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Iodine in PDB 3b2i: Iodide Derivative of Human Lfabp

Protein crystallography data

The structure of Iodide Derivative of Human Lfabp, PDB code: 3b2i 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 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.968, 57.895, 75.025, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Iodide Derivative of Human Lfabp (pdb code 3b2i). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Iodide Derivative of Human Lfabp, PDB code: 3b2i:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 1 out of 8 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:26.1
occ:0.60
 I A:IOD134 3.1 38.9 0.2
NZ A:LYS96 3.3 19.3 0.5
N A:MET74 3.8 23.9 1.0
CE A:MET113 3.8 27.3 1.0
CB A:MET74 3.9 25.3 1.0
CB A:THR73 3.9 23.2 1.0
CG A:MET74 3.9 28.5 1.0
CE A:LYS96 4.1 20.9 0.5
CE1 A:PHE95 4.2 23.3 1.0
CD1 A:ILE98 4.2 22.3 1.0
CE2 A:PHE18 4.3 25.6 1.0
NZ A:LYS96 4.4 25.8 0.5
CA A:MET74 4.5 24.6 1.0
CD1 A:ILE22 4.6 32.7 1.0
CG2 A:THR73 4.6 23.1 1.0
CA A:THR73 4.6 22.8 1.0
OG1 A:THR73 4.7 23.1 1.0
C A:THR73 4.7 23.2 1.0
CG1 A:ILE22 4.7 32.0 1.0
CZ A:PHE18 4.7 25.6 1.0
CG2 A:ILE22 4.8 31.7 1.0
CF A:PLM150 4.9 33.7 0.7
CZ A:PHE95 4.9 23.9 1.0
CB A:ILE22 5.0 31.7 1.0

Iodine binding site 2 out of 8 in 3b2i

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Iodine binding site 2 out of 8 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:28.2
occ:0.40
 OE2 A:GLU13 3.4 31.2 1.0
OG A:SER11 3.5 22.1 1.0
CG A:GLU13 3.6 27.2 1.0
O A:HOH138 3.7 20.5 0.5
CD1 A:ILE123 3.7 19.2 1.0
CA A:GLN12 3.9 22.3 1.0
C A:GLN12 3.9 22.8 1.0
CD A:GLU13 4.0 30.4 1.0
O A:LYS121 4.0 19.3 1.0
N A:GLU13 4.0 23.3 1.0
O A:SER11 4.0 21.0 1.0
N A:GLN12 4.1 21.6 1.0
C A:SER11 4.1 21.1 1.0
CG1 A:ILE123 4.2 18.2 1.0
CB A:SER11 4.2 20.6 1.0
CG A:LYS121 4.4 19.7 1.0
CB A:GLU13 4.4 24.9 1.0
CD A:LYS121 4.4 21.1 1.0
O A:GLN12 4.4 22.9 1.0
CE A:LYS121 4.6 22.7 1.0
C A:LYS121 4.6 19.0 1.0
CB A:LYS121 4.8 19.2 1.0
CA A:GLU13 4.8 24.3 1.0
CA A:SER11 4.8 20.9 1.0
N A:ILE123 4.9 18.1 1.0
CB A:ILE123 4.9 18.1 1.0

Iodine binding site 3 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 3 out of 8 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:36.3
occ:0.30
 I A:IOD132 0.0 36.3 0.3
I A:IOD132 1.6 41.2 0.2
O A:HOH179 3.4 31.4 1.0
N A:GLN12 3.6 21.6 1.0
NZ A:LYS36 3.9 23.9 1.0
CG A:GLN12 3.9 22.8 1.0
CE A:LYS36 4.1 23.6 1.0
CA A:SER11 4.1 20.9 1.0
O A:GLN12 4.3 22.9 1.0
O A:HOH243 4.3 33.7 1.0
C A:SER11 4.3 21.1 1.0
CA A:GLN12 4.6 22.3 1.0
NE2 A:GLN12 4.6 24.3 1.0
O A:LYS33 4.7 27.6 1.0
CB A:GLN12 4.7 21.9 1.0
CD A:GLN12 4.8 22.6 1.0
C A:GLN12 4.9 22.8 1.0
O A:GLN10 4.9 20.1 1.0
CB A:SER11 4.9 20.6 1.0
CD A:LYS36 5.0 23.9 1.0

Iodine binding site 4 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 4 out of 8 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:41.2
occ:0.20
 I A:IOD132 0.0 41.2 0.2
I A:IOD132 1.6 36.3 0.3
N A:GLN12 3.2 21.6 1.0
CA A:SER11 3.6 20.9 1.0
O A:GLN12 3.6 22.9 1.0
CB A:SER11 3.9 20.6 1.0
C A:SER11 3.9 21.1 1.0
CA A:GLN12 4.3 22.3 1.0
C A:GLN12 4.4 22.8 1.0
CG A:GLN12 4.6 22.8 1.0
O A:GLN10 4.7 20.1 1.0
N A:SER11 4.8 20.3 1.0
CB A:GLN12 5.0 21.9 1.0
O A:HOH179 5.0 31.4 1.0
CE A:LYS36 5.0 23.6 1.0

