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Iodine in PDB 3nte: Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein

Protein crystallography data

The structure of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein, PDB code: 3nte was solved by L.Betts, J.I.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.05 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.910, 86.532, 55.589, 90.00, 99.73, 90.00
R / Rfree (%) 20.4 / 25.3

Other elements in 3nte:

The structure of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein also contains other interesting chemical elements:

Iron (Fe) 23 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein (pdb code 3nte). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 23 binding sites of Iodine where determined in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein, PDB code: 3nte:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 23 in 3nte

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Iodine binding site 1 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I222

b:41.4
occ:1.00
N A:SER178 3.6 37.0 1.0
OG A:SER178 3.8 45.1 1.0
CG2 A:VAL181 3.9 36.0 1.0
CA A:ALA177 4.1 39.9 1.0
CB A:SER178 4.2 41.4 1.0
CB B:GLU29 4.2 38.0 1.0
CG B:GLU29 4.2 43.7 1.0
CG A:PRO147 4.3 33.8 1.0
CB A:ALA177 4.3 39.3 1.0
C A:ALA177 4.4 37.4 1.0
CA B:VAL26 4.5 33.4 1.0
CB A:VAL181 4.5 36.2 1.0
CG2 B:VAL26 4.5 34.2 1.0
CA A:SER178 4.6 38.1 1.0
CG B:LYS30 4.7 42.9 1.0
CE B:LYS30 4.8 46.6 1.0
O B:LYS25 4.8 36.2 1.0
N B:VAL26 4.9 33.8 1.0
CG1 A:VAL181 4.9 37.8 1.0
CG B:LYS25 5.0 38.9 1.0

Iodine binding site 2 out of 23 in 3nte

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Iodine binding site 2 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I223

b:35.1
occ:0.84
FE A:FE243 2.6 32.2 0.6
O A:HOH260 3.1 26.8 0.8
I A:IOD230 3.6 36.5 0.4
CG1 A:ILE129 4.2 18.7 1.0
CZ3 A:TRP80 4.6 32.3 1.0
CD1 A:ILE129 4.9 18.8 1.0
CG2 A:ILE129 4.9 24.2 1.0

Iodine binding site 3 out of 23 in 3nte

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Iodine binding site 3 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I224

b:45.6
occ:0.91
O A:HOH302 2.4 29.6 1.0
O B:HOH281 2.7 48.1 1.0
N A:GLU35 4.0 26.3 1.0
C A:PRO34 4.0 27.2 1.0
O A:PRO34 4.0 27.3 1.0
CB A:PRO34 4.1 27.8 1.0
CA A:GLU35 4.1 28.5 1.0
CG A:GLU35 4.1 32.6 1.0
CG A:PRO38 4.2 30.4 1.0
O A:HOH277 4.5 31.4 1.0
CG B:PRO34 4.7 30.2 1.0
FE A:FE238 4.7 39.2 0.6
CB A:GLU35 4.7 30.9 1.0
CD A:PRO38 4.7 28.0 1.0
CG2 B:THR148 4.7 43.3 1.0
CA A:PRO34 4.7 27.0 1.0
O B:HOH262 4.9 54.9 1.0

Iodine binding site 4 out of 23 in 3nte

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Iodine binding site 4 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I225

b:41.8
occ:0.25
O A:HOH341 2.8 50.7 1.0
N A:PRO1 3.1 36.5 1.0
CD A:PRO1 3.1 40.4 1.0
CG A:PRO1 3.4 39.7 1.0
CB A:PRO1 3.5 38.1 1.0
CA A:PRO1 3.8 36.0 1.0
OD2 A:ASP51 3.9 34.4 1.0
CG1 A:ILE15 4.0 47.2 1.0
CG2 A:ILE15 4.1 45.5 1.0
CG A:ASP51 4.1 30.6 1.0
CA A:ALA47 4.1 27.6 1.0
CA A:ILE15 4.2 38.5 1.0
O A:GLU45 4.2 25.0 1.0
CB A:ILE15 4.3 44.9 1.0
FE A:FE244 4.3 52.1 0.5
N A:ALA47 4.3 27.2 1.0
CB A:ALA47 4.4 25.7 1.0
CB A:ASP51 4.4 25.4 1.0
OD1 A:ASP51 4.5 31.5 1.0
N A:ILE15 4.6 38.7 1.0
C A:GLY46 4.7 30.4 1.0
O A:HOH342 4.7 49.5 1.0
O A:GLY46 4.8 29.7 1.0
CD1 A:ILE15 4.9 49.0 1.0
O A:GLN13 4.9 35.2 1.0

Iodine binding site 5 out of 23 in 3nte

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Iodine binding site 5 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I226

b:60.1
occ:0.30
NH1 A:ARG173 2.9 43.0 0.5
CD A:ARG173 3.2 40.6 0.5
NZ A:LYS182 3.4 37.1 1.0
CZ A:ARG173 3.7 42.0 0.5
CD A:LYS182 3.8 35.1 1.0
NE A:ARG173 3.8 42.6 0.5
CE A:LYS182 4.0 36.3 1.0
O A:HOH298 4.0 37.7 1.0
CA A:ARG173 4.1 36.6 0.5
CA A:ARG173 4.2 36.7 0.5
CG A:ARG173 4.4 37.9 0.5
CG A:ARG173 4.4 38.8 0.5
NE2 A:GLN179 4.5 54.1 1.0
O A:LEU172 4.6 33.7 1.0
CB A:ARG173 4.6 37.5 0.5
CG A:LEU172 4.7 43.9 1.0
N A:ARG173 4.7 35.0 1.0
CD2 A:LEU172 4.7 46.1 1.0
C A:LEU172 4.8 34.3 1.0
CB A:ARG173 4.9 37.2 0.5
O A:ARG173 4.9 40.8 1.0
NH2 A:ARG173 4.9 42.5 0.5
C A:ARG173 5.0 35.7 1.0

