Iodine in PDB 5jyd: Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia

The structure of Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia, PDB code: 5jyd was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.800, 107.820, 117.690, 90.00, 97.63, 90.00
R / Rfree (%)	14.1 / 17.4

The structure of Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia (pdb code 5jyd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 54 binding sites of Iodine where determined in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia, PDB code: 5jyd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I903 b:25.2 occ:0.89 CG2 A:VAL207 3.4 9.3 0.6 NE2 A:GLN208 3.9 15.2 1.0 NH1 A:ARG211 4.0 42.6 1.0 N A:PRO251 4.1 12.2 1.0 O A:HOH1072 4.1 43.3 1.0 O A:HOH1066 4.1 31.9 1.0 C A:GLY250 4.2 11.2 1.0 CD A:PRO251 4.3 16.2 1.0 CG A:GLN208 4.3 10.9 1.0 CA A:PRO251 4.4 9.9 1.0 O A:HOH1216 4.5 41.6 1.0 CB A:PRO251 4.5 11.1 1.0 CA A:GLY250 4.5 9.2 1.0 CG1 A:VAL207 4.6 10.3 0.4 CB A:VAL207 4.6 9.5 0.4 CD A:ARG211 4.6 25.6 1.0 CD A:GLN208 4.6 14.6 1.0 O A:GLY250 4.7 12.6 1.0 C4N A:NAD901 4.7 26.1 1.0 OG A:SER206 4.8 9.9 1.0 OH A:TYR270 4.8 21.7 1.0 CB A:VAL207 4.9 9.8 0.6 CG A:PRO251 4.9 14.0 1.0

Iodine binding site 2 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I904 b:20.7 occ:0.66 O A:HOH1182 3.7 27.0 1.0 NH1 A:ARG211 3.9 42.6 1.0 CA A:ALA271 4.1 16.0 1.0 NH2 A:ARG211 4.2 49.9 1.0 CB A:SER274 4.2 21.8 1.0 O A:HOH1154 4.3 24.2 1.0 CG A:PRO251 4.4 14.0 1.0 CD2 A:LEU311 4.4 15.6 1.0 CZ A:ARG211 4.5 45.9 1.0 CB A:ALA271 4.5 15.4 1.0 N A:SER274 4.6 19.7 1.0 CD1 A:LEU311 4.7 16.7 1.0 CA A:SER274 4.7 17.7 1.0 C A:ALA271 4.9 18.3 1.0 N A:ALA271 4.9 18.9 1.0

Iodine binding site 3 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:13.7 occ:0.45 I C:IOD905 2.8 12.4 0.5 O A:HOH1205 3.7 29.9 1.0 O C:HOH1041 3.8 13.0 1.0 O A:ALA224 4.1 7.8 1.0 CB A:ALA224 4.1 7.6 1.0 CD1 A:ILE227 4.1 9.5 1.0 CA A:ALA224 4.2 6.8 1.0 CG2 A:ILE227 4.2 10.0 1.0 CB A:ILE227 4.2 8.0 1.0 CG1 A:VAL210 4.3 20.4 1.0 CB C:ALA224 4.5 11.1 1.0 C A:ALA224 4.6 7.4 1.0 CB A:ALA209 4.6 11.5 1.0 NH1 A:ARG231 4.7 14.7 1.0 CG1 A:ILE227 4.8 10.5 1.0 CG1 C:VAL210 4.9 19.4 1.0 O A:ALA209 4.9 12.7 1.0 CZ A:PHE314 5.0 10.9 1.0

Iodine binding site 4 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I906 b:20.1 occ:1.00 O A:HOH1280 3.5 25.3 1.0 O G:HOH1093 3.5 24.5 1.0 NH1 G:ARG141 3.7 22.9 1.0 N A:VAL103 3.8 16.4 1.0 CD A:PRO102 3.9 13.9 1.0 CD G:ARG137 4.0 20.8 1.0 CD G:ARG141 4.0 19.1 1.0 CB A:VAL103 4.0 18.4 1.0 N A:PRO102 4.1 13.9 1.0 CB G:ARG137 4.2 16.6 1.0 CG A:PRO102 4.2 15.4 1.0 CB A:PRO102 4.2 17.1 1.0 CG1 A:VAL103 4.2 17.2 1.0 CB A:LEU101 4.4 14.2 1.0 CZ G:ARG141 4.4 21.8 1.0 NE G:ARG141 4.5 24.3 1.0 CA A:VAL103 4.6 17.7 1.0 CG G:ARG137 4.6 21.6 1.0 CD2 A:LEU101 4.6 16.0 1.0 CA A:PRO102 4.6 14.9 1.0 C A:PRO102 4.7 17.9 1.0 C A:LEU101 4.8 14.9 1.0 O A:HOH1013 4.9 26.2 1.0

