Atomistry » Sodium » PDB 4i05-4ii8 » 4ief
Atomistry »
  Sodium »
    PDB 4i05-4ii8 »
      4ief »

Sodium in PDB 4ief: Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains

Enzymatic activity of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains

All present enzymatic activity of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains:
3.4.22.37;

Protein crystallography data

The structure of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief was solved by I.De Diego, F.T.Veillard, T.Guevara, B.Potempa, M.Sztukowska, 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) 33.67 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.420, 133.140, 109.830, 90.00, 90.52, 90.00
R / Rfree (%) 18.9 / 22.5

Other elements in 4ief:

The structure of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Barium (Ba) 4 atoms
Chlorine (Cl) 1 atom
Calcium (Ca) 14 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains (pdb code 4ief). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains, PDB code: 4ief:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4ief

Go back to Sodium Binding Sites List in 4ief
Sodium binding site 1 out of 3 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na706

b:38.3
occ:1.00
O H:HOH911 2.2 26.8 1.0
OD1 H:ASP258 2.4 34.4 1.0
O F:HOH810 3.0 28.1 1.0
OE1 F:GLU254 3.3 83.0 1.0
CG H:ASP258 3.4 31.7 1.0
OE2 F:GLU254 3.5 85.3 1.0
CD F:GLU254 3.6 82.5 1.0
OD2 H:ASP258 3.7 33.8 1.0
O H:ASP614 4.0 37.3 1.0
MG H:MG705 4.1 50.4 1.0
CG H:GLU254 4.3 47.5 1.0
CD H:GLU254 4.4 77.8 1.0
OE2 H:GLU254 4.4 73.6 1.0
NA F:NA708 4.4 42.9 1.0
O H:GLU254 4.6 33.3 1.0
CB H:ASP258 4.7 28.5 1.0
CG F:GLU254 4.9 48.2 1.0
CA H:GLY615 4.9 33.9 1.0
OE1 H:GLU254 4.9 86.1 1.0
O H:GLY615 4.9 38.8 1.0
C H:GLY615 5.0 39.1 1.0

Sodium binding site 2 out of 3 in 4ief

Go back to Sodium Binding Sites List in 4ief
Sodium binding site 2 out of 3 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na707

b:63.5
occ:1.00
O H:HOH922 2.4 67.6 1.0
O F:HOH829 2.5 46.4 1.0
O H:HOH921 2.5 66.0 1.0
O F:HOH929 2.6 32.7 1.0
OD1 H:ASP255 2.6 51.0 1.0
OD2 H:ASP255 2.9 58.4 1.0
CG F:ASP616 3.1 58.7 1.0
CB F:ASP616 3.1 40.1 1.0
CG H:ASP255 3.1 49.4 1.0
OD1 F:ASP616 3.3 61.1 1.0
OD2 F:ASP616 3.6 67.1 1.0
OD2 F:ASP613 4.0 44.3 1.0
O F:ASP613 4.2 34.2 1.0
CA F:ASP616 4.6 36.3 1.0
CB H:ASP255 4.6 31.4 1.0
CG F:ASP613 4.7 39.5 1.0

Sodium binding site 3 out of 3 in 4ief

Go back to Sodium Binding Sites List in 4ief
Sodium binding site 3 out of 3 in the Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex of Porphyromonas Gingivalis Rgpb Pro- and Mature Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na708

b:42.9
occ:1.00
OD1 F:ASP258 2.2 44.3 1.0
OE1 H:GLU254 3.0 86.1 1.0
CG F:ASP258 3.2 41.5 1.0
O F:HOH810 3.2 28.1 1.0
OE2 H:GLU254 3.4 73.6 1.0
CD H:GLU254 3.4 77.8 1.0
OD2 F:ASP258 3.4 47.0 1.0
MG H:MG705 3.9 50.4 1.0
CG F:GLU254 4.0 48.2 1.0
CD F:GLU254 4.2 82.5 1.0
OE2 F:GLU254 4.4 85.3 1.0
NA F:NA706 4.4 38.3 1.0
O F:ASP614 4.5 37.3 1.0
O F:GLU254 4.6 32.1 1.0
CB F:ASP258 4.6 31.1 1.0
CG H:GLU254 4.7 47.5 1.0
OE1 F:GLU254 4.8 83.0 1.0
CA F:ASP258 5.0 28.0 1.0

Reference:

I.De Diego, F.T.Veillard, T.Guevara, B.Potempa, M.Sztukowska, J.Potempa, F.X.Gomis-Ruth. Porphyromonas Gingivalis Virulence Factor Gingipain Rgpb Shows A Unique Zymogenic Mechanism For Cysteine Peptidases. J.Biol.Chem. V. 288 14287 2013.
ISSN: ISSN 0021-9258
PubMed: 23558682
DOI: 10.1074/JBC.M112.444927
Page generated: Tue Dec 15 06:44:32 2020

Last articles

Zn in 7NA9
Zn in 7LZP
Zn in 7M1H
Zn in 7L6V
Zn in 7CM0
V in 7P8R
Ni in 7L19
Na in 7T88
Na in 7MJ5
Na in 7L00
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy