Iodine in PDB 6axr: Structure of the P122A Mutant of the Hiv-1 Capsid Protein

The structure of Structure of the P122A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axr 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)	46.91 / 2.30
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.728, 92.728, 57.791, 90.00, 90.00, 120.00
R / Rfree (%)	24 / 26.8

The structure of Structure of the P122A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Iodine atom in the Structure of the P122A Mutant of the Hiv-1 Capsid Protein (pdb code 6axr). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Structure of the P122A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axr:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:71.2 occ:0.85 N A:LYS158 3.6 83.5 1.0 CD A:PRO157 3.7 84.9 1.0 CA A:GLY156 3.8 81.8 1.0 N A:GLU159 3.8 76.2 1.0 N A:PRO157 3.9 82.7 1.0 CB A:LYS158 4.0 88.5 1.0 C A:GLY156 4.0 82.3 1.0 CA A:LYS158 4.1 83.8 1.0 C A:LYS158 4.1 80.8 1.0 CG A:PRO157 4.3 85.7 1.0 CB A:GLU159 4.4 71.1 1.0 CA A:GLU159 4.5 72.5 1.0 C A:PRO157 4.6 82.1 1.0 O A:GLY156 4.7 81.7 1.0 CA A:PRO157 4.8 83.0 1.0 CG A:LYS158 4.8 91.8 1.0 N A:GLY156 4.9 78.0 1.0 O A:LYS158 5.0 81.9 1.0

Iodine binding site 2 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:54.4 occ:0.61 NH1 A:ARG173 3.8 53.1 1.0 CG A:LYS170 4.0 73.3 1.0 OE1 A:GLU35 4.0 73.5 1.0 CD A:ARG173 4.1 52.8 1.0 OG A:SER33 4.6 74.1 1.0 CB A:LYS170 4.6 67.5 1.0 CD A:PRO34 4.6 65.4 1.0 CG A:PRO34 4.6 65.3 1.0 CA A:LYS170 4.6 62.5 1.0 CD A:LYS170 4.7 78.1 1.0 CZ A:ARG173 4.7 53.2 1.0 CE A:LYS170 4.8 82.3 1.0 CB A:PRO34 4.8 65.6 1.0 NE A:ARG173 4.9 53.1 1.0

Iodine binding site 3 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:64.8 occ:0.47 CA A:PRO38 3.9 64.0 1.0 CG2 A:ILE37 3.9 59.9 1.0 N A:PRO38 4.1 62.2 1.0 CB A:SER41 4.2 62.9 1.0 CD1 A:ILE135 4.2 56.3 1.0 O A:ILE37 4.3 58.1 1.0 C A:ILE37 4.3 59.6 1.0 CB A:PRO38 4.3 65.8 1.0 OG A:SER41 4.6 62.7 1.0 CD A:PRO38 4.6 62.9 1.0 CG2 A:ILE135 4.7 55.3 1.0 CB A:ILE37 4.8 60.7 1.0

Iodine binding site 4 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:60.8 occ:0.40 CG A:MET144 3.7 82.5 1.0 SD A:MET144 4.0 81.9 1.0 CE1 A:TYR145 4.2 91.4 1.0 CD1 A:TYR145 4.5 91.1 1.0 O A:MET144 4.5 81.2 1.0

Iodine binding site 5 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:72.0 occ:0.37 CE A:LYS182 3.7 73.3 1.0 CA A:ARG173 3.9 55.1 1.0 N A:ARG173 3.9 56.6 1.0 CD A:LYS182 4.1 73.4 1.0 CB A:ARG173 4.2 54.5 1.0 CD2 A:LEU172 4.2 57.6 1.0 CG A:LEU172 4.2 57.6 1.0 C A:LEU172 4.3 56.3 1.0 O A:LEU172 4.4 55.7 1.0 O A:TYR169 4.5 56.9 1.0 CB A:LEU172 4.6 57.7 1.0 CG A:ARG173 4.6 53.9 1.0 O A:HOH433 4.7 61.0 1.0 CD1 A:TYR169 4.8 56.9 1.0 NZ A:LYS182 5.0 74.2 1.0

Iodine binding site 6 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:0.2 occ:0.45 NH1 A:ARG18 3.3 0.0 1.0 CG A:ARG18 4.0 0.1 1.0 CD A:ARG18 4.1 0.3 1.0 CB A:ALA22 4.4 70.4 1.0 CZ A:ARG18 4.5 0.9 1.0 NE A:ARG18 4.8 0.8 1.0 O A:ARG18 4.9 81.0 1.0

Iodine binding site 7 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:85.3 occ:0.37 CD A:ARG18 3.6 0.3 1.0 NE A:ARG18 4.0 0.8 1.0 CG A:ARG18 4.8 0.1 1.0

Iodine binding site 8 out of 8 in the Structure of the P122A 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 P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:0.8 occ:0.52 CD A:PRO125 4.3 89.3 1.0 CH2 A:TRP80 4.3 64.6 1.0 CD1 A:ILE129 4.4 62.9 1.0 CG2 A:ILE124 4.5 0.3 1.0 CA A:ILE124 4.7 0.8 1.0 CG1 A:ILE124 4.9 1.0 1.0 CZ3 A:TRP80 4.9 66.0 1.0 O A:PRO123 4.9 0.5 1.0 O A:HOH439 4.9 72.6 1.0 CB A:ILE124 5.0 0.2 1.0

M.Novikova, L.J.Adams, J.Fontana, A.T.Gres, M.Balasubramaniam, D.C.Winkler, S.B.Kudchodkar, F.Soheilian, S.G.Sarafianos, A.C.Steven, E.O.Freed. Identification of A Structural Element in Hiv-1 Gag Required For Virus Particle Assembly and Maturation. Mbio V. 9 2018.
ISSN: ESSN 2150-7511
PubMed: 30327442
DOI: 10.1128/MBIO.01567-18