Sodium in PDB 3pa8: Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor

The structure of Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor, PDB code: 3pa8 was solved by P.J.Lupardus, K.C.Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.310, 45.480, 87.230, 90.00, 103.53, 90.00
R / Rfree (%)	18.5 / 23.3

The structure of Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor (pdb code 3pa8). 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 C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor, PDB code: 3pa8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor


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 C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na256 b:35.3 occ:1.00 O A:HOH274 2.7 20.5 1.0 O24 A:IHP257 2.8 27.5 1.0 O45 A:IHP257 2.8 29.1 1.0 O A:HOH262 2.8 17.6 1.0 O15 A:IHP257 3.0 28.6 1.0 NH2 A:ARG208 3.5 22.8 1.0 P4 A:IHP257 3.5 30.5 1.0 O34 A:IHP257 3.6 27.8 1.0 P5 A:IHP257 3.6 29.3 1.0 CB A:LYS221 3.6 22.7 1.0 O14 A:IHP257 3.7 28.0 1.0 NE A:ARG208 3.7 23.3 1.0 C4 A:IHP257 3.8 29.1 1.0 CD A:LYS221 3.9 23.1 1.0 CZ A:ARG208 4.0 24.0 1.0 C5 A:IHP257 4.0 27.9 1.0 O A:HOH310 4.2 29.4 1.0 O A:ARG209 4.2 24.6 1.0 N A:ARG209 4.2 23.2 1.0 CG A:LYS221 4.3 23.4 1.0 CB A:ARG208 4.4 24.0 1.0 CE A:LYS221 4.5 23.1 1.0 O25 A:IHP257 4.5 27.0 1.0 NZ A:LYS221 4.7 19.5 1.0 O35 A:IHP257 4.7 27.5 1.0 N A:LYS221 4.7 24.1 1.0 CA A:ARG208 4.7 23.6 1.0 CA A:LYS221 4.7 23.5 1.0 NZ A:LYS57 4.8 19.9 1.0 CD A:ARG208 4.8 25.7 1.0 O46 A:IHP257 4.9 27.7 1.0 CG A:ARG208 4.9 25.0 1.0 C A:ARG208 4.9 23.8 1.0 CA A:ARG209 4.9 23.5 1.0 CB A:ARG209 4.9 23.0 1.0 C6 A:IHP257 4.9 28.0 1.0 O44 A:IHP257 5.0 29.6 1.0

Sodium binding site 2 out of 2 in the Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor


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 C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na255 b:34.3 occ:1.00 O46 B:IHP256 2.7 28.2 1.0 O B:HOH308 2.7 23.1 1.0 O B:HOH259 2.8 19.6 1.0 O B:HOH305 2.9 25.4 1.0 O15 B:IHP256 3.1 28.1 1.0 NH2 B:ARG209 3.6 24.5 1.0 P6 B:IHP256 3.8 28.5 1.0 CG B:LYS221 3.8 21.2 1.0 O25 B:IHP256 3.8 26.4 1.0 CD B:LYS221 3.8 20.2 1.0 O45 B:IHP256 3.9 28.0 1.0 P5 B:IHP256 3.9 28.9 1.0 CB B:LYS221 3.9 21.7 1.0 NE B:ARG209 3.9 24.4 1.0 CZ B:ARG209 4.0 24.5 1.0 O26 B:IHP256 4.0 29.1 1.0 C5 B:IHP256 4.1 27.2 1.0 C6 B:IHP256 4.1 28.0 1.0 CB B:ARG209 4.1 19.8 1.0 OG B:SER231 4.2 30.3 1.0 O16 B:IHP256 4.3 27.1 1.0 O B:ARG209 4.5 22.1 1.0 O B:HOH276 4.5 21.9 1.0 C4 B:IHP256 4.6 28.0 1.0 O B:HOH306 4.7 28.8 1.0 CA B:LYS221 4.7 22.6 1.0 O24 B:IHP256 4.8 29.9 1.0 CG B:ARG209 4.8 21.0 1.0 CD B:ARG209 4.9 22.8 1.0 CA B:ARG209 4.9 20.4 1.0 N B:ARG209 4.9 20.2 1.0 NH1 B:ARG209 5.0 26.3 1.0

A.W.Puri, P.J.Lupardus, E.Deu, V.E.Albrow, K.C.Garcia, M.Bogyo, A.Shen. Rational Design of Inhibitors and Activity-Based Probes Targeting Clostridium Difficile Virulence Factor Tcdb. Chem.Biol. V. 17 1201 2010.
ISSN: ISSN 1074-5521
PubMed: 21095570
DOI: 10.1016/J.CHEMBIOL.2010.09.011