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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4rbm:

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

Nickel (Ni) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains, PDB code: 4rbm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4rbm

Go back to Sodium Binding Sites List in 4rbm
Sodium binding site 1 out of 3 in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains


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) Catalytic and Immunoglobulin Superfamily-Like Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:10.7
occ:1.00
 O A:VAL521 2.3 10.6 1.0
OD2 A:ASP542 2.4 11.5 1.0
OG1 A:THR536 2.4 11.2 1.0
O A:SER537 2.4 10.9 1.0
O A:HOH1275 2.4 10.1 1.0
OH A:TYR402 2.6 9.9 1.0
CB A:THR536 3.3 13.2 1.0
CG A:ASP542 3.4 12.3 1.0
CZ A:TYR402 3.5 13.5 1.0
C A:VAL521 3.5 12.6 1.0
C A:SER537 3.6 13.6 1.0
OD1 A:ASP542 3.7 11.2 1.0
C A:THR536 3.9 13.7 1.0
O A:THR536 3.9 11.6 1.0
CA A:GLY522 4.1 9.9 1.0
CE1 A:TYR402 4.1 10.3 1.0
N A:GLY539 4.1 9.2 1.0
O A:HOH837 4.2 13.5 1.0
N A:SER537 4.2 10.9 1.0
N A:GLY522 4.2 9.9 1.0
CA A:THR536 4.2 8.7 1.0
CE2 A:TYR402 4.3 10.0 1.0
CA A:MET538 4.3 8.0 1.0
O A:HOH833 4.4 14.5 1.0
N A:MET538 4.4 9.6 1.0
O A:PHE533 4.4 12.8 1.0
CG2 A:THR536 4.5 9.9 1.0
CA A:SER537 4.5 11.5 1.0
C A:MET538 4.6 11.7 1.0
CA A:VAL521 4.6 8.4 1.0
CB A:ASP542 4.7 9.1 1.0
O A:THR532 4.8 10.6 1.0
CD1 A:PHE533 4.8 14.0 1.0
CA A:PHE533 4.9 9.7 1.0
N A:THR536 4.9 9.9 1.0

Sodium binding site 2 out of 3 in 4rbm

Go back to Sodium Binding Sites List in 4rbm
Sodium binding site 2 out of 3 in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains


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) Catalytic and Immunoglobulin Superfamily-Like Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:12.5
occ:1.00
 O A:LEU546 2.4 12.7 1.0
O A:SER549 2.4 9.9 1.0
OD1 A:ASN551 2.4 10.5 1.0
O A:THR544 2.5 9.2 1.0
O A:TYR550 2.5 9.0 1.0
O A:ALA543 2.7 10.7 1.0
C A:TYR550 3.2 10.5 1.0
C A:THR544 3.2 10.6 1.0
CG A:ASN551 3.4 17.4 1.0
C A:LEU546 3.4 12.6 1.0
N A:LEU546 3.5 9.1 1.0
C A:SER549 3.5 10.7 1.0
NH1 A:ARG597 3.7 14.6 1.0
C A:ALA543 3.8 10.3 1.0
CA A:THR544 3.8 8.2 1.0
N A:ASN551 3.9 9.1 1.0
CA A:LEU546 3.9 9.1 1.0
CA A:TYR550 4.0 8.0 1.0
CA A:ASN551 4.0 8.9 1.0
CB A:TYR550 4.0 8.5 1.0
N A:PHE545 4.0 7.8 1.0
CB A:LEU546 4.1 9.5 1.0
ND2 A:ASN551 4.2 12.6 1.0
N A:TYR550 4.2 8.4 1.0
C A:PHE545 4.2 12.4 1.0
N A:THR544 4.3 9.1 1.0
CB A:ASN551 4.4 8.8 1.0
CZ A:ARG597 4.4 24.0 1.0
O A:HOH844 4.4 11.2 1.0
CA A:PHE545 4.5 7.8 1.0
N A:SER549 4.5 9.3 1.0
N A:GLU547 4.6 10.8 1.0
CA A:SER549 4.7 8.3 1.0
NH2 A:ARG597 4.9 20.8 1.0
CA A:GLU547 4.9 11.0 1.0
C A:GLU547 4.9 15.7 1.0

Sodium binding site 3 out of 3 in 4rbm

Go back to Sodium Binding Sites List in 4rbm
Sodium binding site 3 out of 3 in the Porphyromonas Gingivalis Gingipain K (Kgp) Catalytic and Immunoglobulin Superfamily-Like Domains


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) Catalytic and Immunoglobulin Superfamily-Like Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:16.1
occ:1.00
 O A:HOH1060 2.2 36.5 1.0
O A:HOH904 2.2 24.8 1.0
O A:THR415 2.3 12.6 1.0
O A:HOH1204 2.4 31.9 1.0
O A:HOH891 2.9 21.9 1.0
C A:THR415 3.3 14.1 1.0
O1 A:GOL716 3.8 51.0 1.0
CA A:THR415 3.9 11.4 1.0
C1 A:GOL716 4.2 51.6 1.0
O A:HOH1106 4.3 40.9 1.0
N A:ASP416 4.5 11.0 1.0
CB A:THR415 4.6 15.5 1.0
O2 A:GOL716 4.6 55.0 1.0
O A:TYR414 4.7 15.9 1.0
O A:HOH1079 4.7 39.1 1.0
CA A:ASP416 4.9 10.8 1.0
O A:HOH1124 5.0 38.6 1.0

Reference:

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
Page generated: Tue Dec 15 07:10:02 2020

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