Iodine in PDB 3vg6: Barium Derivative of Human Lfabp

The structure of Barium Derivative of Human Lfabp, PDB code: 3vg6 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 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.216, 57.240, 74.491, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 29.5

The structure of Barium Derivative of Human Lfabp also contains other interesting chemical elements:

Barium

(Ba)

2 atoms

The binding sites of Iodine atom in the Barium Derivative of Human Lfabp (pdb code 3vg6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Barium Derivative of Human Lfabp, PDB code: 3vg6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Barium 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 Barium Derivative of Human Lfabp within 5.0Å range: probe atom residue distance (Å) B Occ A:I132 b:44.9 occ:0.50 I A:IOD132 0.0 44.9 0.5 I A:IOD132 1.5 41.7 0.5 I A:IOD134 3.2 52.0 0.3 CE A:MET113 3.7 32.1 1.0 CB A:THR73 3.9 31.5 1.0 CD1 A:ILE22 4.0 43.8 1.0 CE1 A:PHE95 4.1 26.4 1.0 CE2 A:PHE18 4.1 36.3 1.0 CD1 A:ILE98 4.2 31.4 1.0 N A:MET74 4.2 32.5 1.0 CB A:MET74 4.3 33.4 0.5 CG2 A:THR73 4.5 29.9 1.0 CZ A:PHE18 4.5 36.1 1.0 CG1 A:ILE22 4.6 44.0 1.0 OG1 A:THR73 4.6 31.5 1.0 CZ A:PHE95 4.6 26.1 1.0 CG2 A:ILE22 4.7 43.8 1.0 CB A:ILE22 4.7 44.4 1.0 CA A:THR73 4.9 31.3 1.0 CA A:MET74 4.9 33.1 0.5 CG A:MET74 4.9 35.5 0.5

Iodine binding site 2 out of 5 in the Barium 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 Barium Derivative of Human Lfabp within 5.0Å range: probe atom residue distance (Å) B Occ A:I132 b:41.7 occ:0.50 I A:IOD132 0.0 41.7 0.5 I A:IOD132 1.5 44.9 0.5 N A:MET74 3.4 32.5 1.0 CE A:MET113 3.5 32.1 1.0 CB A:MET74 3.6 33.4 0.5 CB A:THR73 3.7 31.5 1.0 CG A:MET74 3.9 35.5 0.5 CG A:PLM150 4.0 31.1 0.7 CA A:MET74 4.1 33.1 0.5 CA A:THR73 4.2 31.3 1.0 C A:THR73 4.3 32.0 1.0 I A:IOD134 4.4 52.0 0.3 CG2 A:THR73 4.4 29.9 1.0 CE1 A:PHE95 4.6 26.4 1.0 CE A:PLM150 4.6 32.2 0.7 OG1 A:THR73 4.7 31.5 1.0 CZ A:PHE95 4.7 26.1 1.0 CE2 A:PHE18 4.7 36.3 1.0 CD1 A:ILE22 4.8 43.8 1.0 CF A:PLM150 4.9 32.2 0.7 SD A:MET113 4.9 33.7 1.0

Iodine binding site 3 out of 5 in the Barium 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 Barium Derivative of Human Lfabp within 5.0Å range: probe atom residue distance (Å) B Occ A:I133 b:36.4 occ:0.30 OG1 A:THR51 3.0 30.5 1.0 O A:GLU40 3.5 27.9 1.0 O A:LYS49 3.6 27.1 1.0 N A:THR51 3.8 28.7 1.0 C A:LYS49 3.9 27.4 1.0 CG2 A:VAL42 3.9 24.8 1.0 CA A:PHE50 4.0 28.2 1.0 CB A:THR51 4.0 29.6 1.0 C A:GLU40 4.1 27.2 1.0 C A:PHE50 4.1 28.7 1.0 CB A:LYS49 4.1 28.1 1.0 N A:PHE50 4.1 27.4 1.0 CB A:GLU40 4.2 27.7 1.0 NE2 A:GLN60 4.3 31.7 0.5 N A:VAL42 4.5 25.2 1.0 CA A:THR51 4.5 29.1 1.0 N A:ILE41 4.7 26.8 1.0 OE1 A:GLU40 4.7 36.9 1.0 CA A:LYS49 4.7 27.7 1.0 CA A:ILE41 4.8 26.0 1.0 CB A:VAL42 4.8 25.0 1.0 C A:ILE41 4.8 25.4 1.0 CA A:GLU40 4.8 28.1 1.0 CD A:GLN60 4.9 32.2 0.5 O A:PHE50 5.0 29.1 1.0

Iodine binding site 4 out of 5 in the Barium 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 Barium Derivative of Human Lfabp within 5.0Å range: probe atom residue distance (Å) B Occ A:I134 b:52.0 occ:0.27 CD A:LYS96 2.9 29.3 0.5 CE A:LYS96 2.9 30.2 0.5 I A:IOD132 3.2 44.9 0.5 OG1 A:THR73 3.6 31.5 1.0 CB A:THR73 3.9 31.5 1.0 CD1 A:ILE98 4.0 31.4 1.0 CB A:ILE22 4.2 44.4 1.0 CG2 A:THR73 4.2 29.9 1.0 CG A:LYS96 4.3 29.6 0.5 NZ A:LYS96 4.3 30.4 0.5 I A:IOD132 4.4 41.7 0.5 CD1 A:ILE22 4.4 43.8 1.0 CG2 A:ILE22 4.5 43.8 1.0 CE1 A:PHE95 4.5 26.4 1.0 OG1 A:THR75 4.5 32.1 1.0 CG2 A:THR75 4.6 31.0 1.0 O A:ILE22 4.7 44.8 1.0 CB A:LYS96 4.8 29.2 0.5 CG A:LYS96 4.8 29.6 0.5 CD1 A:PHE95 4.8 25.9 1.0 CG1 A:ILE22 4.9 44.0 1.0 CB A:LYS96 4.9 29.2 0.5 NZ A:LYS96 4.9 31.6 0.5

Iodine binding site 5 out of 5 in the Barium 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 Barium Derivative of Human Lfabp within 5.0Å range: probe atom residue distance (Å) B Occ A:I135 b:39.1 occ:0.28 NZ A:LYS121 2.9 40.5 1.0 OG A:SER11 3.4 33.2 1.0 OE2 A:GLU13 3.8 46.4 1.0 CG A:GLU13 3.8 39.5 1.0 CA A:GLN12 3.8 34.6 1.0 CD1 A:ILE123 3.9 26.1 1.0 N A:GLN12 3.9 34.0 1.0 C A:GLN12 3.9 35.3 1.0 N A:GLU13 4.0 35.9 1.0 C A:SER11 4.0 33.2 1.0 O A:LYS121 4.1 26.0 1.0 CG1 A:ILE123 4.1 24.4 1.0 O A:SER11 4.1 33.2 1.0 CB A:SER11 4.2 32.9 1.0 CE A:LYS121 4.2 37.9 1.0 CD A:GLU13 4.3 43.8 1.0 CG A:LYS121 4.4 29.8 1.0 CB A:GLU13 4.5 36.8 1.0 O A:GLN12 4.5 35.7 1.0 C A:LYS121 4.6 26.1 1.0 CB A:ILE123 4.7 24.0 1.0 CD A:LYS121 4.7 34.7 1.0 N A:ILE123 4.7 24.5 1.0 CA A:SER11 4.8 32.8 1.0 CA A:GLU13 4.8 36.6 1.0 CB A:LYS121 4.9 27.1 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