Iodine in PDB 3oib: Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak

The structure of Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak, PDB code: 3oib was solved by Seattle Structural 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)	40.12 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.590, 64.490, 83.600, 90.00, 111.99, 90.00
R / Rfree (%)	15.2 / 20

The structure of Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak (pdb code 3oib). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 30 binding sites of Iodine where determined in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak, PDB code: 3oib:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:18.6 occ:1.00 O A:HOH802 3.3 22.4 1.0 NZ A:LYS65 3.4 14.8 1.0 N A:LEU62 3.7 8.4 1.0 CA A:LEU62 4.0 7.7 1.0 CG A:GLU61 4.0 18.5 1.0 CG A:PRO59 4.1 10.1 1.0 CE A:LYS65 4.1 12.7 1.0 C A:GLU61 4.2 9.8 1.0 CB A:PRO59 4.2 11.5 1.0 CB A:LEU62 4.2 7.1 1.0 CB A:GLU61 4.2 12.9 1.0 CD A:LYS65 4.3 9.9 1.0 CZ2 A:TRP52 4.4 9.7 1.0 CD1 A:LEU62 4.4 6.3 1.0 O A:GLU61 4.7 10.1 1.0 CA A:GLU61 4.7 11.6 1.0 CD A:PRO59 4.8 9.9 1.0 CH2 A:TRP52 4.8 9.0 1.0 O A:HOH925 4.9 33.0 1.0 CG A:LEU62 4.9 6.6 1.0 O A:HOH864 4.9 25.8 1.0

Iodine binding site 2 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:23.1 occ:1.00 CD A:ARG311 3.8 10.5 1.0 O A:HOH613 3.9 31.2 1.0 NE A:ARG311 4.1 12.2 1.0 CB A:ARG311 4.1 8.8 1.0 O A:ALA307 4.2 12.1 1.0 C A:ALA307 4.4 11.9 1.0 CB A:ALA307 4.5 12.3 1.0 CA A:GLY308 4.5 10.9 1.0 N A:GLY308 4.5 11.7 1.0 CG A:ARG311 4.5 9.2 1.0

Iodine binding site 3 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:22.9 occ:1.00 O A:HOH687 3.1 31.6 1.0 O A:HOH719 3.3 22.6 1.0 NH2 A:ARG373 3.4 15.2 1.0 ND1 A:HIS50 3.6 21.4 0.5 CE1 A:HIS50 3.6 21.1 0.5 CG A:HIS50 3.7 17.1 0.5 NE2 A:HIS50 3.8 19.1 0.5 CD2 A:HIS50 3.9 18.2 0.5 N A:HIS50 3.9 13.2 1.0 CA A:HIS50 3.9 13.6 0.5 CA A:HIS50 3.9 13.7 0.5 CD A:ARG373 4.0 11.8 1.0 C A:ALA49 4.1 12.2 1.0 CG A:GLU53 4.1 7.6 1.0 CB A:ALA49 4.2 12.1 1.0 O A:ALA49 4.2 10.1 1.0 CB A:HIS50 4.4 14.4 0.5 CB A:HIS50 4.4 14.5 0.5 CZ A:ARG373 4.4 12.0 1.0 CG A:PRO103 4.6 8.0 1.0 NE A:ARG373 4.6 11.6 1.0 O A:HOH694 4.6 41.5 1.0 CB A:GLU53 4.7 8.1 1.0 CA A:ALA49 4.8 12.1 1.0 CD2 A:HIS50 4.9 18.0 0.5 CD A:GLU53 4.9 8.6 1.0 O A:HOH650 5.0 8.7 1.0 CG A:HIS50 5.0 16.3 0.5 O A:HOH857 5.0 24.5 1.0

Iodine binding site 4 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:40.9 occ:0.75 OD1 A:ASP79 2.6 26.8 0.5 O A:HOH934 3.1 30.8 1.0 CG A:ASP79 3.3 24.6 0.5 OD2 A:ASP79 3.7 27.0 0.5 CB A:ALA80 3.8 18.8 1.0 N A:ALA80 3.9 20.2 1.0 CD1 A:ILE129 3.9 15.9 1.0 CB A:ASP79 3.9 22.6 0.5 C A:ASP79 4.0 21.5 1.0 CA A:ALA80 4.1 18.7 1.0 CB A:ASP79 4.3 23.2 0.5 O A:ASP79 4.3 22.4 1.0 NE2 A:GLN126 4.5 18.9 0.5 CG A:PRO77 4.5 17.0 1.0 CA A:ASP79 4.6 21.8 0.5 CA A:ASP79 4.6 22.1 0.5 CB A:PRO77 4.7 17.8 1.0 CG2 A:ILE121 4.9 11.1 1.0 CG2 A:ILE129 4.9 13.6 1.0 NE2 A:GLN126 5.0 22.4 0.5 OE1 A:GLN126 5.0 20.9 0.5

Iodine binding site 5 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:37.1 occ:0.59 O B:HOH817 2.9 31.2 1.0 OE1 A:GLU368 3.3 37.7 1.0 NH1 B:ARG218 3.4 37.3 1.0 O B:ASP221 3.7 16.6 1.0 N B:ASP221 3.7 18.3 1.0 CB A:GLU368 3.9 22.2 1.0 CB A:MET366 4.0 13.7 1.0 N A:GLU368 4.0 19.2 1.0 CD A:GLU368 4.0 32.3 1.0 CG A:GLU368 4.0 25.8 1.0 CB B:ASP221 4.2 20.4 1.0 CD2 B:LEU220 4.2 18.5 1.0 CZ B:ARG218 4.2 35.7 1.0 N A:ALA367 4.3 16.2 1.0 CA B:ASP221 4.4 18.0 1.0 SD A:MET366 4.4 19.9 0.9 C B:ASP221 4.5 16.2 1.0 CA B:LEU220 4.5 17.8 1.0 CG A:MET366 4.6 17.1 1.0 CA A:GLU368 4.6 20.3 1.0 C B:LEU220 4.6 17.3 1.0 NH2 B:ARG218 4.6 36.3 1.0 CA A:MET366 4.7 13.7 1.0 CB B:LEU220 4.7 17.2 1.0 C A:MET366 4.7 14.4 1.0 C A:ALA367 4.9 18.3 1.0 CA A:ALA367 4.9 17.1 1.0 CB A:ALA367 5.0 16.3 1.0

