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Iodine in PDB 1gwg: Tri-Iodide Derivative of Apoferritin

Protein crystallography data

The structure of Tri-Iodide Derivative of Apoferritin, PDB code: 1gwg was solved by G.Evans, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.14 / 2.01
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.190, 181.190, 181.190, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.8

Other elements in 1gwg:

The structure of Tri-Iodide Derivative of Apoferritin also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Tri-Iodide Derivative of Apoferritin (pdb code 1gwg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Tri-Iodide Derivative of Apoferritin, PDB code: 1gwg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 1gwg

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Iodine binding site 1 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1172

b:25.7
occ:0.30
 O A:HOH2016 2.7 35.1 1.0
O A:HOH2044 3.2 24.5 1.0
N A:LEU93 3.6 9.4 1.0
CD A:GLU163 3.7 24.8 1.0
O A:HOH2043 3.7 37.0 1.0
CB A:THR91 3.8 12.4 1.0
CB A:LEU93 3.8 13.4 1.0
O A:HOH2145 3.9 39.9 1.0
N A:THR92 3.9 8.6 1.0
OE1 A:GLU163 3.9 28.6 1.0
CG A:GLU163 3.9 16.8 1.0
OE2 A:GLU163 4.0 14.6 1.0
CG2 A:ILE151 4.0 14.4 1.0
OG1 A:THR91 4.0 9.4 1.0
CB A:GLU163 4.0 13.4 1.0
CB A:THR92 4.1 11.7 1.0
CA A:LEU93 4.3 11.8 1.0
CA A:THR92 4.4 8.8 1.0
C A:THR92 4.4 11.0 1.0
CG1 A:VAL155 4.5 33.4 1.0
C A:THR91 4.6 10.9 1.0
CG2 A:THR91 4.7 14.8 1.0
CA A:GLU163 4.7 12.7 1.0
OG1 A:THR92 4.7 11.6 1.0
CA A:THR91 4.7 11.7 1.0
O A:HOH2101 4.8 22.5 1.0

Iodine binding site 2 out of 9 in 1gwg

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Iodine binding site 2 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1173

b:43.5
occ:0.38
 O A:HOH2052 2.9 28.9 1.0
N A:PRO123 3.7 17.7 1.0
CA A:PRO123 3.7 17.1 1.0
SG A:CYS126 3.9 37.2 1.0
N A:ASP122 4.0 18.5 1.0
CD A:PRO123 4.0 18.2 1.0
C A:ASP122 4.0 19.4 1.0
CB A:PRO123 4.1 18.5 1.0
CA A:SER118 4.2 17.0 1.0
O A:ASP122 4.2 18.5 1.0
C A:ALA121 4.3 22.7 1.0
CA A:ALA121 4.3 22.6 1.0
O A:GLY117 4.4 18.6 1.0
O A:HOH2118 4.5 38.2 1.0
CG A:PRO123 4.6 20.5 1.0
CB A:CYS126 4.6 30.5 1.0
CA A:ASP122 4.7 17.1 1.0
O A:SER118 4.8 26.2 1.0
N A:SER118 4.8 18.1 1.0
CB A:SER118 4.8 21.3 1.0
C A:GLY117 4.9 19.8 1.0
OG A:SER118 4.9 49.1 1.0
C A:SER118 5.0 23.6 1.0

Iodine binding site 3 out of 9 in 1gwg

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Iodine binding site 3 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1174

b:32.3
occ:0.28
 SG A:CYS48 2.2 17.5 1.0
I A:IOD1175 2.9 65.5 0.4
CD2 A:HIS49 3.0 17.6 0.5
CB A:CYS48 3.3 11.3 1.0
O A:HOH2051 3.4 27.0 1.0
I A:IOD1177 3.5 36.8 0.2
NE2 A:HIS49 3.6 17.8 0.5
N A:HIS49 3.7 10.6 0.5
N A:HIS49 3.8 10.5 0.5
C A:CYS48 3.8 13.3 1.0
CG A:HIS49 4.0 17.0 0.5
O A:CYS48 4.1 12.8 1.0
CA A:HIS49 4.2 11.1 0.5
CA A:HIS49 4.2 11.3 0.5
CD A:ARG52 4.2 33.9 1.0
CA A:CYS48 4.2 9.7 1.0
O A:GLU45 4.5 11.9 1.0
CG A:ARG52 4.5 20.0 1.0
CB A:HIS49 4.6 13.3 0.5
ND1 A:HIS49 4.7 18.9 0.5
CB A:HIS49 4.7 13.7 0.5
CE1 A:HIS49 4.7 17.5 0.5
ND1 A:HIS49 5.0 19.6 0.5

