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Iodine in PDB 3b2j: Iodide Derivative of Human Lfabp

Protein crystallography data

The structure of Iodide Derivative of Human Lfabp, PDB code: 3b2j 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.982, 57.608, 75.984, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 29.2

Iodine Binding Sites:

The binding sites of Iodine atom in the Iodide Derivative of Human Lfabp (pdb code 3b2j). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Iodide Derivative of Human Lfabp, PDB code: 3b2j:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 1 out of 7 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:41.8
occ:0.45
 I A:IOD130 0.0 41.8 0.5
I A:IOD130 1.3 23.3 0.6
CG A:PLM150 3.4 26.3 0.7
CG A:MET74 3.5 26.6 1.0
N A:MET74 3.5 23.0 1.0
CE A:MET113 3.6 21.4 0.5
CB A:MET74 3.8 24.2 1.0
CB A:THR73 4.0 22.4 1.0
CA A:MET74 4.2 23.6 1.0
CA A:THR73 4.4 22.1 1.0
C A:THR73 4.4 22.4 1.0
CE1 A:PHE95 4.4 25.5 1.0
SD A:MET113 4.5 22.4 0.5
CF A:PLM150 4.5 26.6 0.7
I A:IOD134 4.6 43.1 0.2
CE A:MET74 4.6 32.2 1.0
CG2 A:THR73 4.6 21.7 1.0
CE A:MET113 4.7 22.4 0.5
CE A:MET19 4.7 25.5 1.0
CE2 A:PHE18 4.8 23.3 1.0
NZ A:LYS96 4.8 23.3 0.5
CZ A:PHE95 4.8 25.3 1.0
SD A:MET74 4.9 33.0 1.0
SD A:MET113 4.9 21.0 0.5
OG1 A:THR73 5.0 22.4 1.0

Iodine binding site 2 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 2 out of 7 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:23.3
occ:0.55
 I A:IOD130 0.0 23.3 0.6
I A:IOD130 1.3 41.8 0.5
I A:IOD134 3.4 43.1 0.2
NZ A:LYS96 3.7 23.3 0.5
N A:MET74 3.8 23.0 1.0
CB A:THR73 3.9 22.4 1.0
CE A:MET113 4.0 21.4 0.5
CB A:MET74 4.2 24.2 1.0
CD1 A:ILE98 4.3 21.2 1.0
CE2 A:PHE18 4.3 23.3 1.0
CG A:MET74 4.4 26.6 1.0
CE1 A:PHE95 4.4 25.5 1.0
CD1 A:ILE22 4.4 27.6 1.0
CE A:LYS96 4.5 23.1 0.5
CG2 A:THR73 4.5 21.7 1.0
CG1 A:ILE22 4.5 27.8 1.0
CG A:PLM150 4.5 26.3 0.7
OG1 A:THR73 4.6 22.4 1.0
CA A:MET74 4.6 23.6 1.0
CA A:THR73 4.6 22.1 1.0
C A:THR73 4.7 22.4 1.0
CZ A:PHE18 4.9 22.6 1.0
CG2 A:ILE22 4.9 27.6 1.0
CB A:ILE22 4.9 28.0 1.0
CE A:MET19 4.9 25.5 1.0

Iodine binding site 3 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 3 out of 7 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:32.4
occ:0.60
 OE2 A:GLU13 3.5 28.6 1.0
OG A:SER11 3.5 20.6 1.0
CG A:GLU13 3.6 25.2 1.0
CD1 A:ILE123 3.7 19.4 1.0
CA A:GLN12 3.9 20.0 1.0
C A:GLN12 3.9 20.6 1.0
N A:GLN12 4.0 19.8 1.0
C A:SER11 4.0 19.9 1.0
CB A:SER11 4.0 20.0 1.0
CD A:GLU13 4.0 27.7 1.0
O A:SER11 4.0 19.6 1.0
N A:GLU13 4.0 21.3 1.0
CG1 A:ILE123 4.2 18.4 1.0
O A:LYS121 4.2 17.9 1.0
CG A:LYS121 4.4 19.4 1.0
O A:GLN12 4.4 20.5 1.0
CE A:LYS121 4.4 20.6 1.0
CB A:GLU13 4.4 22.5 1.0
CD A:LYS121 4.5 20.2 1.0
CA A:SER11 4.7 19.7 1.0
CB A:LYS121 4.8 18.4 1.0
CA A:GLU13 4.8 21.9 1.0
C A:LYS121 4.8 17.9 1.0
O A:HOH257 4.8 2.8 0.2
N A:ILE123 4.9 17.9 1.0
CB A:ILE123 4.9 18.6 1.0

