Atomistry » Iodine » PDB 2y6q-3cgp » 3b2j
Atomistry »
  Iodine »
    PDB 2y6q-3cgp »
      3b2j »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy