Sodium in PDB 3eeb: Structure of the V. Cholerae Rtx Cysteine Protease Domain

The structure of Structure of the V. Cholerae Rtx Cysteine Protease Domain, PDB code: 3eeb was solved by P.J.Lupardus, A.Shen, M.Bogyo, K.C.Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.491, 66.099, 136.051, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.3

The binding sites of Sodium atom in the Structure of the V. Cholerae Rtx Cysteine Protease Domain (pdb code 3eeb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the V. Cholerae Rtx Cysteine Protease Domain, PDB code: 3eeb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the V. Cholerae Rtx Cysteine Protease Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the V. Cholerae Rtx Cysteine Protease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:49.0 occ:1.00 O32 A:IHP210 1.9 41.2 1.0 O31 A:IHP210 2.0 32.8 1.0 O A:HOH286 2.3 44.8 1.0 O A:GLU27 2.4 46.9 1.0 O A:HOH284 2.6 36.2 1.0 P1 A:IHP210 3.1 31.5 1.0 P2 A:IHP210 3.4 38.7 1.0 O21 A:IHP210 3.4 32.5 1.0 O11 A:IHP210 3.6 32.9 1.0 C A:GLU27 3.6 46.5 1.0 C2 A:IHP210 4.1 31.9 1.0 O A:HOH285 4.1 35.5 1.0 O42 A:IHP210 4.1 37.1 1.0 O12 A:IHP210 4.2 34.4 1.0 CA A:THR28 4.2 44.1 1.0 O A:HOH212 4.3 42.7 1.0 O22 A:IHP210 4.3 38.4 1.0 N A:THR28 4.3 45.3 1.0 C1 A:IHP210 4.4 31.8 1.0 O41 A:IHP210 4.4 32.3 1.0 NZ A:LYS54 4.5 33.8 1.0 N A:GLU27 4.6 47.0 1.0 NE2 A:HIS55 4.7 39.0 1.0 CA A:GLU27 4.7 47.2 1.0 O A:GLY25 4.7 47.7 1.0 CE1 A:HIS55 4.8 38.4 1.0 CB A:THR28 4.8 44.1 1.0

Sodium binding site 2 out of 2 in the Structure of the V. Cholerae Rtx Cysteine Protease Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the V. Cholerae Rtx Cysteine Protease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na211 b:26.2 occ:1.00 O31 B:IHP210 2.1 25.1 1.0 O32 B:IHP210 2.1 22.7 1.0 O B:GLU27 2.3 23.2 1.0 O B:HOH283 2.4 51.6 1.0 O B:HOH293 2.5 35.3 1.0 P1 B:IHP210 3.2 25.8 1.0 C B:GLU27 3.5 23.3 1.0 O21 B:IHP210 3.5 25.3 1.0 O11 B:IHP210 3.6 25.6 1.0 P2 B:IHP210 3.6 22.6 1.0 C2 B:IHP210 4.0 23.6 1.0 O12 B:IHP210 4.2 22.4 1.0 O B:HOH243 4.2 14.8 1.0 C1 B:IHP210 4.3 23.7 1.0 CA B:THR28 4.3 21.4 1.0 N B:THR28 4.4 22.0 1.0 N B:GLU27 4.4 25.9 1.0 O42 B:IHP210 4.4 23.7 1.0 O41 B:IHP210 4.5 25.2 1.0 O22 B:IHP210 4.5 23.0 1.0 CA B:GLU27 4.6 24.2 1.0 C B:GLY26 4.7 27.5 1.0 NZ B:LYS54 4.9 16.7 1.0

P.J.Lupardus, A.Shen, M.Bogyo, K.C.Garcia. Small Molecule-Induced Allosteric Activation of the Vibrio Cholerae Rtx Cysteine Protease Domain Science V. 322 265 2008.
ISSN: ISSN 0036-8075
PubMed: 18845756
DOI: 10.1126/SCIENCE.1162403