Iodine binding site 6 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:30.9 occ:0.58 O A:HOH951 3.1 39.9 1.0 NZ A:LYS141 3.4 16.6 1.0 O A:HOH908 3.7 32.4 1.0 O A:ASP186 3.8 6.9 1.0 CE A:LYS141 3.9 17.0 1.0 CE1 A:TYR132 3.9 8.9 1.0 OD1 A:ASP208 4.1 15.5 1.0 CB A:ASP186 4.1 8.8 1.0 CD A:LYS141 4.1 13.7 1.0 CG A:ASP208 4.2 12.8 1.0 C A:ASP186 4.3 7.8 1.0 CD1 A:TYR132 4.4 8.0 1.0 CB A:TYR187 4.5 7.7 1.0 OD2 A:ASP208 4.6 18.5 1.0 CD1 A:TYR187 4.6 8.4 1.0 CB A:ASP208 4.7 9.8 1.0 CA A:ASP186 4.8 8.2 1.0 N A:TYR187 4.9 7.3 1.0 CZ A:TYR132 5.0 9.6 1.0

Iodine binding site 7 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:40.2 occ:0.57 O A:HOH814 3.2 16.4 1.0 CG2 A:VAL324 4.3 12.3 1.0 CG2 A:VAL265 4.4 7.9 1.0 O A:HOH944 4.4 34.0 1.0 CA A:ALA262 4.6 17.5 1.0 CB A:GLN327 4.6 21.7 1.0 CG1 A:VAL261 4.7 22.7 1.0 CB A:VAL265 4.7 9.0 1.0 CG1 A:VAL265 4.8 7.7 1.0 CG1 A:VAL324 4.8 11.4 1.0 CA A:GLY87 4.8 12.3 1.0 CA A:VAL324 4.8 12.7 1.0 CB A:VAL324 4.9 12.1 1.0 N A:ALA262 4.9 18.5 1.0 CB A:ALA262 4.9 18.4 1.0

Iodine binding site 8 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:44.3 occ:0.54 O A:HOH673 2.7 26.5 1.0 ND2 A:ASN288 3.7 27.5 1.0 CD A:ARG287 3.9 23.9 1.0 CG A:GLU284 4.5 22.1 1.0 NH1 A:ARG287 4.5 28.5 1.0 CB A:ARG287 4.5 21.7 1.0 CA A:GLU284 4.6 16.2 1.0 CG A:ASN288 4.7 29.8 1.0 CB A:GLU284 4.8 16.8 1.0 CG A:ARG287 4.8 23.0 1.0 O A:GLU284 4.9 16.3 1.0 O A:HOH788 4.9 47.7 1.0 OD1 A:ASN288 4.9 36.5 1.0

Iodine binding site 9 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:39.0 occ:0.46 I A:IOD514 2.8 33.0 0.4 N A:ALA175 3.6 11.6 1.0 CB A:ARG160 3.6 22.1 1.0 OE1 A:GLU149 3.8 10.6 1.0 OG1 A:THR161 3.9 13.8 1.0 O A:ALA175 4.0 11.3 1.0 N A:THR161 4.0 16.9 1.0 CA A:GLY174 4.0 12.2 1.0 CD A:GLU149 4.0 12.9 1.0 C A:ARG160 4.2 19.3 1.0 C A:GLY174 4.2 11.7 1.0 CB A:ALA175 4.3 10.9 1.0 CA A:ALA175 4.3 10.7 1.0 OE2 A:GLU149 4.4 8.7 1.0 NE A:ARG160 4.4 35.5 1.0 CD A:ARG160 4.4 32.4 1.0 CA A:THR161 4.4 15.5 1.0 CA A:ARG160 4.5 20.9 1.0 C A:ALA175 4.6 11.0 1.0 CB A:GLU149 4.7 15.4 1.0 CG A:GLU149 4.7 14.0 1.0 CG A:ARG160 4.7 26.6 1.0 O A:ARG160 4.8 17.5 1.0 O A:HOH737 4.8 38.2 1.0 CB A:THR161 4.8 14.7 1.0 N A:ARG160 4.9 21.2 1.0

Iodine binding site 10 out of 30 in the Crystal Structure of A Putative Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak


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 Acyl-Coa Dehydrogenase From Mycobacterium Smegmatis, Iodide Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:41.7 occ:0.43 O A:HOH759 3.6 13.2 1.0 CG A:GLU284 3.9 22.1 1.0 CA A:TRP285 3.9 15.0 1.0 N A:TRP285 4.2 14.7 1.0 CE3 A:TRP285 4.2 15.1 1.0 O A:GLU284 4.3 16.3 1.0 CD A:GLU284 4.3 27.2 1.0 C A:GLU284 4.3 15.9 1.0 OE1 A:GLU284 4.4 28.5 1.0 CB A:TRP285 4.4 14.5 1.0 CB A:ASN288 4.6 28.7 1.0 ND2 A:ASN288 4.7 27.5 1.0 CB A:GLU284 4.8 16.8 1.0 CD2 A:TRP285 5.0 14.3 1.0

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J Struct Funct Genomics 2011.
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7