Chlorine in PDB 5w4o: Structure of the R18A Mutant of the Hiv-1 Capsid Protein

The structure of Structure of the R18A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4o 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)	46.46 / 2.09
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.921, 92.921, 58.053, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 24.6

The structure of Structure of the R18A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Iodine

(I)

9 atoms

The binding sites of Chlorine atom in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein (pdb code 5w4o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl310 b:47.0 occ:1.00 O A:GLY60 2.8 45.8 1.0 O A:HOH503 3.0 72.2 1.0 O A:HOH470 3.2 49.3 1.0 CD2 A:HIS62 3.6 47.6 1.0 NE2 A:HIS62 3.8 48.1 1.0 CG A:GLU28 3.9 67.1 1.0 C A:GLY60 4.0 45.3 1.0 CG1 A:VAL27 4.1 46.5 1.0 CA A:GLU28 4.2 56.1 1.0 N A:GLU28 4.4 49.8 1.0 O A:VAL27 4.5 45.1 1.0 N A:GLY60 4.5 39.9 1.0 C A:VAL27 4.5 45.9 1.0 CG1 A:VAL59 4.6 40.4 1.0 CB A:GLU28 4.6 62.2 1.0 O A:HOH489 4.6 67.1 1.0 CA A:GLY60 4.8 42.2 1.0 CG A:HIS62 4.9 47.2 1.0 CB A:VAL27 4.9 44.4 1.0 N A:GLY61 5.0 46.1 1.0

Chlorine binding site 2 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl311 b:65.2 occ:1.00 O A:HOH417 3.6 48.8 1.0 CL A:CL315 3.9 91.3 1.0 CG2 A:ILE124 4.0 57.4 1.0 CH2 A:TRP80 4.2 51.5 1.0 CD A:PRO125 4.3 62.4 1.0 CG1 A:ILE124 4.5 61.9 1.0 CA A:ILE124 4.5 66.8 1.0 CB A:ILE124 4.5 61.9 1.0 CD1 A:ILE129 4.7 46.5 1.0 CZ2 A:TRP80 4.8 50.8 1.0

Chlorine binding site 3 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl312 b:72.6 occ:1.00 O A:HOH427 3.4 38.5 1.0 I A:IOD307 3.6 71.7 0.3 CD1 A:ILE153 3.9 39.5 1.0 O A:ASP152 4.0 55.0 1.0 CG2 A:THR148 4.1 61.7 1.0 NH1 A:ARG167 4.3 41.4 1.0 C A:ASP152 4.6 53.4 1.0 CB A:THR148 4.8 60.3 1.0 CB A:ASP152 4.8 58.9 1.0 O A:HOH478 4.9 50.2 1.0

Chlorine binding site 4 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl313 b:52.9 occ:1.00 O A:HOH435 2.8 48.4 1.0 NH2 A:ARG173 3.4 44.3 1.0 CG A:PRO38 4.3 45.7 1.0 CZ A:ARG173 4.3 45.3 1.0 NE A:ARG173 4.3 44.9 1.0 CD A:PRO38 4.4 43.9 1.0 O A:HOH460 4.4 57.7 1.0 CB A:PRO38 4.7 44.6 1.0

Chlorine binding site 5 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl314 b:94.4 occ:1.00 N A:PHE32 3.1 58.9 1.0 CB A:ALA31 3.4 60.6 1.0 CB A:PHE32 3.5 54.8 1.0 CA A:PHE32 3.6 55.0 1.0 C A:PHE32 3.7 51.3 1.0 O A:PHE32 3.9 51.8 1.0 CB A:TYR145 4.0 57.7 1.0 CD2 A:TYR145 4.1 63.2 1.0 CD2 A:PHE32 4.2 51.4 1.0 C A:ALA31 4.2 61.4 1.0 O A:HOH421 4.3 45.7 1.0 N A:SER33 4.3 49.6 1.0 CG A:PHE32 4.3 53.5 1.0 CA A:ALA31 4.5 60.2 1.0 CG A:TYR145 4.6 62.1 1.0 O A:TYR145 4.6 54.0 1.0 O A:LYS30 4.8 60.5 1.0

Chlorine binding site 6 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl315 b:91.3 occ:1.00 O A:HOH511 3.5 58.4 1.0 CD1 A:ILE129 3.7 46.5 1.0 CL A:CL311 3.9 65.2 1.0 CG1 A:ILE129 4.2 48.0 1.0 CZ3 A:TRP80 4.2 50.1 1.0 CH2 A:TRP80 4.3 51.5 1.0 NH2 A:ARG132 4.7 73.1 1.0

Chlorine binding site 7 out of 7 in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl316 b:76.5 occ:1.00 O A:HOH434 2.7 42.6 1.0 N A:ARG162 3.5 41.9 1.0 N A:PHE161 3.6 43.1 1.0 CB A:ARG162 3.8 51.0 1.0 O A:HOH431 3.9 54.7 1.0 CB A:PRO160 4.1 49.5 1.0 O A:GLN219 4.1 87.2 1.0 CB A:PHE161 4.2 40.7 1.0 CA A:ARG162 4.2 44.2 1.0 CA A:PHE161 4.3 42.7 1.0 C A:PRO160 4.3 49.0 1.0 CA A:GLN219 4.3 79.6 1.0 O A:CYS218 4.3 66.2 1.0 C A:PHE161 4.3 41.6 1.0 CA A:PRO160 4.4 49.3 1.0 C A:GLN219 4.7 85.5 1.0 CG A:GLN219 4.8 86.0 1.0 NE A:ARG162 4.9 70.4 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