Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Structure of the C. Difficile Tcdb Cysteine Protease Domain in Complex with A Peptide Inhibitor, PDB code: 3pa8:

Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca255 b:29.0 occ:1.00 O23 A:IHP257 2.1 29.6 1.0 O33 B:IHP256 2.3 32.8 1.0 O32 A:IHP257 2.4 30.7 1.0 O B:HOH258 2.4 26.9 1.0 O32 B:IHP256 2.4 28.5 1.0 O A:HOH260 2.5 46.4 1.0 O42 B:IHP256 3.3 31.5 1.0 P2 B:IHP256 3.4 29.4 1.0 O42 A:IHP257 3.4 31.8 1.0 P3 A:IHP257 3.4 30.1 1.0 P2 A:IHP257 3.4 29.2 1.0 P3 B:IHP256 3.5 30.3 1.0 O43 A:IHP257 3.8 29.3 1.0 O13 A:IHP257 3.8 29.5 1.0 O13 B:IHP256 3.8 27.4 1.0 O23 B:IHP256 4.0 29.0 1.0 O A:HOH291 4.1 47.0 1.0 O B:HOH349 4.2 40.8 1.0 O12 B:IHP256 4.4 27.9 1.0 O12 A:IHP257 4.4 28.6 1.0 O22 B:IHP256 4.5 28.9 1.0 NZ A:LYS221 4.5 19.5 1.0 O22 A:IHP257 4.5 27.8 1.0 NZ B:LYS221 4.5 19.4 1.0 O33 A:IHP257 4.7 28.6 1.0 C2 A:IHP257 4.7 29.1 1.0 C2 B:IHP256 4.7 28.4 1.0 O B:HOH266 4.7 44.1 1.0 O43 B:IHP256 4.8 29.7 1.0 C3 A:IHP257 4.9 26.8 1.0 O B:HOH353 4.9 42.0 1.0 C3 B:IHP256 4.9 28.2 1.0 O B:HOH272 4.9 37.7 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