Iodine binding site 5 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I907 b:29.9 occ:0.42 O A:HOH1146 3.5 18.1 1.0 O A:HOH1127 3.6 30.3 1.0 O C:HOH1280 4.0 31.1 1.0 CG2 C:THR170 4.0 17.4 1.0 CZ2 A:TRP186 4.1 12.8 1.0 OD2 C:ASP174 4.2 14.0 1.0 CE2 A:TYR182 4.2 13.2 1.0 CE A:LYS178 4.4 19.6 1.0 CH2 A:TRP186 4.4 11.7 1.0 O A:HOH1273 4.4 38.7 1.0 CG C:ASP174 4.5 17.5 1.0 CD2 A:TYR182 4.5 10.4 1.0 NZ A:LYS178 4.7 22.8 1.0 CB C:ASP174 4.8 13.5 1.0

Iodine binding site 6 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I908 b:22.4 occ:0.41 O A:HOH1246 3.2 34.7 1.0 O A:HOH1149 3.4 20.4 1.0 O A:HOH1235 3.5 36.2 1.0 NH2 A:ARG83 3.7 15.9 1.0 CG A:GLU58 4.3 16.9 1.0 CD1 A:LEU114 4.4 14.1 1.0 CB A:GLU110 4.4 13.6 1.0 CD A:GLU110 4.4 23.0 1.0 OE1 A:GLU110 4.5 20.5 1.0 CG A:GLU110 4.5 16.8 1.0 OE2 A:GLU110 4.8 26.0 1.0 O A:HOH1278 4.8 27.7 1.0 CG A:LEU114 4.8 14.5 1.0 CD2 A:LEU114 4.9 21.9 1.0 OE2 A:GLU58 4.9 15.8 1.0 CZ A:ARG83 4.9 13.5 1.0 NH2 A:ARG53 5.0 30.8 0.5

Iodine binding site 7 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:I909 b:23.6 occ:0.40 O D:HOH1300 3.6 32.9 1.0 O A:HOH1106 3.6 41.3 1.0 O B:HOH1254 3.8 24.5 1.0 CE B:LYS235 4.0 10.7 1.0 CD2 A:LEU311 4.1 15.6 1.0 CD B:LYS235 4.1 10.4 1.0 CG A:PRO275 4.1 25.9 1.0 CD A:PRO275 4.1 22.3 1.0 O A:GLY310 4.7 12.7 1.0 CG B:LYS235 4.7 9.7 1.0 O A:HOH1028 4.7 26.1 1.0 CA A:LEU311 4.8 12.7 1.0 O A:GLY273 5.0 23.7 1.0 O D:HOH1137 5.0 18.9 1.0

Iodine binding site 8 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ B:I903 b:15.4 occ:0.41 I D:IOD903 2.8 13.6 0.6 O D:HOH1052 3.7 12.5 1.0 CB B:ALA224 4.0 8.5 1.0 O B:ALA224 4.1 8.7 1.0 CD1 B:ILE227 4.2 10.7 1.0 CA B:ALA224 4.2 9.6 1.0 CB B:ILE227 4.2 10.5 1.0 CG2 B:ILE227 4.2 9.8 1.0 O D:HOH1277 4.4 35.7 1.0 CG1 B:VAL210 4.4 22.3 1.0 C B:ALA224 4.6 10.8 1.0 CB D:ALA224 4.6 7.8 1.0 CB B:ALA209 4.6 11.1 1.0 NH1 B:ARG231 4.6 13.3 1.0 CG1 B:ILE227 4.8 12.3 1.0 CG1 D:VAL210 4.9 19.6 1.0 O B:ALA209 4.9 13.1 1.0

Iodine binding site 9 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ B:I904 b:33.3 occ:0.55 O B:HOH1194 3.1 41.3 1.0 O B:HOH1197 3.5 36.7 1.0 O B:HOH1142 3.6 22.5 1.0 NH2 B:ARG83 3.7 26.1 1.0 CD B:GLU110 4.2 25.5 1.0 OE2 B:GLU110 4.2 26.1 1.0 CG B:GLU58 4.2 20.2 1.0 CB B:GLU110 4.3 23.7 1.0 CG B:GLU110 4.5 24.7 1.0 OE1 B:GLU110 4.5 28.0 1.0 CD1 B:LEU114 4.6 23.6 1.0 O B:HOH1248 4.6 44.8 1.0 OE2 B:GLU58 4.7 22.9 1.0 CD B:GLU58 4.9 24.5 1.0 CZ B:ARG83 5.0 23.7 1.0 O B:HOH1253 5.0 29.6 1.0 NH2 B:ARG53 5.0 43.0 1.0

Iodine binding site 10 out of 54 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ B:I905 b:33.9 occ:0.42 O B:HOH1018 3.6 22.2 1.0 O D:HOH1265 3.9 33.2 1.0 CG2 D:THR170 4.0 19.8 1.0 CZ2 B:TRP186 4.1 19.4 1.0 OD2 D:ASP174 4.2 18.4 1.0 CE1 B:TYR182 4.2 16.2 1.0 CH2 B:TRP186 4.4 20.6 1.0 CG D:ASP174 4.4 20.6 1.0 CE B:LYS178 4.4 25.1 1.0 CD1 B:TYR182 4.5 15.8 1.0 CB D:ASP174 4.7 16.9 1.0 NZ B:LYS178 4.8 24.8 1.0 OD1 D:ASP174 4.9 24.7 1.0

Ssgcid, J.Y.Yano, D.Lorimer, T.E.Edwards. Tbd To Be Published.