Iodine binding site 4 out of 9 in 1gwg

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Iodine binding site 4 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1175

b:65.5
occ:0.36
 I A:IOD1177 2.3 36.8 0.2
I A:IOD1174 2.9 32.3 0.3
OD1 A:ASP38 3.0 18.0 1.0
I A:IOD1176 3.1 43.2 0.4
SG A:CYS48 3.6 17.5 1.0
O A:HOH2051 3.8 27.0 1.0
CG A:ASP38 3.8 14.7 1.0
CB A:CYS48 3.9 11.3 1.0
CB A:ASP38 4.0 10.1 1.0
CG A:GLU45 4.1 34.4 1.0
CA A:GLU45 4.2 10.9 1.0
CA A:ASP38 4.3 8.8 1.0
CB A:GLU45 4.4 13.9 1.0
NE2 A:HIS49 4.8 17.8 0.5
O A:GLU45 4.8 11.9 1.0
OD2 A:ASP38 4.9 18.7 1.0
CD2 A:HIS49 4.9 17.6 0.5

Iodine binding site 5 out of 9 in 1gwg

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Iodine binding site 5 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1176

b:43.2
occ:0.43
 I A:IOD1175 3.1 65.5 0.4
O A:HOH2055 3.7 36.1 1.0
CA A:GLU45 3.7 10.9 1.0
N A:GLU45 3.8 8.6 1.0
OD1 A:ASP38 3.8 18.0 1.0
CB A:GLU45 3.8 13.9 1.0
CA A:ASP38 3.9 8.8 1.0
O A:PHE37 4.0 11.2 1.0
CA A:ALA43 4.2 5.6 1.0
N A:LEU44 4.2 8.8 1.0
C A:ALA43 4.3 9.3 1.0
C A:LEU44 4.4 8.3 1.0
O A:ASP38 4.5 10.2 1.0
O A:HOH2056 4.5 11.1 1.0
C A:ASP38 4.5 8.6 1.0
CG A:GLU45 4.6 34.4 1.0
CG A:ASP38 4.6 14.7 1.0
CB A:ASP38 4.7 10.1 1.0
I A:IOD1177 4.7 36.8 0.2
C A:PHE37 4.8 11.7 1.0
N A:ASP38 4.8 10.9 1.0
CB A:ALA43 4.8 5.5 1.0
O A:LEU44 4.9 8.3 1.0
CA A:LEU44 5.0 6.8 1.0
O A:ALA43 5.0 10.8 1.0

Iodine binding site 6 out of 9 in 1gwg

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Iodine binding site 6 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1177

b:36.8
occ:0.18
 I A:IOD1175 2.3 65.5 0.4
I A:IOD1174 3.5 32.3 0.3
O A:HOH2051 3.6 27.0 1.0
NE2 A:HIS49 3.8 17.8 0.5
OD1 A:ASP38 4.2 18.0 1.0
CG A:GLU45 4.2 34.4 1.0
CD2 A:HIS49 4.5 17.6 0.5
CD A:GLU45 4.5 79.4 1.0
I A:IOD1176 4.7 43.2 0.4
CE1 A:HIS49 4.7 17.5 0.5
OE2 A:GLU45 4.8 96.6 1.0

Iodine binding site 7 out of 9 in 1gwg

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Iodine binding site 7 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1180

b:22.1
occ:0.64
 CD A:CD1178 2.8 19.1 0.5
O A:HOH2081 3.8 14.9 1.0
OD2 A:ASP80 4.2 20.1 1.0
OD1 A:ASP80 4.4 13.0 1.0
CG A:ASP80 4.7 15.3 1.0

Iodine binding site 8 out of 9 in 1gwg

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Iodine binding site 8 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1181

b:32.0
occ:0.13
 O A:HOH2032 2.8 37.8 1.0
I A:IOD1182 3.1 39.6 0.3
CD1 A:LEU81 4.4 24.1 1.0
O A:HOH2036 4.8 8.0 0.3

Iodine binding site 9 out of 9 in 1gwg

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Iodine binding site 9 out of 9 in the Tri-Iodide Derivative of Apoferritin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Tri-Iodide Derivative of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1182

b:39.6
occ:0.35
 O A:HOH2036 2.5 8.0 0.3
O A:HOH2032 2.7 37.8 1.0
I A:IOD1181 3.1 32.0 0.1
OG A:SER27 3.7 16.9 1.0
CA A:TYR28 4.1 8.9 1.0
N A:TYR28 4.1 9.8 1.0
CD2 A:LEU31 4.1 16.3 1.0
C A:SER27 4.2 10.9 1.0
O A:SER27 4.3 9.5 1.0
CB A:SER27 4.4 8.3 1.0
CD1 A:TYR28 4.5 11.0 1.0
CB A:LEU31 4.6 12.2 1.0
CB A:TYR28 4.6 9.5 1.0
CG A:LEU31 4.9 16.6 1.0
CG A:TYR28 4.9 11.8 1.0
CA A:SER27 5.0 7.8 1.0

Reference:

G.Evans, G.Bricogne. Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods For Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Acta Crystallogr.,Sect.D V. 58 976 2002.
ISSN: ISSN 0907-4449
PubMed: 12037300
DOI: 10.1107/S0907444902005486
Page generated: Sun Aug 11 12:12:20 2024

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