Iodine in PDB 5suo: Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae

The structure of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae, PDB code: 5suo was solved by M.Robb, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.79 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.910, 40.200, 93.890, 90.00, 98.77, 90.00
R / Rfree (%)	21.1 / 26.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae (pdb code 5suo). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 21 binding sites of Iodine where determined in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae, PDB code: 5suo:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:17.4 occ:1.00 O A:HOH727 3.4 13.2 1.0 N A:GLY291 3.7 12.7 1.0 CA A:PRO287 3.9 11.4 1.0 CG A:GLU411 4.1 19.1 1.0 O A:GLY286 4.1 10.5 1.0 CA A:GLY291 4.1 12.9 1.0 CA A:SER408 4.1 18.6 1.0 CZ A:PHE311 4.2 13.2 1.0 N A:PRO287 4.3 11.0 1.0 C A:GLY286 4.3 10.9 1.0 CE2 A:PHE311 4.4 13.4 1.0 CB A:GLU411 4.5 18.7 1.0 N A:SER408 4.5 18.4 1.0 CB A:SER408 4.5 18.4 1.0 C A:TYR290 4.6 12.5 1.0 O A:PRO287 4.7 11.5 1.0 CB A:PRO287 4.7 11.2 1.0 O A:ASN407 4.8 17.2 1.0 C A:PRO287 4.8 11.5 1.0 CA A:TYR290 4.8 12.4 1.0 C A:ASN407 4.8 18.9 1.0 CG1 A:VAL285 4.8 10.3 1.0 CG A:PRO287 4.9 11.4 1.0 N A:TYR290 5.0 12.2 1.0

Iodine binding site 2 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:16.5 occ:0.77 N A:GLY205 3.6 12.2 1.0 O A:HOH678 3.8 11.5 1.0 CB A:PHE208 4.0 11.1 1.0 CG1 A:VAL207 4.1 14.0 1.0 CA A:ILE204 4.1 11.1 1.0 CD1 A:PHE208 4.2 11.0 1.0 CB A:ILE204 4.2 11.1 1.0 CA A:PHE208 4.3 11.4 1.0 N A:PHE208 4.3 11.8 1.0 C A:ILE204 4.3 11.6 1.0 CA A:GLY205 4.5 12.5 1.0 CG2 A:ILE204 4.5 10.5 1.0 O A:GLY205 4.5 12.0 1.0 CG A:PHE208 4.6 11.1 1.0 O A:HOH747 4.7 22.8 1.0 C A:GLY205 4.8 12.3 1.0 O A:ALA203 4.9 11.1 1.0 C A:VAL207 4.9 12.6 1.0

Iodine binding site 3 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:29.4 occ:1.00 O A:HOH744 3.2 12.8 1.0 O A:HOH710 3.6 22.3 1.0 CB A:PRO356 3.8 12.8 1.0 O A:GLU57 3.8 15.0 1.0 CB A:ASN61 3.9 18.5 1.0 CA A:PRO356 4.0 12.6 1.0 C A:GLU57 4.0 16.0 1.0 CD2 A:LEU58 4.1 14.1 1.0 N A:LEU58 4.2 14.9 1.0 CA A:LEU58 4.2 14.2 1.0 CB A:GLU57 4.3 19.1 1.0 N A:PRO356 4.3 12.3 1.0 CG A:ASN61 4.4 20.3 1.0 CD A:PRO356 4.6 12.4 1.0 CG A:PRO356 4.6 13.0 1.0 OD1 A:ASN61 4.7 21.0 1.0 O A:HOH718 4.7 16.0 1.0 CA A:GLU57 4.8 17.5 1.0 O A:HOH758 4.9 9.7 1.0 CG A:LEU58 5.0 14.5 1.0

Iodine binding site 4 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:23.9 occ:0.69 NZ A:LYS367 3.1 22.8 1.0 CD1 A:ILE364 3.8 22.0 1.0 CZ A:ARG370 4.0 18.1 1.0 CB A:GLU398 4.0 19.4 1.0 CB A:ARG370 4.0 16.2 1.0 NE A:ARG370 4.1 18.8 1.0 CG A:ARG370 4.1 17.1 1.0 CE A:LYS367 4.1 23.6 1.0 CA A:GLU398 4.2 18.0 1.0 CG A:LYS367 4.2 24.7 1.0 NH2 A:ARG370 4.3 19.9 1.0 NH1 A:ARG370 4.4 16.8 1.0 CB A:LYS367 4.4 25.0 1.0 CD A:ARG370 4.4 17.5 1.0 O A:GLU398 4.5 16.4 1.0 CG2 A:ILE364 4.5 22.9 1.0 CD A:LYS367 4.7 23.3 1.0 CG1 A:ILE364 4.8 21.6 1.0 C A:GLU398 4.9 17.2 1.0 CB A:ILE364 4.9 22.1 1.0 O A:HOH601 5.0 8.9 1.0

