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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 Dec 15 12:23:53 2020

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