Iodine in PDB 3b2h: Iodide Derivative of Human Lfabp at High Resolution

The structure of Iodide Derivative of Human Lfabp at High Resolution, PDB code: 3b2h was solved by A.Sharma, M.Yogavel, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.278, 57.104, 74.723, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Iodide Derivative of Human Lfabp at High Resolution (pdb code 3b2h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Iodide Derivative of Human Lfabp at High Resolution, PDB code: 3b2h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I130 b:23.6 occ:0.35 I A:IOD130 0.0 23.6 0.3 I A:IOD130 1.5 24.6 0.3 N A:MET74 3.4 22.9 1.0 CG A:MET74 3.6 27.1 1.0 CB A:MET74 3.8 24.3 1.0 CE A:MET113 3.9 16.4 0.5 CB A:THR73 3.9 21.5 1.0 CE A:MET113 4.1 18.9 0.5 CA A:THR73 4.2 21.5 1.0 CF A:PLM150 4.2 31.6 0.7 CA A:MET74 4.2 23.7 1.0 CE A:MET74 4.3 32.3 1.0 C A:THR73 4.3 22.1 1.0 SD A:MET113 4.5 18.9 0.5 CG2 A:THR73 4.6 22.0 1.0 CE2 A:PHE18 4.7 24.1 1.0 I A:IOD134 4.8 34.8 0.3 CZ A:PHE95 4.8 21.7 1.0 CE1 A:PHE95 4.8 21.9 1.0 SD A:MET74 4.8 33.1 1.0 OG1 A:THR73 5.0 21.9 1.0

Iodine binding site 2 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I130 b:24.6 occ:0.35 I A:IOD130 0.0 24.6 0.3 I A:IOD130 1.5 23.6 0.3 I A:IOD134 3.5 34.8 0.3 CB A:THR73 3.8 21.5 1.0 N A:MET74 3.9 22.9 1.0 CE A:MET113 4.1 16.4 0.5 CE2 A:PHE18 4.1 24.1 1.0 CE1 A:PHE95 4.3 21.9 1.0 CG2 A:THR73 4.4 22.0 1.0 CD1 A:ILE22 4.4 30.1 1.0 CB A:MET74 4.4 24.3 1.0 CZ A:PHE18 4.5 23.9 1.0 CD1 A:ILE98 4.5 20.0 1.0 CA A:THR73 4.6 21.5 1.0 OG1 A:THR73 4.6 21.9 1.0 CZ A:PHE95 4.6 21.7 1.0 CG A:MET74 4.6 27.1 1.0 CE A:MET113 4.7 18.9 0.5 CG1 A:ILE22 4.8 29.3 1.0 C A:THR73 4.8 22.1 1.0 CA A:MET74 4.8 23.7 1.0 CG2 A:ILE22 4.9 29.0 1.0 SD A:MET113 4.9 18.9 0.5 CB A:ILE22 5.0 29.1 1.0

Iodine binding site 3 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I131 b:46.0 occ:0.50 N A:GLN12 3.7 19.2 1.0 O A:HOH162 3.7 45.0 1.0 O A:HOH288 3.8 23.9 1.0 CA A:SER11 3.9 18.7 1.0 O A:GLN12 4.2 21.0 1.0 CG A:GLN12 4.2 20.5 1.0 C A:SER11 4.3 18.9 1.0 NZ A:LYS36 4.4 21.1 1.0 CB A:SER11 4.5 19.0 1.0 CE A:LYS36 4.5 20.3 1.0 O A:HOH173 4.5 39.1 0.5 CA A:GLN12 4.7 20.1 1.0 O A:GLN10 4.7 18.3 1.0 O A:LYS33 4.8 25.2 1.0 C A:GLN12 4.9 20.7 1.0 CB A:GLN12 5.0 20.1 1.0 N A:SER11 5.0 18.3 1.0