Iodine binding site 4 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 4 out of 7 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:32.3
occ:0.35
 OG1 A:THR51 3.1 22.1 1.0
O A:LYS49 3.6 21.2 1.0
N A:THR51 3.8 21.4 1.0
C A:LYS49 3.8 21.3 1.0
O A:GLU40 3.8 21.5 1.0
CA A:PHE50 3.9 21.4 1.0
OE1 A:GLN60 3.9 30.8 1.0
NE2 A:GLN60 4.0 28.3 1.0
N A:PHE50 4.0 21.2 1.0
C A:PHE50 4.0 21.5 1.0
CB A:THR51 4.1 21.3 1.0
CB A:LYS49 4.3 21.6 1.0
CG2 A:VAL42 4.3 20.5 1.0
CD A:GLN60 4.4 27.9 1.0
C A:GLU40 4.4 21.6 1.0
CB A:GLU40 4.5 22.9 1.0
N A:VAL42 4.6 20.0 1.0
CA A:THR51 4.6 21.2 1.0
CB A:VAL42 4.7 19.9 1.0
CA A:LYS49 4.7 21.4 1.0
O A:PHE50 4.8 21.1 1.0
N A:ILE41 4.9 21.0 1.0
C A:ILE41 5.0 20.3 1.0
CA A:ILE41 5.0 20.4 1.0

Iodine binding site 5 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 5 out of 7 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:35.8
occ:0.30
 O A:HOH172 3.5 23.2 1.0
CG2 A:THR129 3.5 30.3 1.0
O A:THR129 3.7 29.4 1.0
CA A:THR129 4.0 29.1 1.0
CA A:GLY5 4.0 20.3 1.0
CB A:THR129 4.3 29.4 1.0
C A:THR129 4.3 29.5 1.0
O A:HOH261 4.3 22.4 0.0
O A:SER4 4.5 20.1 1.0
N A:GLY5 4.6 20.4 1.0
C A:SER4 4.7 20.6 1.0
O A:GLY128 4.8 26.6 1.0
OG1 A:THR129 4.8 30.2 1.0
NH1 A:ARG126 4.9 16.8 1.0
C A:GLY5 5.0 20.1 1.0

Iodine binding site 6 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 6 out of 7 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:43.1
occ:0.20
 NZ A:LYS96 1.0 23.3 0.5
CE A:LYS96 2.5 23.1 0.5
OG1 A:THR73 3.3 22.4 1.0
CD A:LYS96 3.4 22.3 0.5
I A:IOD130 3.4 23.3 0.6
OG1 A:THR75 3.6 22.3 1.0
CB A:THR73 3.7 22.4 1.0
CG2 A:THR75 3.9 22.8 1.0
CB A:ILE22 3.9 28.0 1.0
O A:HOH254 4.1 30.3 1.0
CD1 A:ILE22 4.2 27.6 1.0
CG2 A:ILE22 4.3 27.6 1.0
CB A:THR75 4.3 22.3 1.0
CG2 A:THR73 4.4 21.7 1.0
O A:ILE22 4.4 28.2 1.0
CG1 A:ILE22 4.5 27.8 1.0
I A:IOD130 4.6 41.8 0.5
N A:THR75 4.6 22.9 1.0
OE1 A:GLU77 4.8 23.2 1.0
CD1 A:ILE98 4.8 21.2 1.0
CG A:LYS96 4.8 22.9 0.5
N A:MET74 4.8 23.0 1.0
CB A:GLU77 4.9 20.8 1.0

Iodine binding site 7 out of 7 in 3b2j

Go back to Iodine Binding Sites List in 3b2j
Iodine binding site 7 out of 7 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 7 of Iodide Derivative of Human Lfabp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:38.7
occ:0.35
 O A:HOH232 3.1 32.1 1.0
O A:HOH194 3.6 25.4 1.0
N A:GLN12 3.6 19.8 1.0
CA A:SER11 4.0 19.7 1.0
CG A:GLN12 4.1 19.0 1.0
O A:GLN12 4.1 20.5 1.0
NZ A:LYS36 4.1 22.6 1.0
C A:SER11 4.2 19.9 1.0
CE A:LYS36 4.3 22.3 1.0
CA A:GLN12 4.5 20.0 1.0
CB A:SER11 4.7 20.0 1.0
O A:LYS33 4.7 26.0 1.0
C A:GLN12 4.7 20.6 1.0
O A:GLN10 4.8 18.7 1.0
CB A:GLN12 4.8 19.5 1.0
NE2 A:GLN12 4.8 18.5 1.0
CD A:GLN12 4.9 17.9 1.0
O A:HOH224 4.9 34.0 1.0
N A:SER11 5.0 19.4 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 Aug 11 14:44:13 2024

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