Iodine in PDB 4xfx: Structure of the Native Full-Length Hiv-1 Capsid Protein

The structure of Structure of the Native Full-Length Hiv-1 Capsid Protein, PDB code: 4xfx 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)	19.00 / 2.43
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.328, 92.328, 57.340, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 24.9

The structure of Structure of the Native Full-Length Hiv-1 Capsid Protein 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 (pdb code 4xfx). 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 Native Full-Length Hiv-1 Capsid Protein, PDB code: 4xfx:
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 Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:24.8 occ:0.62 NH1 A:ARG173 3.9 31.8 1.0 CD A:ARG173 4.0 28.2 1.0 OE1 A:GLU35 4.1 36.6 1.0 CG A:LYS170 4.1 41.9 1.0 CG A:PRO34 4.3 31.0 1.0 CB A:PRO34 4.4 31.9 1.0 CA A:LYS170 4.6 33.6 1.0 CB A:LYS170 4.7 38.0 1.0 CD A:PRO34 4.7 32.2 1.0 CZ A:ARG173 4.8 29.2 1.0 OG A:SER33 4.8 41.1 1.0 NE A:ARG173 4.9 29.6 1.0 O A:LYS170 4.9 26.8 1.0 CD A:GLU35 4.9 36.8 1.0 CE A:LYS170 5.0 52.5 1.0

Iodine binding site 2 out of 7 in the Structure of the Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:51.0 occ:0.93 N A:LYS158 3.8 51.6 1.0 N A:GLU159 3.8 43.1 1.0 CD A:PRO157 3.8 54.0 1.0 CA A:GLY156 3.9 45.5 1.0 C A:LYS158 4.0 48.4 1.0 C A:GLY156 4.0 49.4 1.0 N A:PRO157 4.1 51.5 1.0 CA A:LYS158 4.2 53.5 1.0 CB A:LYS158 4.2 59.8 1.0 CB A:GLU159 4.3 41.0 1.0 CA A:GLU159 4.4 40.3 1.0 CG A:PRO157 4.4 55.3 1.0 O A:LYS158 4.7 43.0 1.0 O A:GLY156 4.7 38.6 1.0 C A:PRO157 4.8 50.4 1.0 N A:GLY156 4.9 43.3 1.0 CA A:PRO157 5.0 49.5 1.0

Iodine binding site 3 out of 7 in the Structure of the Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:35.3 occ:0.47 CA A:PRO38 4.0 28.0 1.0 CG2 A:ILE37 4.0 32.7 1.0 N A:PRO38 4.1 27.8 1.0 CB A:SER41 4.2 38.0 1.0 O A:ILE37 4.2 23.7 1.0 C A:ILE37 4.3 27.2 1.0 CD1 A:ILE135 4.5 36.3 1.0 CG A:PRO38 4.6 28.3 1.0 OG A:SER41 4.6 42.2 1.0 CB A:PRO38 4.6 26.9 1.0 CD A:PRO38 4.6 28.5 1.0 CG2 A:ILE135 4.9 29.9 1.0 CB A:ILE37 4.9 32.1 1.0

Iodine binding site 4 out of 7 in the Structure of the Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:89.7 occ:0.61 CB A:ASN21 3.9 37.5 1.0 ND2 A:ASN21 4.0 50.7 1.0 O A:PRO17 4.1 46.8 1.0 C A:PRO17 4.2 41.3 1.0 CA A:ARG18 4.2 52.7 1.0 CG A:ASN21 4.2 43.3 1.0 N A:ARG18 4.3 47.9 1.0 CB A:PRO17 4.4 41.7 1.0 CB A:ARG18 4.4 61.5 1.0 CA A:PRO17 4.9 41.6 1.0

Iodine binding site 5 out of 7 in the Structure of the Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:54.1 occ:0.56 OE1 A:GLN219 3.4 82.1 1.0 O A:HOH446 3.5 25.2 1.0 CD A:ARG162 3.7 66.3 1.0 CD A:GLN219 3.9 88.3 1.0 CE A:MET215 4.0 45.5 1.0 CG A:GLN219 4.1 82.2 1.0 NH1 A:ARG162 4.2 76.4 1.0 O A:HOH466 4.3 35.4 1.0 O A:MET215 4.4 49.9 1.0 CB A:ARG162 4.5 47.0 1.0 CG A:ARG162 4.6 58.4 1.0 CB A:MET215 4.6 47.4 1.0 CB A:GLN219 4.7 73.2 1.0 C A:MET215 4.8 48.8 1.0 NE A:ARG162 4.8 70.0 1.0 NE2 A:GLN219 4.9 95.0 1.0

Iodine binding site 6 out of 7 in the Structure of the Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:70.6 occ:0.49 CA A:ARG173 3.8 27.9 1.0 CG A:LEU172 3.9 27.1 1.0 CD2 A:LEU172 3.9 27.9 1.0 N A:ARG173 3.9 28.5 1.0 C A:LEU172 4.2 26.6 1.0 O A:LEU172 4.3 25.8 1.0 CB A:LEU172 4.3 26.9 1.0 CB A:ARG173 4.4 27.5 1.0 CE A:LYS182 4.5 41.9 1.0 CD A:LYS182 4.5 41.2 1.0 O A:TYR169 4.5 32.3 1.0 CG A:ARG173 4.7 27.4 1.0 NZ A:LYS182 4.8 43.7 1.0 CD1 A:TYR169 4.9 27.4 1.0 CA A:LEU172 4.9 27.7 1.0

Iodine binding site 7 out of 7 in the Structure of the Native 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 Structure of the Native Full-Length Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:93.3 occ:0.67 CD A:PRO17 3.8 41.0 1.0 CB A:SER16 3.9 37.3 1.0 CG A:PRO17 4.2 42.3 1.0 CG A:ARG18 4.2 60.7 1.0 N A:PRO17 4.3 42.0 1.0 CD A:ARG18 4.4 70.2 1.0 N A:ARG18 4.4 47.9 1.0 OG A:SER16 4.5 37.9 1.0 CB A:PRO17 4.5 41.7 1.0 CB A:ARG18 4.7 61.5 1.0 CA A:SER16 4.8 37.8 1.0 C A:SER16 4.9 38.3 1.0 CA A:PRO17 5.0 41.6 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