Iodine in PDB 3b2k: Iodide Derivative of Human Lfabp

The structure of Iodide Derivative of Human Lfabp, PDB code: 3b2k 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 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.352, 57.070, 74.892, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 27.5

The binding sites of Iodine atom in the Iodide Derivative of Human Lfabp (pdb code 3b2k). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Iodide Derivative of Human Lfabp, PDB code: 3b2k:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Iodide Derivative of Human Lfabp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I130 b:24.7 occ:0.40 I A:IOD130 0.0 24.7 0.4 I A:IOD130 1.6 24.4 0.4 N A:MET74 3.4 21.6 1.0 CG A:MET74 3.5 26.0 1.0 CB A:MET74 3.7 23.2 1.0 CF A:PLM150 3.9 29.8 0.7 CB A:THR73 3.9 20.3 1.0 CG A:PLM150 4.0 29.7 0.7 CE A:MET113 4.1 20.5 1.0 CA A:MET74 4.2 22.6 1.0 CA A:THR73 4.2 20.1 1.0 C A:THR73 4.3 20.7 1.0 C3 A:PLM151 4.6 37.4 0.6 CE2 A:PHE18 4.6 23.6 1.0 CG2 A:THR73 4.7 19.9 1.0 C2 A:PLM151 4.8 37.5 0.6 SD A:MET113 4.8 19.5 1.0 SD A:MET74 4.8 33.4 1.0 I A:IOD133 4.8 39.5 0.2 CD1 A:ILE22 4.8 28.8 1.0 OG1 A:THR73 4.9 20.3 1.0 CE1 A:PHE95 4.9 17.9 1.0 CZ A:PHE95 4.9 18.7 1.0 CE A:MET19 4.9 24.8 1.0

Iodine binding site 2 out of 6 in the Iodide Derivative of Human Lfabp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I130 b:24.4 occ:0.40 I A:IOD130 0.0 24.4 0.4 I A:IOD130 1.6 24.7 0.4 I A:IOD133 3.4 39.5 0.2 CB A:THR73 3.9 20.3 1.0 CD1 A:ILE22 3.9 28.8 1.0 N A:MET74 4.0 21.6 1.0 CE2 A:PHE18 4.0 23.6 1.0 CE1 A:PHE95 4.3 17.9 1.0 CZ A:PHE18 4.4 23.6 1.0 CB A:MET74 4.4 23.2 1.0 OG1 A:THR73 4.5 20.3 1.0 CD1 A:ILE98 4.5 19.1 1.0 CG2 A:THR73 4.5 19.9 1.0 CG1 A:ILE22 4.6 28.6 1.0 CG2 A:ILE22 4.6 28.3 1.0 CG A:MET74 4.7 26.0 1.0 CA A:THR73 4.7 20.1 1.0 CE A:MET113 4.7 20.5 1.0 CB A:ILE22 4.8 28.3 1.0 CZ A:PHE95 4.8 18.7 1.0 CA A:MET74 4.8 22.6 1.0 C A:THR73 4.9 20.7 1.0

Iodine binding site 3 out of 6 in the Iodide Derivative of Human Lfabp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I131 b:44.6 occ:0.30 N A:GLN12 3.6 17.9 1.0 CA A:SER11 3.8 17.1 1.0 O A:GLN12 4.0 18.7 1.0 O A:HOH287 4.2 27.7 1.0 C A:SER11 4.2 17.4 1.0 CG A:GLN12 4.2 18.0 1.0 CB A:SER11 4.4 17.1 1.0 CA A:GLN12 4.6 18.3 1.0 NZ A:LYS36 4.7 15.1 1.0 O A:GLN10 4.7 15.2 1.0 C A:GLN12 4.7 18.9 1.0 CE A:LYS36 4.8 16.0 1.0 O A:HOH311 4.8 37.9 1.0 N A:SER11 4.9 16.3 1.0 CB A:GLN12 4.9 18.1 1.0

Iodine binding site 4 out of 6 in the Iodide Derivative of Human Lfabp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I132 b:37.1 occ:0.50 O A:HOH252 3.5 16.0 1.0 O A:ASN97 3.6 18.4 1.0 CB A:ASN97 4.0 17.8 1.0 CA A:ASN97 4.2 17.7 1.0 ND2 A:ASN97 4.2 17.8 1.0 C A:ASN97 4.3 17.7 1.0 O A:HOH322 4.4 11.3 0.5 CG A:ASN97 4.4 17.5 1.0 O A:HOH322 4.6 15.5 0.5

Iodine binding site 5 out of 6 in the Iodide Derivative of Human Lfabp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I133 b:39.5 occ:0.25 I A:IOD130 3.4 24.4 0.4 OG1 A:THR73 3.5 20.3 1.0 CB A:THR73 3.8 20.3 1.0 CB A:ILE22 4.0 28.3 1.0 O A:HOH140 4.1 29.6 1.0 CD1 A:ILE98 4.2 19.1 1.0 CG2 A:THR73 4.2 19.9 1.0 CD1 A:ILE22 4.2 28.8 1.0 CG2 A:ILE22 4.3 28.3 1.0 NZ A:LYS96 4.4 24.6 1.0 OG1 A:THR75 4.4 21.4 1.0 CG A:LYS96 4.5 20.0 1.0 CG2 A:THR75 4.6 20.9 1.0 CE1 A:PHE95 4.6 17.9 1.0 O A:ILE22 4.7 28.4 1.0 CG1 A:ILE22 4.7 28.6 1.0 I A:IOD130 4.8 24.7 0.4 CB A:LYS96 4.8 18.7 1.0 O A:HOH137 4.8 27.7 1.0 CD1 A:PHE95 5.0 17.8 1.0

Iodine binding site 6 out of 6 in the Iodide Derivative of Human Lfabp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I134 b:32.7 occ:0.43 O A:HOH198 2.7 35.4 1.0 OG1 A:THR51 3.1 18.9 1.0 O A:GLU40 3.7 14.9 1.0 O A:LYS49 3.8 15.6 1.0 N A:THR51 3.8 17.2 1.0 C A:LYS49 4.0 15.3 1.0 CA A:PHE50 4.0 16.6 1.0 C A:PHE50 4.1 16.7 1.0 N A:PHE50 4.1 15.7 1.0 CB A:THR51 4.1 17.8 1.0 CB A:LYS49 4.1 15.3 0.5 CG2 A:VAL42 4.2 13.9 1.0 CB A:LYS49 4.2 15.2 0.5 C A:GLU40 4.3 14.9 1.0 CB A:GLU40 4.3 15.2 0.5 NE2 A:GLN60 4.4 19.1 0.3 CB A:GLU40 4.5 15.1 0.5 CG A:GLU40 4.5 15.8 0.5 CA A:THR51 4.6 17.6 1.0 N A:VAL42 4.6 13.8 1.0 O A:HOH206 4.7 38.4 1.0 CA A:LYS49 4.7 15.1 0.5 OE2 A:GLU40 4.7 17.8 0.5 CA A:LYS49 4.7 15.1 0.5 O A:HOH197 4.8 92.2 0.5 CB A:VAL42 4.8 13.7 1.0 CD A:GLU40 4.9 16.8 0.5 O A:PHE50 4.9 16.8 1.0 N A:ILE41 4.9 14.8 1.0 C A:ILE41 5.0 13.8 1.0 CA A:ILE41 5.0 14.2 1.0

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