Zinc in PDB 2ygt: Clostridium Perfringens Delta-Toxin

The structure of Clostridium Perfringens Delta-Toxin, PDB code: 2ygt was solved by J.Huyet, C.E.Naylor, M.Gibert, M.R.Popoff, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.48 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.932, 49.664, 58.477, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.8

The binding sites of Zinc atom in the Clostridium Perfringens Delta-Toxin (pdb code 2ygt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Clostridium Perfringens Delta-Toxin, PDB code: 2ygt:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Clostridium Perfringens Delta-Toxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Clostridium Perfringens Delta-Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1291 b:38.6 occ:1.00 OD1 A:ASP52 2.2 24.3 1.0 NE2 A:HIS284 2.3 27.2 1.0 OD2 A:ASP52 2.8 39.2 1.0 CG A:ASP52 2.8 27.4 1.0 CD2 A:HIS284 3.0 18.7 1.0 O A:HOH2220 3.0 36.7 1.0 O A:TRP281 3.3 21.4 1.0 O A:HOH2211 3.4 43.8 1.0 CE1 A:HIS284 3.4 24.8 1.0 O A:HOH2034 3.7 47.2 1.0 CG A:HIS284 4.2 28.6 1.0 CB A:ASP52 4.3 23.0 1.0 O A:HOH2033 4.3 15.8 1.0 ND1 A:HIS284 4.4 23.9 1.0 C A:TRP281 4.5 40.0 1.0 O A:HOH2083 4.7 55.0 1.0 CE2 A:TYR30 4.8 34.7 1.0 O A:GLU282 4.9 31.1 1.0 CD2 A:TYR30 4.9 25.5 1.0 CA A:ASP52 4.9 22.7 1.0 SD A:MET59 4.9 30.2 1.0

Zinc binding site 2 out of 3 in the Clostridium Perfringens Delta-Toxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Clostridium Perfringens Delta-Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1292 b:23.8 occ:1.00 OD2 A:ASP164 2.2 27.2 1.0 O A:HOH2134 2.3 22.9 1.0 O A:HOH2080 2.4 13.7 1.0 O A:HOH2082 2.5 23.1 1.0 CG A:ASP164 3.1 26.7 1.0 OD1 A:ASP164 3.4 26.4 1.0 OD1 A:ASP108 3.8 20.5 1.0 O A:HOH2133 4.1 19.6 1.0 O A:HOH2085 4.1 25.2 1.0 OE1 A:GLN161 4.2 18.2 1.0 CB A:ASP164 4.5 23.8 1.0 O A:SER109 4.5 21.0 1.0 CG A:LYS112 4.5 30.9 1.0 OG A:SER109 4.7 17.1 1.0 CD A:LYS112 4.7 33.9 1.0 N A:SER109 4.8 20.1 1.0 CG A:ASP108 4.8 22.7 1.0 CE A:LYS112 4.9 29.2 1.0

Zinc binding site 3 out of 3 in the Clostridium Perfringens Delta-Toxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Clostridium Perfringens Delta-Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1297 b:22.9 occ:1.00 N3 A:IMD1293 1.9 54.9 0.5 O A:HOH2219 2.3 11.3 1.0 O A:HOH3001 2.4 14.1 1.0 C4 A:IMD1293 2.6 49.7 0.5 C2 A:IMD1293 3.1 52.6 0.5 C5 A:IMD1293 3.8 49.7 0.5 O A:GLN288 3.9 22.4 1.0 N1 A:IMD1293 4.0 54.9 0.5 CD A:ARG287 4.3 24.6 1.0 NH1 A:ARG287 4.3 20.9 1.0 CB A:ARG287 4.5 20.8 1.0 CG A:ARG287 4.8 20.5 1.0

J.Huyet, C.E.Naylor, C.G.Savva, M.Gibert, M.R.Popoff, A.K.Basak. Structural Insights Into Clostridium Perfringens Delta Toxin Pore Formation. Plos One V. 8 66673 2013.
ISSN: ESSN 1932-6203
PubMed: 23805259
DOI: 10.1371/JOURNAL.PONE.0066673