Iodine in PDB 4p0d: The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions

The structure of The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions, PDB code: 4p0d was solved by P.G.Young, N.J.Moreland, J.M.Loh, A.Bell, P.Atatoa-Carr, T.Proft, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	104.240, 104.240, 84.220, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 25

The structure of The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iodine atom in the The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions (pdb code 4p0d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions, PDB code: 4p0d:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions within 5.0Å range: probe atom residue distance (Å) B Occ A:I601 b:13.6 occ:0.80 OG1 A:THR215 3.6 17.8 1.0 N A:THR215 3.7 18.2 1.0 O A:HOH859 3.7 15.9 1.0 CG A:PRO319 3.8 15.4 1.0 CB A:PRO319 3.8 15.8 1.0 OD1 A:ASN141 3.9 19.0 1.0 CD A:PRO142 4.0 18.8 1.0 CG2 A:THR215 4.0 17.9 1.0 O A:TYR140 4.0 16.4 1.0 CA A:ASN141 4.2 18.3 1.0 CB A:THR215 4.2 18.6 1.0 CD A:PRO319 4.2 15.6 1.0 CA A:TYR214 4.3 16.8 1.0 CB A:ALA218 4.4 18.7 1.0 C A:TYR214 4.5 17.5 1.0 CA A:THR215 4.5 19.1 1.0 CG A:ASN141 4.7 19.3 1.0 CG2 A:THR320 4.7 18.8 1.0 CG A:PRO142 4.7 19.0 1.0 C A:TYR140 4.8 16.5 1.0 N A:ASN141 4.8 17.1 1.0 CB A:ASN141 4.8 18.8 1.0 O A:SER213 4.8 16.9 1.0 CB A:TYR214 4.9 15.9 1.0 N A:PRO142 4.9 18.5 1.0 CD1 A:TYR214 4.9 14.3 1.0 CA A:PRO319 5.0 15.9 1.0

Iodine binding site 2 out of 3 in the The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions within 5.0Å range: probe atom residue distance (Å) B Occ A:I602 b:34.9 occ:0.60 ND2 A:ASN236 3.4 21.9 1.0 CG2 A:VAL295 3.5 13.4 0.5 O A:HOH779 3.7 19.8 1.0 CB A:ASN236 3.9 18.7 1.0 OH A:TYR464 4.0 21.6 1.0 CG2 A:VAL202 4.0 15.0 1.0 O A:HOH1089 4.1 19.1 1.0 O A:HOH926 4.1 36.0 1.0 CE2 A:TYR464 4.1 19.8 1.0 CG A:ASN236 4.2 20.6 1.0 CB A:LYS293 4.2 15.9 1.0 CG1 A:VAL202 4.3 14.8 1.0 CD A:LYS293 4.5 20.5 1.0 CZ A:TYR464 4.6 20.2 1.0 CB A:VAL295 4.8 13.2 0.5 CB A:VAL202 4.8 14.3 1.0 C A:ALA294 4.9 13.4 1.0 C A:LYS293 4.9 13.7 1.0 CB A:VAL295 4.9 13.3 0.5 N A:VAL295 5.0 13.6 0.5 N A:VAL295 5.0 13.5 0.5

Iodine binding site 3 out of 3 in the The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes Has A Modular Three-Domain Structure Decorated with Variable Loops and Extensions within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:29.5 occ:0.30 CG2 A:THR422 3.7 27.3 1.0 O A:HOH991 3.7 27.1 1.0 ND2 A:ASN424 3.7 22.6 1.0 N A:GLY399 3.9 18.9 1.0 CA A:GLY399 4.0 19.4 1.0 O A:ALA423 4.0 23.1 1.0 C A:GLY399 4.4 19.8 1.0 CB A:ASN424 4.4 25.0 1.0 O A:GLY399 4.4 21.2 1.0 CG A:ASN424 4.6 24.0 1.0 C A:SER398 4.6 19.7 1.0 CB A:SER398 4.8 19.1 1.0 C A:ALA423 4.9 23.1 1.0

P.G.Young, N.J.Moreland, J.M.Loh, A.Bell, P.Atatoa Carr, T.Proft, E.N.Baker. Structural Conservation, Variability, and Immunogenicity of the T6 Backbone Pilin of Serotype M6 Streptococcus Pyogenes. Infect.Immun. V. 82 2949 2014.
ISSN: ESSN 1098-5522
PubMed: 24778112
DOI: 10.1128/IAI.01706-14