Iodine binding site 4 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I132 b:27.6 occ:0.40 OG1 A:THR51 3.2 21.7 1.0 O A:GLU40 3.6 17.0 1.0 OE2 A:GLU40 3.8 21.7 0.5 N A:THR51 3.9 18.6 1.0 O A:LYS49 3.9 17.1 1.0 CB A:THR51 4.0 19.8 1.0 CA A:PHE50 4.0 18.1 1.0 C A:LYS49 4.0 16.9 1.0 CG2 A:VAL42 4.1 15.9 1.0 C A:PHE50 4.1 18.4 1.0 CD A:GLU40 4.2 20.2 0.5 N A:PHE50 4.2 17.4 1.0 CB A:LYS49 4.2 17.1 1.0 O A:HOH147 4.2 29.6 0.5 CG A:GLU40 4.3 18.4 0.5 C A:GLU40 4.3 16.8 1.0 CB A:GLU40 4.5 17.0 0.5 CB A:GLU40 4.5 17.2 0.5 NE2 A:GLN60 4.5 21.4 0.5 CA A:THR51 4.6 19.5 1.0 N A:VAL42 4.6 15.2 1.0 CB A:VAL42 4.8 15.2 1.0 O A:PHE50 4.8 18.4 1.0 CA A:LYS49 4.8 16.7 1.0 OE1 A:GLU40 4.9 21.1 0.5 N A:ILE41 4.9 16.3 1.0 O A:HOH215 5.0 30.8 0.5 CA A:ILE41 5.0 16.0 1.0 C A:ILE41 5.0 15.4 1.0

Iodine binding site 5 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I133 b:30.5 occ:0.40 O A:HOH350 2.5 23.5 0.5 O A:HOH350 3.4 21.6 0.5 O A:HOH231 3.5 17.2 1.0 O A:ASN97 3.6 20.5 1.0 CB A:ASN97 3.9 20.3 1.0 CA A:ASN97 4.1 20.2 1.0 C A:ASN97 4.2 20.1 1.0 ND2 A:ASN97 4.3 20.6 1.0 O A:HOH349 4.3 32.5 1.0 CG A:ASN97 4.4 20.3 1.0

Iodine binding site 6 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I134 b:34.8 occ:0.30 NZ A:LYS96 2.6 22.5 0.5 CE A:LYS96 3.0 22.2 0.5 CD A:LYS96 3.3 21.7 0.5 I A:IOD130 3.5 24.6 0.3 OG1 A:THR73 3.5 21.9 1.0 CB A:THR73 3.8 21.5 1.0 CG2 A:THR73 4.0 22.0 1.0 CB A:ILE22 4.1 29.1 1.0 CD1 A:ILE98 4.1 20.0 1.0 CG2 A:ILE22 4.2 29.0 1.0 O A:HOH329 4.3 32.9 1.0 OG1 A:THR75 4.4 22.6 1.0 CE1 A:PHE95 4.5 21.9 1.0 CD1 A:ILE22 4.6 30.1 1.0 CG2 A:THR75 4.6 22.4 1.0 CG A:LYS96 4.6 21.2 0.5 CG A:LYS96 4.7 21.2 0.5 I A:IOD130 4.8 23.6 0.3 O A:ILE22 4.8 29.2 1.0 NZ A:LYS96 4.8 22.3 0.5 CG1 A:ILE22 4.8 29.3 1.0 CB A:LYS96 4.9 20.7 0.5 CB A:LYS96 4.9 20.7 0.5 CD1 A:PHE95 4.9 21.5 1.0

Iodine binding site 7 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I135 b:45.0 occ:0.25 I A:IOD135 0.0 45.0 0.2 I A:IOD135 1.7 43.5 0.2 NZ A:LYS121 2.3 20.9 0.5 CG A:LYS121 2.9 17.4 0.5 CE A:LYS121 3.1 20.2 0.5 O A:LYS121 3.3 16.5 1.0 CD A:LYS121 3.3 19.4 0.5 CB A:LYS121 3.6 16.7 0.5 CB A:LYS121 3.6 16.8 0.5 CD A:LYS121 3.7 19.8 0.5 CG A:GLU13 3.7 24.5 1.0 CG A:LYS121 3.7 17.7 0.5 C A:LYS121 3.7 16.4 1.0 CG1 A:ILE123 3.8 16.3 1.0 CD1 A:ILE123 3.8 19.3 1.0 CD A:GLU13 3.8 27.8 1.0 N A:GLU13 3.9 21.0 1.0 OE2 A:GLU13 3.9 29.0 1.0 CA A:GLN12 4.1 20.1 1.0 CB A:GLU13 4.2 22.2 1.0 C A:GLN12 4.2 20.7 1.0 CA A:LYS121 4.3 16.5 0.5 CA A:LYS121 4.3 16.6 0.5 O A:HOH356 4.3 34.2 1.0 O A:SER11 4.4 18.2 1.0 N A:ARG122 4.4 15.9 1.0 OE1 A:GLU13 4.5 28.9 1.0 OG A:SER11 4.5 19.5 1.0 N A:GLN12 4.5 19.2 1.0 O A:HOH160 4.6 39.8 1.0 C A:SER11 4.6 18.9 1.0 N A:ILE123 4.6 15.2 1.0 CA A:GLU13 4.7 21.9 1.0 CA A:ARG122 4.7 15.7 1.0 C A:ARG122 4.8 15.6 1.0 CB A:ILE123 4.8 15.5 1.0

