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Iodine in PDB 5w4o: Structure of the R18A Mutant of the Hiv-1 Capsid Protein

Protein crystallography data

The structure of Structure of the R18A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4o was solved by A.T.Gres, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 2.09
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 92.921, 92.921, 58.053, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 24.6

Other elements in 5w4o:

The structure of Structure of the R18A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein (pdb code 5w4o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5w4o

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Iodine binding site 1 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:48.7
occ:0.94
 CG A:LYS158 3.5 74.7 1.0
N A:LYS158 3.6 54.9 1.0
CD A:PRO157 3.7 50.7 1.0
N A:GLU159 3.8 53.4 1.0
CA A:GLY156 3.8 43.1 1.0
N A:PRO157 3.8 49.4 1.0
C A:GLY156 3.9 45.6 1.0
CE A:LYS158 4.1 90.6 1.0
CG A:PRO157 4.1 58.1 1.0
CB A:LYS158 4.2 67.1 1.0
CA A:LYS158 4.2 58.0 1.0
C A:LYS158 4.2 55.4 1.0
CD A:LYS158 4.3 83.5 1.0
CB A:GLU159 4.3 49.5 1.0
CA A:GLU159 4.4 51.1 1.0
C A:PRO157 4.6 53.0 1.0
O A:GLY156 4.7 44.1 1.0
CA A:PRO157 4.7 52.7 1.0
N A:GLY156 4.9 40.3 1.0

Iodine binding site 2 out of 9 in 5w4o

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Iodine binding site 2 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:45.5
occ:0.78
 NH1 A:ARG173 3.7 48.3 1.0
CG A:LYS170 3.9 58.9 1.0
CD A:ARG173 4.1 45.0 1.0
OE1 A:GLU35 4.1 50.4 1.0
CG A:PRO34 4.4 47.4 1.0
CB A:LYS170 4.5 50.8 1.0
CD A:LYS170 4.5 65.3 1.0
CB A:PRO34 4.6 45.8 1.0
CD A:PRO34 4.6 45.7 1.0
OG A:SER33 4.7 56.8 1.0
CA A:LYS170 4.7 41.6 1.0
CZ A:ARG173 4.7 45.3 1.0
CE A:LYS170 4.7 70.9 1.0
NE A:ARG173 4.8 44.9 1.0
CD A:GLU35 5.0 50.9 1.0

Iodine binding site 3 out of 9 in 5w4o

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Iodine binding site 3 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:52.8
occ:0.52
 CG2 A:ILE37 3.9 45.0 1.0
CA A:PRO38 4.0 44.5 1.0
N A:PRO38 4.1 44.1 1.0
CB A:SER41 4.2 49.3 1.0
O A:ILE37 4.2 41.6 1.0
C A:ILE37 4.3 42.2 1.0
CD1 A:ILE135 4.3 45.0 1.0
CB A:PRO38 4.4 44.6 1.0
OG A:SER41 4.5 52.8 1.0
CD A:PRO38 4.6 43.9 1.0
CG2 A:ILE135 4.7 39.5 1.0
CB A:ILE37 4.8 45.4 1.0

Iodine binding site 4 out of 9 in 5w4o

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Iodine binding site 4 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:57.1
occ:0.55
 CE1 A:TYR145 4.0 65.7 1.0
CG A:MET144 4.2 66.8 1.0
CD1 A:TYR145 4.3 64.5 1.0
CE A:MET144 4.3 72.9 1.0
O A:MET144 4.3 60.3 1.0
SD A:MET144 4.8 67.5 1.0

Iodine binding site 5 out of 9 in 5w4o

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Iodine binding site 5 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:94.0
occ:0.42
 CA A:ASN21 3.8 48.2 1.0
CB A:ASN21 3.8 52.2 1.0
OD1 A:ASN21 3.8 61.1 1.0
O A:HOH502 4.0 52.8 1.0
N A:ASN21 4.0 44.8 1.0
CG A:ASN21 4.3 57.7 1.0
C A:LEU20 4.5 41.0 1.0
CB A:LEU20 4.7 44.6 1.0
O A:HOH500 4.7 60.9 1.0
O A:LEU20 4.9 41.6 1.0
O A:PRO17 4.9 49.2 1.0

