Atomistry » Sodium » PDB 6hz1-6ic1 » 6i9a
Atomistry »
  Sodium »
    PDB 6hz1-6ic1 »
      6i9a »

Sodium 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:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 6i9a

Go back to Sodium Binding Sites List in 6i9a
Sodium 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 Sodium with other atoms in the Na 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:Na703

b:9.3
occ:1.00
O A:LEU546 2.3 10.5 1.0
O A:SER549 2.3 10.1 1.0
OD1 A:ASN551 2.4 9.8 1.0
O A:THR544 2.5 9.2 1.0
O A:TYR550 2.5 8.7 1.0
O A:ALA543 2.7 8.8 1.0
C A:TYR550 3.1 8.2 1.0
C A:THR544 3.1 8.4 1.0
C A:LEU546 3.4 9.9 1.0
CG A:ASN551 3.5 9.1 1.0
C A:SER549 3.5 9.8 1.0
N A:LEU546 3.6 9.3 1.0
CA A:THR544 3.8 9.0 1.0
C A:ALA543 3.8 8.9 1.0
N A:ASN551 3.8 8.4 1.0
NH1 A:ARG597 3.8 12.3 1.0
CA A:LEU546 3.9 10.1 1.0
CA A:TYR550 3.9 8.9 1.0
CA A:ASN551 4.0 8.6 1.0
CB A:TYR550 4.0 9.4 1.0
N A:PHE545 4.0 8.7 1.0
CB A:LEU546 4.0 10.8 1.0
N A:TYR550 4.1 9.1 1.0
C A:PHE545 4.2 9.3 1.0
ND2 A:ASN551 4.2 10.6 1.0
N A:THR544 4.3 8.8 1.0
CZ A:ARG597 4.4 14.6 1.0
CB A:ASN551 4.4 9.2 1.0
O A:HOH1141 4.4 10.2 1.0
CA A:PHE545 4.4 9.5 1.0
N A:GLU547 4.5 11.6 1.0
N A:SER549 4.6 11.4 1.0
CA A:SER549 4.7 10.5 1.0
NH2 A:ARG597 4.8 15.8 1.0
CA A:GLU547 4.9 13.2 0.5
CA A:GLU547 4.9 12.7 0.5
C A:GLU547 4.9 12.8 1.0
O A:PHE545 5.0 10.7 1.0

Sodium binding site 2 out of 4 in 6i9a

Go back to Sodium Binding Sites List in 6i9a
Sodium 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 Sodium with other atoms in the Na 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:Na704

b:8.9
occ:1.00
O A:VAL521 2.3 9.9 1.0
OD2 A:ASP542 2.3 9.5 1.0
O A:SER537 2.4 9.1 1.0
OG1 A:THR536 2.4 10.3 1.0
O A:HOH1150 2.4 10.6 1.0
OH A:TYR402 2.5 9.6 1.0
CG A:ASP542 3.4 8.6 1.0
CB A:THR536 3.4 10.1 1.0
CZ A:TYR402 3.4 8.9 1.0
C A:SER537 3.5 9.1 1.0
C A:VAL521 3.5 8.8 1.0
OD1 A:ASP542 3.7 9.2 1.0
C A:THR536 3.9 9.6 1.0
O A:THR536 4.0 10.4 1.0
CA A:GLY522 4.1 8.9 1.0
CE1 A:TYR402 4.1 8.9 1.0
N A:GLY539 4.1 8.5 1.0
O A:HOH849 4.1 10.1 1.0
CE2 A:TYR402 4.2 9.0 1.0
N A:SER537 4.2 9.4 1.0
CA A:THR536 4.2 9.8 1.0
N A:GLY522 4.3 8.5 1.0
CA A:MET538 4.3 9.1 1.0
O A:HOH1354 4.3 13.9 1.0
N A:MET538 4.4 8.9 1.0
CA A:SER537 4.5 9.8 1.0
CG2 A:THR536 4.5 12.0 1.0
O A:PHE533 4.6 12.9 1.0
C A:MET538 4.6 8.8 1.0
CG1 A:VAL521 4.7 9.3 0.5
CA A:VAL521 4.7 9.0 0.5
CB A:ASP542 4.7 8.4 1.0
CA A:VAL521 4.7 8.7 0.5
CA A:PHE533 4.8 11.8 1.0
CD1 A:PHE533 4.8 12.4 1.0
O A:THR532 4.8 10.9 1.0
N A:THR536 4.9 10.8 1.0

