Iodine in PDB 5w4q: Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein

The structure of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4q 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)	47.03 / 2.29
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.055, 92.055, 58.253, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.5

The structure of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Iodine atom in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein (pdb code 5w4q). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4q:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:56.9 occ:0.91 N A:ALA92 3.6 72.5 1.0 CB A:GLN95 3.7 87.7 1.0 CG A:GLN95 3.8 93.8 1.0 CB A:ALA92 3.9 77.0 1.0 CA A:ALA92 4.3 76.7 1.0 CA A:ILE91 4.4 69.2 1.0 CD A:GLN95 4.5 95.2 1.0 C A:ILE91 4.5 69.1 1.0 CG2 A:ILE91 4.6 59.8 1.0 CD1 A:ILE91 4.8 63.7 1.0 O A:PRO90 4.8 77.9 1.0 OE1 A:GLN95 4.8 94.9 1.0

Iodine binding site 2 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:46.0 occ:0.63 OE1 A:GLU35 3.7 64.0 1.0 NH1 A:ARG173 3.7 46.2 1.0 CG A:LYS170 3.9 57.2 1.0 NZ A:LYS170 4.0 74.7 1.0 CD A:ARG173 4.1 34.5 1.0 OG A:SER33 4.4 69.6 1.0 CG A:PRO34 4.5 52.9 1.0 CD A:PRO34 4.5 49.0 1.0 CB A:LYS170 4.7 52.2 1.0 CB A:PRO34 4.7 47.6 1.0 CZ A:ARG173 4.7 46.3 1.0 CA A:LYS170 4.7 47.1 1.0 CD A:GLU35 4.7 61.7 1.0 CE A:LYS170 4.8 67.8 1.0 NE A:ARG173 4.8 45.8 1.0 CD A:LYS170 4.9 59.6 1.0

Iodine binding site 3 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:62.6 occ:0.57 O A:HOH452 3.1 57.9 1.0 NE2 A:GLN219 3.6 98.4 1.0 NH2 A:ARG162 3.6 74.9 1.0 CG A:GLN219 3.6 94.8 1.0 NE A:ARG162 3.8 74.7 1.0 CE A:MET215 3.9 53.8 1.0 CD A:GLN219 4.1 97.8 1.0 CZ A:ARG162 4.1 75.0 1.0 O A:MET215 4.3 61.5 1.0 CL A:CL312 4.4 81.2 1.0 CB A:MET215 4.6 55.1 1.0 CB A:ARG162 4.7 48.0 1.0 C A:MET215 4.9 62.5 1.0 CD A:ARG162 5.0 70.0 1.0 CB A:GLN219 5.0 91.2 1.0 CG A:ARG162 5.0 59.7 1.0

Iodine binding site 4 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:67.5 occ:0.61 CG2 A:ILE37 3.8 43.5 1.0 O A:HOH457 3.9 62.3 1.0 CA A:PRO38 3.9 40.8 1.0 N A:PRO38 4.1 41.2 1.0 CB A:SER41 4.1 51.4 1.0 O A:ILE37 4.1 39.0 1.0 C A:ILE37 4.2 40.6 1.0 CD1 A:ILE135 4.2 46.5 1.0 CB A:PRO38 4.4 48.8 1.0 OG A:SER41 4.4 58.1 1.0 CD A:PRO38 4.6 44.6 1.0 CG2 A:ILE135 4.6 33.8 1.0 CB A:ILE37 4.7 49.5 1.0 CG1 A:ILE135 5.0 36.5 1.0

Iodine binding site 5 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:85.5 occ:0.43 OE2 A:GLU29 3.3 98.3 1.0 CG2 A:VAL26 3.9 54.8 1.0 CB A:VAL26 4.0 45.3 1.0 CE A:LYS30 4.2 67.1 1.0 CA A:VAL26 4.2 48.1 1.0 CD A:GLU29 4.2 94.4 1.0 CD A:LYS30 4.6 66.4 1.0 OE1 A:GLU29 4.7 96.5 1.0 N A:VAL26 4.7 50.6 1.0 CG A:LYS30 4.7 64.0 1.0 NZ A:LYS30 4.8 73.4 1.0 CB A:GLU29 4.9 68.6 1.0

Iodine binding site 6 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:68.4 occ:0.38 NZ A:LYS182 3.4 76.0 1.0 CA A:ARG173 3.6 44.3 1.0 N A:ARG173 3.8 50.8 1.0 CE A:LYS182 3.9 72.7 1.0 CB A:ARG173 4.0 40.7 1.0 CG A:LEU172 4.1 50.4 1.0 C A:LEU172 4.1 49.0 1.0 CD2 A:LEU172 4.2 44.9 1.0 O A:LEU172 4.2 45.1 1.0 CB A:LEU172 4.5 46.3 1.0 CG A:ARG173 4.5 36.0 1.0 CD A:LYS182 4.5 73.7 1.0 O A:TYR169 4.5 46.9 1.0 O A:HOH417 4.5 55.4 1.0 C A:ARG173 5.0 42.9 1.0 CA A:LEU172 5.0 45.8 1.0

Iodine binding site 7 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:88.2 occ:0.37 O A:HOH429 3.4 54.0 1.0 O A:ASP152 3.7 62.4 1.0 CL A:CL313 3.8 71.0 1.0 CD1 A:ILE153 3.9 44.9 1.0 CG2 A:THR148 4.1 74.8 1.0 NH2 A:ARG167 4.2 51.2 1.0 C A:ASP152 4.5 57.5 1.0 CB A:ASP152 4.7 59.1 1.0 CB A:THR148 4.9 73.1 1.0 CA A:ILE153 4.9 49.4 1.0

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