Iodine binding site 8 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I135 b:43.5 occ:0.25 I A:IOD135 0.0 43.5 0.2 I A:IOD135 1.7 45.0 0.2 NZ A:LYS121 3.1 20.9 0.5 OG A:SER11 3.2 19.5 1.0 O A:HOH160 3.2 39.8 1.0 O A:HOH356 3.3 34.2 1.0 N A:GLN12 3.8 19.2 1.0 CG A:GLU13 3.8 24.5 1.0 C A:SER11 3.8 18.9 1.0 CA A:GLN12 3.8 20.1 1.0 CB A:SER11 3.8 19.0 1.0 CD1 A:ILE123 3.8 19.3 1.0 O A:SER11 3.9 18.2 1.0 C A:GLN12 4.0 20.7 1.0 OE2 A:GLU13 4.0 29.0 1.0 CG1 A:ILE123 4.1 16.3 1.0 N A:GLU13 4.2 21.0 1.0 CD A:GLU13 4.2 27.8 1.0 O A:LYS121 4.3 16.5 1.0 CE A:LYS121 4.3 20.2 0.5 CA A:SER11 4.5 18.7 1.0 O A:GLN12 4.5 21.0 1.0 CG A:LYS121 4.6 17.4 0.5 CB A:GLU13 4.7 22.2 1.0 CB A:ILE123 4.8 15.5 1.0 CD A:LYS121 4.9 19.4 0.5 CA A:GLU13 4.9 21.9 1.0

Iodine binding site 9 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I136 b:34.1 occ:0.30 O A:HOH347 2.6 22.1 1.0 NE2 A:GLN84 2.8 16.3 1.0 N A:LEU85 2.9 15.1 1.0 O A:LEU85 2.9 16.2 1.0 CA A:LEU85 3.6 15.7 1.0 CG1 A:VAL65 3.6 14.8 1.0 C A:LEU85 3.6 16.0 1.0 CB A:GLN84 3.7 15.0 1.0 CA A:GLN84 3.7 14.7 1.0 C A:GLN84 3.7 14.9 1.0 CB A:LEU85 3.9 15.8 1.0 CD A:GLN84 4.0 16.8 1.0 CG A:GLN84 4.4 15.9 1.0 O A:HOH240 4.5 17.0 1.0 O A:HOH348 4.8 38.6 1.0 O A:GLN84 4.9 15.0 1.0 N A:GLU86 4.9 16.4 1.0 CG A:LEU85 5.0 16.0 1.0

Iodine binding site 10 out of 14 in the Iodide Derivative of Human Lfabp at High Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Iodide Derivative of Human Lfabp at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I137 b:31.6 occ:0.25 O A:HOH234 3.4 23.6 1.0 OXT A:THR129 3.9 29.9 1.0 CA A:GLY5 4.0 15.2 1.0 CA A:THR129 4.1 29.1 1.0 O A:HOH205 4.1 21.4 0.5 CB A:THR129 4.3 29.2 1.0 O A:SER4 4.4 15.5 1.0 C A:THR129 4.4 29.4 1.0 N A:GLY5 4.5 14.9 1.0 C A:SER4 4.7 15.1 1.0 O A:GLY128 4.7 27.1 1.0 CG2 A:THR129 4.8 29.5 1.0 NH1 A:ARG126 4.9 15.9 1.0 O A:HOH159 5.0 24.8 0.5

A.Sharma, M.Yogavel, A.Sharma. Utility of Anion and Cation Combinations For Phasing of Protein Structures. J.Struct.Funct.Genom. V. 13 135 2012.
ISSN: ISSN 1345-711X
PubMed: 22562242
DOI: 10.1007/S10969-012-9137-3