PHE341 3.5 10.7 1.0
OD2 B:ASP339 3.7 12.7 1.0
OD2 B:ASP337 4.0 20.1 1.0
N B:PHE341 4.1 11.6 1.0
CA B:PHE341 4.2 10.9 1.0
CB B:PHE341 4.2 11.7 1.0
N B:ASP337 4.3 13.2 1.0
O B:HOH805 4.3 26.4 1.0
CG B:GLU343 4.3 11.2 1.0
C B:PRO342 4.4 10.1 1.0
O B:ASP339 4.4 13.4 1.0
O B:ASP337 4.4 15.8 1.0
N B:GLU343 4.5 9.7 1.0
N B:PRO342 4.5 10.3 1.0
O B:PRO342 4.6 11.2 1.0
CB B:ASP337 4.6 15.1 1.0
C B:ASP337 4.6 14.1 1.0
C B:ASP339 4.6 11.9 1.0
N B:VAL336 4.6 11.3 1.0
O B:HOH860 4.6 25.2 1.0
N B:ASP339 4.6 13.9 1.0
CB B:ASP339 4.7 11.6 1.0
CA B:ASP337 4.7 14.2 1.0
CA B:PRO342 4.7 10.1 1.0
O B:HOH887 4.7 32.0 1.0
CA B:ALA335 4.8 12.6 1.0
CA B:ASP339 4.9 12.4 1.0

Calcium binding site 4 out of 4 in 6i9a

Go back to Calcium Binding Sites List in 6i9a
Calcium binding site 4 out of 4 in the Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Porphyromonas Gingivalis Gingipain K (Kgp) in Complex with Inhibitor Kyt-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:9.9
occ:1.00
 O B:PHE482 2.4 9.8 1.0
O B:HOH1191 2.4 11.9 1.0
O B:HOH1137 2.4 11.7 1.0
OE2 B:GLU491 2.4 10.0 1.0
O B:HOH1043 2.5 11.6 1.0
OD1 B:ASP313 2.5 10.2 1.0
OD2 B:ASP313 2.5 10.4 1.0
OE1 B:GLU491 2.6 10.4 1.0
CG B:ASP313 2.9 11.1 1.0
CD B:GLU491 2.9 10.3 1.0
C B:PHE482 3.4 9.6 1.0
CA B:PHE482 4.1 9.9 1.0
O B:HOH1187 4.4 20.0 1.0
N B:ASP483 4.4 10.1 1.0
CG B:GLU491 4.4 9.8 1.0
CB B:ASP313 4.4 10.2 1.0
CB B:PHE482 4.4 11.0 1.0
NH2 B:ARG495 4.4 10.9 1.0
O B:HOH1334 4.5 16.9 1.0
O B:HOH1197 4.5 12.9 1.0
CA B:ASP483 4.5 11.2 1.0
OG B:SER350 4.6 10.3 1.0
OG1 B:THR314 4.6 12.9 1.0
CA B:PRO487 4.7 11.2 1.0
O B:TYR484 4.7 12.2 1.0
O B:HOH1329 4.8 31.5 1.0
N B:TYR484 4.9 10.9 1.0
C B:ASP483 5.0 11.9 1.0

Reference:

T.Guevara, A.Rodriguez-Banqueri, A.M.Lasica, M.Ksiazek, B.A.Potempa, J.Potempa, F.X.Gomis-Ruth. Structural Determinants of Inhibition of Porphyromonas Gingivalis Gingipain K By Kyt-36, A Potent, Selective, and Bioavailable Peptidase Inhibitor. Sci Rep V. 9 4935 2019.
ISSN: ESSN 2045-2322
PubMed: 30894633
DOI: 10.1038/S41598-019-41354-3
Page generated: Tue Jul 16 09:21:03 2024

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