Iodine binding site 6 out of 9 in 5w4o

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Iodine binding site 6 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:78.9
occ:0.41
 OG A:SER146 3.3 47.5 1.0
OG1 A:THR148 3.3 61.6 1.0
CD A:PRO147 3.8 55.3 1.0
CB A:ALA174 4.0 46.0 1.0
CA A:THR171 4.2 34.0 1.0
OG1 A:THR171 4.3 39.3 1.0
CB A:SER146 4.3 46.9 1.0
CG A:PRO147 4.4 57.4 1.0
N A:PRO147 4.6 55.3 1.0
N A:THR148 4.6 59.9 1.0
N A:THR171 4.6 35.0 1.0
CB A:THR148 4.7 60.3 1.0
CB A:THR171 4.7 39.4 1.0
CG A:LYS170 4.7 58.9 1.0
CE A:LYS170 4.7 70.9 1.0
O A:LYS170 4.7 39.7 1.0
CA A:SER146 4.7 49.3 1.0
O A:HOH468 4.8 62.6 1.0
CG2 A:THR171 4.8 40.6 1.0
C A:LYS170 4.9 38.6 1.0
C A:SER146 5.0 49.3 1.0
O A:THR148 5.0 52.0 1.0

Iodine binding site 7 out of 9 in 5w4o

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Iodine binding site 7 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:71.7
occ:0.32
 O A:HOH468 3.3 62.6 1.0
NH1 A:ARG167 3.5 41.4 1.0
CL A:CL312 3.6 72.6 1.0
CD A:ARG167 3.8 37.2 1.0
CD1 A:ILE153 4.0 39.5 1.0
CG2 A:THR148 4.3 61.7 1.0
CB A:ARG167 4.4 34.4 1.0
CG A:ARG167 4.4 36.8 1.0
CZ A:ARG167 4.5 41.0 1.0
O A:HOH486 4.5 57.3 1.0
NE A:ARG167 4.6 36.6 1.0

Iodine binding site 8 out of 9 in 5w4o

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Iodine binding site 8 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:64.1
occ:0.43
 CA A:ARG173 3.7 43.5 1.0
O A:HOH484 3.8 57.9 1.0
N A:ARG173 3.9 42.5 1.0
NZ A:LYS182 3.9 62.2 1.0
CG A:LEU172 4.0 42.5 1.0
O A:LEU172 4.0 42.4 1.0
C A:LEU172 4.0 40.0 1.0
CD2 A:LEU172 4.1 42.5 1.0
CB A:ARG173 4.2 43.9 1.0
CD A:LYS182 4.2 62.7 1.0
O A:HOH422 4.4 54.4 1.0
CE A:LYS182 4.5 62.6 1.0
CB A:LEU172 4.5 41.5 1.0
CG A:ARG173 4.5 45.5 1.0
O A:TYR169 4.6 32.0 1.0
CA A:LEU172 5.0 38.4 1.0
C A:ARG173 5.0 42.9 1.0

Iodine binding site 9 out of 9 in 5w4o

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Iodine binding site 9 out of 9 in the Structure of the R18A Mutant of the 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 Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:77.7
occ:0.42
 O A:HOH444 3.3 44.8 1.0
ND2 A:ASN57 3.3 35.9 1.0
CG A:ASN57 4.3 38.5 1.0
CB A:ASN57 4.3 37.3 1.0
OG1 A:THR54 4.4 44.1 1.0
CA A:THR54 4.4 40.1 1.0
O A:ASN53 4.5 34.0 1.0
N A:THR54 4.6 40.4 1.0
C A:ASN53 4.7 38.4 1.0
CB A:THR54 5.0 43.8 1.0

Reference:

P.Craveur, A.T.Gres, K.A.Kirby, D.Liu, J.A.Hammond, Y.Deng, S.Forli, D.S.Goodsell, J.R.Williamson, S.G.Sarafianos, A.J.Olson. Novel Intersubunit Interaction Critical For Hiv-1 Core Assembly Defines A Potentially Targetable Inhibitor Binding Pocket. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 30862755
DOI: 10.1128/MBIO.02858-18
Page generated: Sun Aug 11 22:17:13 2024

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