Sodium binding site 3 out of 4 in 6i9a

Go back to Sodium Binding Sites List in 6i9a
Sodium 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 Sodium with other atoms in the Na 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:Na703

b:9.5
occ:1.00
O B:LEU546 2.3 11.2 1.0
O B:SER549 2.4 9.7 1.0
OD1 B:ASN551 2.4 9.0 1.0
O B:THR544 2.5 8.8 1.0
O B:TYR550 2.5 8.8 1.0
O B:ALA543 2.7 9.0 1.0
C B:TYR550 3.1 8.6 1.0
C B:THR544 3.1 8.6 1.0
C B:LEU546 3.4 10.3 1.0
CG B:ASN551 3.5 9.0 1.0
C B:SER549 3.6 9.7 1.0
N B:LEU546 3.6 9.3 1.0
NH1 B:ARG597 3.8 13.9 1.0
C B:ALA543 3.8 8.4 1.0
CA B:THR544 3.8 8.9 1.0
N B:ASN551 3.8 8.0 1.0
CA B:LEU546 3.9 9.9 1.0
CA B:TYR550 3.9 8.7 1.0
CA B:ASN551 4.0 8.3 1.0
CB B:LEU546 4.0 10.8 1.0
CB B:TYR550 4.0 9.4 1.0
N B:PHE545 4.0 9.0 1.0
N B:TYR550 4.2 9.4 1.0
C B:PHE545 4.2 9.3 1.0
ND2 B:ASN551 4.2 10.3 1.0
N B:THR544 4.3 8.7 1.0
CZ B:ARG597 4.3 17.3 1.0
CB B:ASN551 4.4 9.0 1.0
O B:HOH1119 4.4 10.7 1.0
CA B:PHE545 4.5 9.0 1.0
N B:GLU547 4.5 12.2 1.0
N B:SER549 4.6 11.1 1.0
CA B:SER549 4.7 11.3 1.0
NH2 B:ARG597 4.8 18.7 1.0
CA B:GLU547 4.9 13.4 0.5
CA B:GLU547 4.9 13.2 0.5
C B:GLU547 4.9 12.8 1.0
O B:PHE545 4.9 10.7 1.0

Sodium binding site 4 out of 4 in 6i9a

Go back to Sodium Binding Sites List in 6i9a
Sodium 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 Sodium with other atoms in the Na 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:Na704

b:9.5
occ:1.00
OD2 B:ASP542 2.3 9.5 1.0
O B:VAL521 2.3 10.2 1.0
OG1 B:THR536 2.4 10.4 1.0
O B:SER537 2.4 9.9 1.0
O B:HOH1077 2.4 10.7 1.0
OH B:TYR402 2.5 10.0 1.0
CG B:ASP542 3.3 8.8 1.0
CB B:THR536 3.4 10.6 1.0
CZ B:TYR402 3.4 9.2 1.0
C B:SER537 3.5 10.1 1.0
C B:VAL521 3.5 9.1 1.0
OD1 B:ASP542 3.7 9.5 1.0
C B:THR536 3.9 10.7 1.0
O B:THR536 4.0 11.1 1.0
N B:GLY539 4.1 8.7 1.0
CA B:GLY522 4.1 9.9 1.0
CE1 B:TYR402 4.1 10.0 1.0
O B:HOH816 4.1 10.9 1.0
N B:GLY522 4.2 9.2 1.0
CE2 B:TYR402 4.2 9.5 1.0
CA B:THR536 4.3 10.5 1.0
N B:SER537 4.3 10.2 1.0
CA B:MET538 4.3 9.4 1.0
O B:HOH1364 4.3 15.5 1.0
N B:MET538 4.4 10.0 1.0
CG2 B:THR536 4.5 11.6 1.0
CA B:SER537 4.5 10.2 1.0
O B:PHE533 4.5 12.1 1.0
C B:MET538 4.5 9.1 1.0
CB B:ASP542 4.6 9.4 1.0
CG1 B:VAL521 4.6 9.6 0.5
CA B:VAL521 4.7 9.7 0.5
CA B:VAL521 4.7 9.2 0.5
O B:THR532 4.7 10.4 1.0
CA B:PHE533 4.8 10.7 1.0
CD1 B:PHE533 4.8 11.2 1.0
N B:THR536 4.9 11.0 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 Oct 8 09:35:06 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy