Iodine in PDB 7m9f: Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261

The structure of Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261, PDB code: 7m9f was solved by 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)	45.71 / 2.70
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	90.9, 90.9, 56.14, 90, 90, 120
R / Rfree (%)	16.9 / 25.3

The structure of Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 (pdb code 7m9f). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261, PDB code: 7m9f:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261


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 Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:75.0 occ:0.85 N A:GLY61 3.7 57.5 1.0 CA A:GLY60 3.7 51.5 1.0 CG A:GLN63 4.0 37.2 1.0 NE2 A:GLN63 4.1 49.5 1.0 CD A:GLN63 4.1 44.4 1.0 C A:GLY60 4.3 59.6 1.0 O A:VAL59 4.7 67.3 1.0 CA A:GLY61 4.8 56.3 1.0 OE1 A:GLN63 4.8 43.6 1.0 N A:GLY60 5.0 50.0 1.0

Iodine binding site 2 out of 5 in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261


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 Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:174.1 occ:0.52 ND2 A:ASN21 3.2 88.8 1.0 NH2 A:ARG18 4.0 97.7 1.0 CG A:ASN21 4.6 75.1 1.0 CZ A:ARG18 4.7 105.5 1.0

Iodine binding site 3 out of 5 in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261


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 Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:118.2 occ:0.78 O A:HOH411 3.3 49.1 1.0

Iodine binding site 4 out of 5 in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261


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 Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:92.4 occ:0.52 NH1 A:ARG162 3.1 100.8 1.0 CZ A:ARG162 3.5 106.7 1.0 CE A:MET215 3.7 78.8 1.0 NE2 A:GLN219 3.8 128.0 1.0 NH2 A:ARG162 4.0 123.8 1.0 NE A:ARG162 4.0 105.3 1.0 CD A:ARG162 4.3 94.4 1.0 CB A:ARG162 4.4 58.9 1.0 CB A:MET215 4.5 72.2 1.0 CD A:GLN219 4.5 126.8 1.0 O A:MET215 4.6 61.8 1.0 CG A:GLN219 4.7 128.1 1.0 C A:MET215 4.9 60.5 1.0 CG A:ARG162 4.9 78.6 1.0

Iodine binding site 5 out of 5 in the Structure of the Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261


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 Wild-Type Native Full-Length Hiv-1 Capsid Protein in Complex with Zw-1261 within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:79.5 occ:0.41 N A:LYS158 3.1 80.7 1.0 CA A:GLY156 3.2 68.0 1.0 N A:PRO157 3.3 85.5 1.0 CD A:PRO157 3.4 83.4 1.0 C A:GLY156 3.4 75.0 1.0 N A:GLU159 3.4 82.8 1.0 CA A:LYS158 3.6 93.3 1.0 CB A:LYS158 3.7 102.9 1.0 C A:LYS158 3.7 88.4 1.0 CG A:PRO157 3.8 80.5 1.0 C A:PRO157 4.1 78.5 1.0 O A:GLY156 4.2 80.2 1.0 CA A:PRO157 4.2 86.0 1.0 CB A:GLU159 4.2 76.7 1.0 CA A:GLU159 4.2 74.9 1.0 N A:GLY156 4.4 60.4 1.0 O A:LYS158 4.5 95.6 1.0 CB A:PRO157 4.6 82.4 1.0 CG A:LYS158 4.6 116.8 1.0

Q.Sun, R.M.Levy, K.A.Kirby, Z.Wang, S.G.Sarafianos, N.Deng. Molecular Dynamics Free Energy Simulations Reveal the Mechanism For the Antiviral Resistance of the M66I Hiv-1 Capsid Mutation. Viruses V. 13 2021.
ISSN: ESSN 1999-4915
PubMed: 34063519
DOI: 10.3390/V13050920