Iodine binding site 5 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 5 out of 8 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:34.4
occ:0.24
 O A:HOH181 3.5 22.1 1.0
O A:HOH276 3.7 32.7 0.5
OXT A:THR129 3.8 31.2 1.0
CA A:THR129 4.0 30.4 1.0
CA A:GLY5 4.0 20.3 1.0
CB A:THR129 4.2 30.7 1.0
C A:THR129 4.4 30.9 1.0
O A:SER4 4.5 20.4 1.0
N A:GLY5 4.6 20.4 1.0
CG2 A:THR129 4.7 30.9 1.0
C A:SER4 4.7 20.5 1.0
NH1 A:ARG126 4.9 20.4 1.0
O A:GLY128 5.0 28.5 1.0
C A:GLY5 5.0 20.2 1.0

Iodine binding site 6 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 6 out of 8 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:38.9
occ:0.22
 NZ A:LYS96 1.0 19.3 0.5
NZ A:LYS96 1.4 25.8 0.5
CE A:LYS96 2.4 20.9 0.5
CE A:LYS96 2.6 25.1 0.5
I A:IOD130 3.1 26.1 0.6
OG1 A:THR73 3.2 23.1 1.0
CD A:LYS96 3.3 21.9 0.5
CD A:LYS96 3.5 24.8 0.5
CB A:THR73 3.5 23.2 1.0
OG1 A:THR75 3.6 23.0 1.0
CB A:ILE22 4.0 31.7 1.0
CG2 A:THR75 4.0 23.6 1.0
CD1 A:ILE22 4.2 32.7 1.0
CG2 A:THR73 4.2 23.1 1.0
CG2 A:ILE22 4.3 31.7 1.0
N A:THR75 4.4 23.8 1.0
N A:MET74 4.4 23.9 1.0
CB A:THR75 4.4 23.5 1.0
CG1 A:ILE22 4.5 32.0 1.0
O A:HOH261 4.6 39.7 1.0
CD1 A:ILE98 4.6 22.3 1.0
CG A:LYS96 4.7 22.7 0.5
CA A:THR73 4.8 22.8 1.0
O A:ILE22 4.8 32.1 1.0
CG A:LYS96 4.9 23.9 0.5
C A:THR73 4.9 23.2 1.0

Iodine binding site 7 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 7 out of 8 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:35.3
occ:0.25
 I A:IOD135 0.0 35.3 0.2
I A:IOD135 2.2 45.8 0.2
OG1 A:THR51 2.9 22.2 1.0
O A:LYS49 3.5 19.2 1.0
O A:GLU40 3.5 22.4 1.0
N A:THR51 3.7 21.4 1.0
C A:LYS49 3.7 19.8 1.0
CA A:PHE50 3.8 21.2 1.0
C A:PHE50 3.9 21.5 1.0
N A:PHE50 3.9 20.3 1.0
CB A:THR51 4.0 22.2 1.0
CG2 A:VAL42 4.1 21.1 1.0
CB A:LYS49 4.1 19.9 1.0
C A:GLU40 4.2 21.9 1.0
NE2 A:GLN60 4.2 25.4 1.0
O A:HOH284 4.3 44.4 1.0
N A:VAL42 4.4 21.1 1.0
OE1 A:GLN60 4.4 27.3 1.0
CB A:GLU40 4.4 22.5 1.0
CA A:THR51 4.5 22.0 1.0
O A:PHE50 4.6 21.0 1.0
CA A:LYS49 4.6 19.8 1.0
CB A:VAL42 4.6 21.4 1.0
N A:ILE41 4.7 21.6 1.0
CA A:ILE41 4.7 21.2 1.0
CD A:GLN60 4.7 25.0 1.0
C A:ILE41 4.8 21.0 1.0
CA A:GLU40 5.0 22.4 1.0

Iodine binding site 8 out of 8 in 3b2i

Go back to Iodine Binding Sites List in 3b2i
Iodine binding site 8 out of 8 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 8 of Iodide Derivative of Human Lfabp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:45.8
occ:0.20
 I A:IOD135 0.0 45.8 0.2
I A:IOD135 2.2 35.3 0.2
NE2 A:GLN60 3.5 25.4 1.0
O A:HOH284 3.6 44.4 1.0
CB A:LYS49 3.7 19.9 1.0
OG1 A:THR51 4.0 22.2 1.0
CD A:LYS49 4.2 24.3 1.0
OE1 A:GLN60 4.3 27.3 1.0
CG2 A:VAL42 4.3 21.1 1.0
CD A:GLN60 4.3 25.0 1.0
CG A:LYS49 4.6 21.3 1.0
C A:LYS49 4.6 19.8 1.0
O A:LYS49 4.7 19.2 1.0
CB A:VAL42 4.7 21.4 1.0
CA A:LYS49 4.8 19.8 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 14:44:09 2024

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