Iodine binding site 6 out of 23 in 3nte

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Iodine binding site 6 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I227

b:41.0
occ:0.30
FE A:FE239 2.6 49.4 0.4
N A:LYS158 3.3 39.6 1.0
N A:GLU159 3.7 34.4 1.0
CA A:LYS158 3.8 43.5 1.0
CD A:PRO157 3.8 36.5 1.0
C A:LYS158 3.8 39.9 1.0
CB A:LYS158 3.8 49.0 1.0
CA A:GLY156 3.9 31.0 1.0
N A:PRO157 3.9 36.0 1.0
C A:GLY156 4.0 33.1 1.0
CG A:PRO157 4.1 37.4 1.0
C A:PRO157 4.4 39.3 1.0
CA A:GLU159 4.4 30.6 1.0
CB A:GLU159 4.5 30.9 1.0
O A:LYS158 4.5 40.7 1.0
O A:GLY156 4.6 35.1 1.0
CA A:PRO157 4.7 39.4 1.0
CG A:LYS158 5.0 53.0 1.0
CB A:PRO157 5.0 37.7 1.0

Iodine binding site 7 out of 23 in 3nte

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Iodine binding site 7 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I228

b:40.9
occ:0.52
O A:HOH292 3.1 21.6 1.0
O A:HOH314 3.2 48.6 1.0
FE A:FE241 3.4 47.4 0.7
O A:HOH331 3.6 31.7 1.0
OE2 A:GLU128 4.4 33.3 1.0
CD A:GLU128 4.6 35.3 1.0
CG A:GLU128 4.7 29.9 1.0
CB A:GLU128 5.0 23.8 1.0

Iodine binding site 8 out of 23 in 3nte

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Iodine binding site 8 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I229

b:49.5
occ:0.51
O A:HOH332 2.7 52.7 1.0
O A:HOH333 2.7 50.1 1.0
OD1 A:ASN74 3.2 49.3 1.0
CA A:GLU71 4.0 30.5 1.0
CG A:ASN74 4.1 45.7 1.0
CG A:LYS70 4.3 40.4 1.0
NZ A:LYS70 4.3 56.0 1.0
CB A:ASN74 4.3 38.6 1.0
CB A:GLU71 4.4 37.5 1.0
N A:GLU71 4.4 23.5 1.0
OE1 A:GLU71 4.4 57.4 1.0
NE2 A:GLN67 4.6 41.8 1.0
O A:LYS70 4.6 26.5 1.0
C A:LYS70 4.7 25.8 1.0
CG A:GLU71 4.9 44.2 1.0

Iodine binding site 9 out of 23 in 3nte

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Iodine binding site 9 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I230

b:36.5
occ:0.38
O A:HOH292 3.1 21.6 1.0
O A:HOH331 3.4 31.7 1.0
I A:IOD223 3.6 35.1 0.8
CG1 A:ILE129 3.7 18.7 1.0
CA A:ILE129 4.0 20.7 1.0
CG A:ARG132 4.0 22.0 1.0
O A:GLU128 4.0 21.4 1.0
N A:ILE129 4.0 22.6 1.0
C A:GLU128 4.1 24.0 1.0
CB A:GLU128 4.2 23.8 1.0
O A:HOH260 4.2 26.8 0.8
CB A:ILE129 4.5 19.1 1.0
O A:HOH358 4.8 24.1 0.7
CA A:GLU128 4.8 24.0 1.0
CD1 A:ILE129 4.8 18.8 1.0
CB A:ARG132 5.0 19.3 1.0

Iodine binding site 10 out of 23 in 3nte

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Iodine binding site 10 out of 23 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I231

b:45.2
occ:0.38
O A:HOH336 2.8 29.3 1.0
O A:HOH321 2.8 50.7 1.0
CG2 A:ILE37 3.6 33.0 1.0
CA A:PRO38 4.1 26.4 1.0
O A:ILE37 4.1 24.1 1.0
CB A:SER41 4.1 29.1 1.0
N A:PRO38 4.2 27.2 1.0
C A:ILE37 4.2 26.0 1.0
O A:HOH308 4.3 39.0 0.9
OG A:SER41 4.4 34.2 1.0
CD1 A:ILE135 4.7 26.0 1.0
CB A:ILE37 4.7 34.1 1.0
CD A:PRO38 4.8 28.0 1.0
CG A:PRO38 4.8 30.4 1.0
CB A:PRO38 4.8 26.7 1.0

Reference:

S.Du, L.Betts, R.Yang, H.Shi, J.Concel, J.Ahn, C.Aiken, P.Zhang, J.I.Yeh. Structure of the Hiv-1 Full-Length Capsid Protein in A Conformationally Trapped Unassembled State Induced By Small-Molecule Binding. J.Mol.Biol. V. 406 371 2011.
ISSN: ISSN 0022-2836
PubMed: 21146540
DOI: 10.1016/J.JMB.2010.11.027
Page generated: Sun Dec 13 19:28:35 2020

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