Iodine in PDB 3vg2: Iodide Derivative of Human Lfabp

The structure of Iodide Derivative of Human Lfabp, PDB code: 3vg2 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.979, 57.781, 74.862, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 31.2

The binding sites of Iodine atom in the Iodide Derivative of Human Lfabp (pdb code 3vg2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Iodide Derivative of Human Lfabp, PDB code: 3vg2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 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:20.6 occ:0.60 N A:MET74 3.7 24.0 1.0 CB A:MET74 3.7 26.5 1.0 NZ A:LYS96 3.9 29.3 1.0 CB A:THR73 3.9 22.0 1.0 CG A:PLM150 4.1 21.8 0.7 CE1 A:PHE95 4.1 22.2 1.0 CD1 A:ILE98 4.2 18.9 1.0 CE2 A:PHE18 4.3 23.3 1.0 CA A:MET74 4.4 25.5 1.0 CE A:MET113 4.5 24.3 1.0 CA A:THR73 4.6 22.3 1.0 CD1 A:ILE22 4.6 35.9 1.0 CZ A:PHE18 4.6 24.5 1.0 C A:THR73 4.6 22.9 1.0 CF A:PLM150 4.6 20.5 0.7 CZ A:PHE95 4.7 21.4 1.0 CG2 A:THR73 4.7 21.6 1.0 CG1 A:ILE22 4.7 34.8 1.0 OG1 A:THR73 4.7 23.3 1.0 CG2 A:ILE22 4.8 34.3 1.0 SD A:MET113 4.9 23.4 1.0 CB A:ILE22 5.0 34.6 1.0 CG A:MET74 5.0 29.3 1.0

Iodine binding site 2 out of 5 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:I131 b:39.1 occ:0.30 N A:GLN12 3.5 19.3 1.0 NZ A:LYS36 3.6 18.9 1.0 CA A:SER11 3.7 19.3 1.0 CE A:LYS36 3.9 21.6 1.0 C A:SER11 4.1 19.4 1.0 CG A:GLN12 4.1 18.7 1.0 O A:GLN12 4.4 21.1 1.0 O A:GLN10 4.4 19.9 1.0 CA A:GLN12 4.5 19.9 1.0 CB A:SER11 4.6 19.2 1.0 N A:SER11 4.6 19.5 1.0 CD A:LYS36 4.6 20.4 1.0 NE2 A:GLN12 4.7 19.6 1.0 CB A:GLN12 4.7 19.2 1.0 O A:LYS33 4.8 25.8 1.0 CD2 A:LEU9 4.8 16.7 1.0 CD A:GLN12 4.9 19.6 1.0 C A:GLN10 4.9 19.1 1.0 C A:GLN12 5.0 21.0 1.0

Iodine binding site 3 out of 5 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:I132 b:26.4 occ:0.20 OG1 A:THR51 3.0 24.0 1.0 CA A:PHE50 3.5 23.9 1.0 N A:THR51 3.5 24.3 1.0 C A:LYS49 3.6 23.7 1.0 O A:LYS49 3.6 23.9 1.0 O A:GLU40 3.6 21.9 1.0 N A:PHE50 3.6 23.7 1.0 C A:PHE50 3.7 24.1 1.0 OE1 A:GLN60 3.9 23.1 1.0 CB A:LYS49 3.9 23.8 1.0 CB A:THR51 4.0 24.9 1.0 CG2 A:VAL42 4.1 19.4 1.0 NE2 A:GLN60 4.1 25.2 1.0 C A:GLU40 4.3 22.0 1.0 CA A:THR51 4.4 25.1 1.0 CA A:LYS49 4.4 23.6 1.0 N A:VAL42 4.4 20.6 1.0 O A:PHE50 4.4 23.5 1.0 CD A:GLN60 4.4 23.6 1.0 CB A:GLU40 4.6 22.4 1.0 CA A:ILE41 4.7 20.9 1.0 N A:ILE41 4.8 22.0 1.0 C A:ILE41 4.9 20.9 1.0 CB A:VAL42 4.9 20.4 1.0 CB A:PHE50 4.9 24.0 1.0

Iodine binding site 4 out of 5 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:I133 b:31.6 occ:0.55 OE2 A:GLU13 3.7 24.8 1.0 OG A:SER11 3.7 18.9 1.0 CD1 A:ILE123 3.8 18.2 1.0 CG A:GLU13 3.8 24.4 1.0 O A:SER11 4.0 18.9 1.0 N A:GLU13 4.0 22.0 1.0 C A:GLN12 4.1 21.0 1.0 C A:SER11 4.1 19.4 1.0 CA A:GLN12 4.1 19.9 1.0 O A:LYS121 4.2 17.9 1.0 CG1 A:ILE123 4.2 16.4 1.0 N A:GLN12 4.2 19.3 1.0 CD A:GLU13 4.2 24.6 1.0 CB A:SER11 4.2 19.2 1.0 CD A:LYS121 4.4 18.9 1.0 CG A:LYS121 4.5 19.3 1.0 CB A:GLU13 4.5 22.5 1.0 O A:GLN12 4.6 21.1 1.0 C A:LYS121 4.7 18.5 1.0 N A:ILE123 4.7 18.3 1.0 CE A:LYS121 4.7 18.7 1.0 CB A:LYS121 4.8 18.4 1.0 CA A:GLU13 4.8 22.9 1.0 CB A:ILE123 4.8 18.4 1.0 CA A:SER11 4.8 19.3 1.0 NZ A:LYS121 5.0 19.2 1.0

Iodine binding site 5 out of 5 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:I134 b:34.2 occ:0.34 O A:HOH149 3.4 12.4 1.0 CA A:GLY5 3.7 18.8 1.0 OG1 A:THR129 3.9 33.9 1.0 O A:THR129 4.2 32.3 1.0 N A:GLY5 4.3 19.9 1.0 CA A:THR129 4.3 32.1 1.0 O A:SER4 4.4 20.1 1.0 C A:SER4 4.5 20.3 1.0 CB A:THR129 4.6 32.5 1.0 C A:THR129 4.8 32.1 1.0 C A:GLY5 4.9 18.1 1.0 NH1 A:ARG126 4.9 18.9 1.0 O A:GLY128 4.9 29.8 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