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Iodine in PDB 3vg6: Barium Derivative of Human Lfabp

Protein crystallography data

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

Other elements in 3vg6:

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

Barium (Ba) 2 atoms

Iodine Binding Sites:

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 3vg6

Go back to Iodine Binding Sites List in 3vg6
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 3vg6

Go back to Iodine Binding Sites List in 3vg6
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 3vg6

Go back to Iodine Binding Sites List in 3vg6
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 3vg6

Go back to Iodine Binding Sites List in 3vg6
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 3vg6

Go back to Iodine Binding Sites List in 3vg6
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

Reference:

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
Page generated: Sun Dec 13 19:31:09 2020

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