Chlorine in PDB 5w4q: Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein

The structure of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4q 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)	47.03 / 2.29
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.055, 92.055, 58.253, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.5

The structure of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Iodine

(I)

7 atoms

The binding sites of Chlorine atom in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein (pdb code 5w4q). 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/E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4q:
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/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:40.9 occ:0.95 O A:GLY60 2.7 52.5 1.0 ND1 A:HIS62 3.6 57.9 1.0 CE1 A:HIS62 3.7 57.4 1.0 C A:GLY60 3.9 53.5 1.0 O A:HOH428 4.1 63.3 1.0 CG1 A:VAL27 4.2 58.5 1.0 CA A:ALA28 4.3 56.1 1.0 N A:GLY60 4.4 48.4 1.0 N A:ALA28 4.6 52.5 1.0 CG1 A:VAL59 4.7 39.2 1.0 CA A:GLY60 4.7 50.9 1.0 O A:VAL27 4.7 45.2 1.0 CB A:ALA28 4.7 55.2 1.0 C A:VAL27 4.7 51.8 1.0 N A:GLY61 4.8 52.8 1.0 CA A:GLY61 4.9 50.4 1.0 CG A:HIS62 4.9 56.7 1.0 C A:GLY61 5.0 38.1 1.0 NE2 A:HIS62 5.0 57.8 1.0

Chlorine binding site 2 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl309 b:94.5 occ:1.00 O A:HOH478 3.1 74.3 1.0 CL A:CL311 3.6 96.4 1.0 CD1 A:ILE129 3.7 61.4 1.0 CG1 A:ILE129 4.2 62.1 1.0 CZ3 A:TRP80 4.3 62.4 1.0 CH2 A:TRP80 4.4 62.3 1.0 NH1 A:ARG132 4.9 74.5 1.0 CG A:PRO125 4.9 59.0 1.0 CD A:PRO125 5.0 62.1 1.0

Chlorine binding site 3 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl310 b:65.5 occ:1.00 O A:HOH439 2.7 54.5 1.0 NH2 A:ARG173 3.3 47.5 1.0 O A:HOH453 4.1 65.6 1.0 NE A:ARG173 4.2 45.8 1.0 CZ A:ARG173 4.2 46.3 1.0 CG A:PRO38 4.3 51.5 1.0 CD A:PRO38 4.4 44.6 1.0 CB A:PRO38 4.6 48.8 1.0

Chlorine binding site 4 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl311 b:96.4 occ:1.00 CL A:CL309 3.6 94.5 1.0 O A:HOH440 3.8 45.3 1.0 CH2 A:TRP80 4.3 62.3 1.0 CG2 A:ILE124 4.5 72.5 1.0 CD A:PRO125 4.7 62.1 1.0

Chlorine binding site 5 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl312 b:81.2 occ:1.00 O A:HOH452 3.0 57.9 1.0 O A:GLN219 3.7 92.5 1.0 O A:HOH408 4.0 64.7 1.0 N A:ARG162 4.0 45.1 1.0 CB A:PRO160 4.0 53.5 1.0 N A:PHE161 4.1 43.6 1.0 CB A:ARG162 4.2 48.0 1.0 CA A:GLN219 4.2 85.4 1.0 O A:CYS218 4.3 67.7 1.0 C A:GLN219 4.4 91.8 1.0 I A:IOD303 4.4 62.6 0.6 CA A:PRO160 4.5 50.2 1.0 C A:PRO160 4.6 46.5 1.0 CA A:ARG162 4.7 48.6 1.0 CA A:PHE161 4.8 45.3 1.0 CB A:PHE161 4.8 38.9 1.0 CG A:GLN219 4.9 94.8 1.0 NE A:ARG162 4.9 74.7 1.0 C A:PHE161 4.9 45.4 1.0

Chlorine binding site 6 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl313 b:71.0 occ:1.00 O A:HOH479 3.0 53.5 1.0 NH2 A:ARG167 3.3 51.2 1.0 CD A:ARG167 3.6 48.6 1.0 CD1 A:ILE153 3.7 44.9 1.0 I A:IOD307 3.8 88.2 0.4 CB A:ARG167 4.1 46.7 1.0 CG2 A:THR148 4.2 74.8 1.0 CG A:ARG167 4.2 51.8 1.0 CZ A:ARG167 4.3 50.7 1.0 NE A:ARG167 4.4 44.0 1.0 OG1 A:THR171 4.8 46.7 1.0 CB A:THR148 5.0 73.1 1.0

Chlorine binding site 7 out of 7 in the Structure of the R18A/E28A 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/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl314 b:74.3 occ:1.00 O A:HOH444 2.5 71.1 1.0 CB A:ALA31 3.6 61.6 1.0 CD2 A:TYR145 3.8 54.3 1.0 CE2 A:TYR145 4.4 54.1 1.0 CD2 A:PHE32 4.5 57.3 1.0 CG A:TYR145 4.7 56.4 1.0 N A:PHE32 4.7 63.4 1.0 NE2 A:HIS62 4.8 57.8 1.0 CD2 A:HIS62 4.8 56.8 1.0 CB A:TYR145 4.8 52.6 1.0 CA A:ALA31 4.9 62.7 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