Iodine binding site 5 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:29.7 occ:0.81 O A:HOH765 3.5 14.1 1.0 O A:HOH672 3.5 18.0 1.0 NE A:ARG297 4.0 25.7 1.0 N A:LEU294 4.1 14.1 1.0 CB A:SER293 4.1 15.1 1.0 CG2 A:VAL400 4.1 14.1 1.0 CA A:LEU294 4.2 14.6 1.0 C A:SER293 4.2 14.5 1.0 CB A:ASN397 4.4 17.9 1.0 CD A:ARG297 4.4 24.1 1.0 O A:SER293 4.4 15.1 1.0 CB A:LEU294 4.7 14.6 1.0 O A:ASP289 4.8 12.5 1.0 CA A:SER293 4.8 14.5 1.0 CD2 A:TYR290 4.9 14.8 1.0 CD1 A:LEU294 4.9 15.2 1.0 ND2 A:ASN397 4.9 19.7 1.0 CG A:ASN397 5.0 19.0 1.0

Iodine binding site 6 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:29.6 occ:0.74 ND2 A:ASN310 3.4 13.5 1.0 CB A:LEU228 4.0 10.6 1.0 CD1 A:ILE312 4.0 13.3 1.0 CG A:ASN213 4.0 10.7 1.0 CB A:ASN213 4.0 10.5 1.0 CB A:ASN310 4.2 12.6 1.0 OD1 A:ASN213 4.2 10.2 1.0 CG A:ASN310 4.3 13.4 1.0 CD1 A:LEU228 4.3 10.8 1.0 ND2 A:ASN213 4.4 10.7 1.0 CG1 A:ILE312 4.5 12.3 1.0 O A:LEU228 4.7 10.7 1.0 CG A:GLU229 4.7 14.8 1.0 C A:LEU228 4.8 11.1 1.0 CG A:LEU228 4.8 10.8 1.0

Iodine binding site 7 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:24.5 occ:0.63 N A:ARG243 3.6 11.0 1.0 CD A:PRO242 3.7 11.4 1.0 CB A:PRO242 3.7 11.2 1.0 NH1 A:ARG243 3.8 10.0 1.0 CG A:PRO242 3.9 11.4 1.0 CD A:ARG243 4.0 10.6 1.0 CG A:ARG243 4.0 10.7 1.0 CB A:ARG243 4.1 10.8 1.0 N A:PRO242 4.1 11.5 1.0 CG1 A:VAL241 4.2 10.5 1.0 CA A:PRO242 4.3 11.3 1.0 C A:PRO242 4.4 11.2 1.0 CA A:ARG243 4.4 11.1 1.0 CZ A:ARG243 4.8 10.3 1.0 O A:HOH795 4.8 8.5 1.0 NE A:ARG243 4.9 10.1 1.0 C A:VAL241 4.9 11.4 1.0

Iodine binding site 8 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:37.3 occ:0.66 OG1 A:THR440 3.0 30.6 1.0 O A:HOH700 3.3 25.6 1.0 O A:ALA436 3.6 24.7 1.0 CB A:THR440 3.8 30.1 1.0 C A:ALA436 3.9 25.0 1.0 N A:ILE437 4.2 25.8 1.0 CA A:ILE437 4.2 26.0 1.0 CB A:GLU469 4.3 32.4 1.0 CB A:ALA436 4.4 23.9 1.0 CG2 A:THR440 4.5 30.1 1.0 CD2 A:LEU466 4.5 25.5 1.0 CB A:ALA471 4.6 23.2 1.0 CA A:ALA436 4.8 24.8 1.0 O A:LYS465 4.8 31.4 1.0 CA A:LEU466 4.8 28.7 1.0 CG1 A:ILE437 4.8 25.9 1.0 O A:LEU466 4.9 29.7 1.0

Iodine binding site 9 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:38.8 occ:0.73 N A:ASP198 3.7 22.8 1.0 CA A:ALA196 3.8 21.7 1.0 C A:ALA196 3.8 22.8 1.0 CB A:ASP198 3.8 26.1 1.0 CD A:PRO197 3.9 24.0 1.0 CB A:ALA196 3.9 22.6 1.0 N A:PRO197 4.0 23.7 1.0 OD2 A:ASP198 4.1 28.8 1.0 CA A:ASP198 4.2 22.7 1.0 O A:ALA196 4.2 22.3 1.0 CG A:ASP198 4.3 28.6 1.0 N A:VAL199 4.5 19.0 1.0 CG2 A:VAL199 4.6 17.9 1.0 C A:PRO197 4.7 22.6 1.0 C A:ASP198 4.8 20.9 1.0 CA A:PRO197 4.9 23.3 1.0

Iodine binding site 10 out of 21 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:30.2 occ:0.61 O A:HOH704 3.7 27.1 1.0 CD1 A:ILE396 3.9 15.8 1.0 ND2 A:ASN369 4.0 26.6 1.0 O A:HOH614 4.2 15.5 1.0 CB A:ASN369 4.3 23.7 1.0 CD1 A:ILE405 4.5 16.1 1.0 O A:GLU368 4.6 23.5 1.0 NE A:ARG370 4.7 18.8 1.0 CG A:ASN369 4.7 25.7 1.0 CD A:ARG370 4.7 17.5 1.0 CG2 A:ILE405 4.8 17.7 1.0

M.Robb, J.K.Hobbs, S.A.Woodiga, S.Shapiro-Ward, M.D.Suits, N.Mcgregor, H.Brumer, H.Yesilkaya, S.J.King, A.B.Boraston. Molecular Characterization of N-Glycan Degradation and Transport in Streptococcus Pneumoniae and Its Contribution to Virulence. Plos Pathog. V. 13 06090 2017.
ISSN: ESSN 1553-7374
PubMed: 28056108
DOI: 10.1371/JOURNAL.PPAT.1006090