Iodine in PDB 4xfz: Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)

The structure of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74), PDB code: 4xfz 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)	45.00 / 2.70
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.181, 92.181, 56.976, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.1

The structure of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iodine atom in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) (pdb code 4xfz). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74), PDB code: 4xfz:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


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 Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:60.3 occ:0.75 NH1 A:ARG173 3.5 60.9 1.0 CG A:LYS170 3.8 72.2 1.0 CD A:ARG173 4.0 54.6 1.0 OE1 A:GLU35 4.3 71.2 1.0 CG A:PRO34 4.3 71.5 1.0 NZ A:LYS170 4.4 93.6 1.0 CD A:PRO34 4.5 69.8 1.0 CZ A:ARG173 4.5 59.1 1.0 CB A:LYS170 4.6 66.8 1.0 CA A:LYS170 4.6 62.8 1.0 NE A:ARG173 4.7 57.4 1.0 CB A:PRO34 4.8 71.3 1.0 O A:LYS170 4.9 64.8 1.0

Iodine binding site 2 out of 6 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


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 Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:90.0 occ:0.78 CD A:PRO157 3.6 98.8 1.0 N A:LYS158 3.6 0.4 1.0 CA A:GLY156 3.7 86.0 1.0 C A:GLY156 3.8 87.5 1.0 N A:PRO157 3.8 94.3 1.0 N A:GLU159 3.9 94.6 1.0 CB A:LYS158 4.1 0.1 1.0 C A:LYS158 4.1 100.0 1.0 CA A:LYS158 4.1 0.6 1.0 CB A:GLU159 4.2 86.0 1.0 CA A:GLU159 4.3 88.6 1.0 CG A:PRO157 4.4 0.2 1.0 O A:GLY156 4.5 83.4 1.0 C A:PRO157 4.7 93.6 1.0 N A:GLY156 4.7 82.8 1.0 CA A:PRO157 4.8 94.7 1.0 O A:LYS158 4.9 0.0 1.0

Iodine binding site 3 out of 6 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


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 Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:99.8 occ:0.67 CG2 A:ILE37 4.1 68.4 1.0 CA A:PRO38 4.1 68.0 1.0 N A:PRO38 4.2 64.2 1.0 CB A:SER41 4.3 67.0 1.0 O A:ILE37 4.4 66.4 1.0 C A:ILE37 4.5 64.3 1.0 OG A:SER41 4.5 69.3 1.0 CB A:PRO38 4.6 69.2 1.0 CG A:PRO38 4.6 72.1 1.0 CD A:PRO38 4.6 67.2 1.0 CD1 A:ILE135 4.9 77.1 1.0 CG2 A:ILE135 5.0 66.8 1.0

Iodine binding site 4 out of 6 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


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 Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:0.3 occ:0.71 CD A:PRO17 3.8 83.1 1.0 CB A:SER16 4.0 72.7 1.0 CG A:PRO17 4.2 87.0 1.0 N A:PRO17 4.4 77.9 1.0 N A:ARG18 4.4 79.8 1.0 OG A:SER16 4.4 74.7 1.0 CG A:ARG18 4.5 88.2 1.0 CB A:ARG18 4.5 84.5 1.0 CD A:ARG18 4.5 97.1 1.0 CB A:PRO17 4.7 85.1 1.0 CA A:SER16 4.8 73.4 1.0 C A:SER16 4.9 72.7 1.0

Iodine binding site 5 out of 6 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


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 Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:96.3 occ:0.49 O A:HOH428 3.6 58.3 1.0 NE2 A:GLN219 3.7 0.7 1.0 NH1 A:ARG162 4.1 0.3 1.0 O A:MET215 4.2 89.5 1.0 CG A:GLN219 4.2 0.5 1.0 CD A:ARG162 4.4 0.3 1.0 CE A:MET215 4.4 86.5 1.0 CD A:GLN219 4.4 0.2 1.0 O A:HOH417 4.4 52.4 1.0 CB A:ARG162 4.5 86.3 1.0 CB A:MET215 4.6 79.8 1.0 C A:MET215 4.7 89.6 1.0 CG A:ARG162 4.7 92.4 1.0 CB A:GLN219 4.8 0.8 1.0

Iodine binding site 6 out of 6 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


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 Native Full-Length Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:0.8 occ:0.63 ND2 A:ASN21 3.7 0.9 1.0 CB A:ASN21 4.1 84.0 1.0 CG A:ASN21 4.1 96.7 1.0 O A:PRO17 4.3 80.2 1.0 CA A:ARG18 4.3 80.0 1.0 N A:ARG18 4.4 79.8 1.0 C A:PRO17 4.4 78.4 1.0 CB A:ARG18 4.5 84.5 1.0 CB A:PRO17 4.6 85.1 1.0 OD1 A:ASN21 5.0 0.5 1.0

A.T.Gres, K.A.Kirby, V.N.Kewalramani, J.J.Tanner, O.Pornillos, S.G.Sarafianos. Structural Virology. X-Ray Crystal Structures of Native Hiv-1 Capsid Protein Reveal Conformational Variability. Science V. 349 99 2015.
ISSN: ESSN 1095-9203
PubMed: 26044298
DOI: 10.1126/SCIENCE.AAA5936