Iodine in PDB 5w4p: Structure of the E28A Mutant of the Hiv-1 Capsid Protein

The structure of Structure of the E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4p 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)	46.34 / 2.19
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.672, 92.672, 57.969, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.6

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

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Structure of the E28A Mutant of the Hiv-1 Capsid Protein (pdb code 5w4p). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Structure of the E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4p:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:58.7 occ:0.94 N A:LYS158 3.7 63.2 1.0 N A:GLU159 3.8 58.6 1.0 CA A:GLY156 3.9 57.7 1.0 CD A:PRO157 3.9 64.1 1.0 N A:PRO157 4.1 62.6 1.0 C A:LYS158 4.1 66.1 1.0 CB A:LYS158 4.1 71.6 1.0 C A:GLY156 4.1 59.1 1.0 CA A:LYS158 4.1 65.8 1.0 CB A:GLU159 4.3 58.2 1.0 CA A:GLU159 4.4 60.6 1.0 CG A:PRO157 4.4 66.0 1.0 C A:PRO157 4.8 64.4 1.0 O A:GLY156 4.8 59.5 1.0 O A:LYS158 4.9 63.6 1.0 N A:GLY156 4.9 55.3 1.0 CA A:PRO157 4.9 63.3 1.0

Iodine binding site 2 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:54.6 occ:0.75 CG A:PRO34 3.8 56.4 1.0 NH1 A:ARG173 3.9 47.7 1.0 OE1 A:GLU35 3.9 68.5 1.0 CG A:LYS170 4.0 56.7 1.0 CD A:ARG173 4.1 47.1 1.0 OG A:SER33 4.5 73.5 1.0 CD A:PRO34 4.6 55.1 1.0 CB A:LYS170 4.6 50.8 1.0 CD A:LYS170 4.7 62.8 1.0 CA A:LYS170 4.7 46.7 1.0 CE A:LYS170 4.8 68.5 1.0 CZ A:ARG173 4.8 48.0 1.0 CD A:GLU35 4.8 67.1 1.0 NE A:ARG173 4.9 50.2 1.0 CB A:PRO34 4.9 54.0 1.0

Iodine binding site 3 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:57.9 occ:0.55 O A:HOH445 3.3 52.2 1.0 NE2 A:GLN219 3.5 96.4 1.0 CG A:GLN219 3.6 93.4 1.0 NH2 A:ARG162 3.9 78.2 1.0 NE A:ARG162 4.0 73.9 1.0 CD A:GLN219 4.0 97.4 1.0 CE A:MET215 4.0 57.7 1.0 O A:MET215 4.3 58.4 1.0 CZ A:ARG162 4.4 76.7 1.0 CL A:CL314 4.4 65.7 0.9 CB A:MET215 4.6 58.4 1.0 CB A:ARG162 4.7 61.1 1.0 C A:MET215 4.9 60.5 1.0 CB A:GLN219 5.0 91.1 1.0

Iodine binding site 4 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:61.0 occ:0.59 CG2 A:ILE37 3.8 51.8 1.0 CA A:PRO38 3.9 48.8 1.0 CB A:SER41 4.0 61.8 1.0 N A:PRO38 4.1 48.5 1.0 O A:ILE37 4.1 45.5 1.0 O A:HOH485 4.1 69.0 1.0 C A:ILE37 4.2 46.8 1.0 CD1 A:ILE135 4.3 52.0 1.0 O A:HOH413 4.4 71.9 1.0 OG A:SER41 4.4 64.2 1.0 CB A:PRO38 4.4 50.4 1.0 CD A:PRO38 4.7 48.6 1.0 CG2 A:ILE135 4.7 46.0 1.0 CB A:ILE37 4.7 53.8 1.0

Iodine binding site 5 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:70.0 occ:0.49 CA A:ARG173 3.8 46.7 1.0 NZ A:LYS182 3.8 63.1 1.0 N A:ARG173 3.9 49.5 1.0 CG A:LEU172 4.0 48.3 1.0 C A:LEU172 4.1 49.7 1.0 O A:LEU172 4.1 49.6 1.0 CD A:LYS182 4.1 63.6 1.0 CD2 A:LEU172 4.2 46.9 1.0 CB A:ARG173 4.2 47.4 1.0 CE A:LYS182 4.4 61.4 1.0 CB A:LEU172 4.5 47.7 1.0 O A:TYR169 4.7 43.2 1.0 CG A:ARG173 4.7 47.5 1.0 O A:HOH427 4.7 58.1 1.0 CA A:LEU172 5.0 46.4 1.0 CD1 A:TYR169 5.0 43.6 1.0

Iodine binding site 6 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:0.6 occ:0.62 NH2 A:ARG18 3.4 0.1 1.0 NE A:ARG18 3.5 96.7 1.0 CZ A:ARG18 3.9 0.3 1.0 CB A:ARG18 4.4 74.8 1.0 O A:ARG18 4.6 58.7 1.0 CD A:ARG18 4.6 89.7 1.0 CG A:ARG18 4.7 80.3 1.0 CB A:ALA22 4.9 55.4 1.0

Iodine binding site 7 out of 12 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:0.2 occ:0.57 CD A:PRO17 3.7 62.3 1.0 CG A:ARG18 3.9 80.3 1.0 CD A:ARG18 3.9 89.7 1.0 CB A:SER16 3.9 68.9 1.0 N A:PRO17 4.2 61.0 1.0 N A:ARG18 4.3 62.5 1.0 CG A:PRO17 4.4 63.2 1.0 OG A:SER16 4.4 67.5 1.0 CB A:ARG18 4.6 74.8 1.0 CB A:PRO17 4.7 62.9 1.0 CA A:SER16 4.8 68.8 1.0 C A:SER16 4.8 64.4 1.0 CA A:PRO17 4.9 61.7 1.0

Iodine binding site 8 out of 12 in the Structure of the 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 8 of Structure of the E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:0.2 occ:0.57 CL A:CL317 3.6 0.0 1.0 CG2 A:ILE124 3.8 69.5 1.0 CL A:CL315 4.0 82.5 1.0 CA A:ILE124 4.1 76.0 1.0 CD A:PRO125 4.2 68.3 1.0 CB A:ILE124 4.3 73.2 1.0 CG1 A:ILE124 4.3 78.2 1.0 O A:PRO123 4.5 0.2 1.0 CH2 A:TRP80 4.5 63.7 1.0 O A:HOH511 4.7 72.8 1.0 CD1 A:ILE129 4.8 58.5 1.0 C A:ILE124 4.8 70.9 1.0 N A:PRO125 4.8 68.4 1.0

Iodine binding site 9 out of 12 in the Structure of the 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 9 of Structure of the E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I309 b:78.7 occ:0.46 CG A:ASN57 3.6 47.5 1.0 CB A:ASN57 3.8 43.7 1.0 ND2 A:ASN57 3.9 46.8 1.0 OD1 A:ASN57 4.0 47.4 1.0 CA A:ASN57 4.8 39.3 1.0 O A:ASN57 5.0 36.3 1.0

Iodine binding site 10 out of 12 in the Structure of the 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 10 of Structure of the E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I310 b:78.6 occ:0.33 O A:HOH429 3.5 52.1 1.0 CL A:CL316 3.7 71.6 1.0 CD1 A:ILE153 3.9 47.5 1.0 O A:ASP152 4.1 61.0 1.0 CG2 A:THR148 4.2 73.3 1.0 NH1 A:ARG167 4.3 52.6 1.0 C A:ASP152 4.6 59.7 1.0 CB A:ASP152 4.7 67.2 1.0 CB A:THR148 4.8 72.1 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