Chlorine 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:

Iodine

(I)

12 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of the E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4p:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl313 b:49.8 occ:1.00 O A:GLY60 2.8 56.4 1.0 O A:HOH455 3.0 61.1 1.0 CD2 A:HIS62 3.5 57.7 1.0 NE2 A:HIS62 3.8 59.6 1.0 CG1 A:VAL27 4.0 53.4 1.0 CA A:ALA28 4.0 60.3 1.0 C A:GLY60 4.0 53.6 1.0 CB A:ALA28 4.3 61.7 1.0 N A:ALA28 4.3 56.7 1.0 O A:HOH436 4.5 53.3 1.0 O A:VAL27 4.5 53.5 1.0 CG1 A:VAL59 4.5 46.2 1.0 C A:VAL27 4.5 54.3 1.0 N A:GLY60 4.6 46.8 1.0 CG A:HIS62 4.8 55.4 1.0 CA A:GLY60 4.8 49.9 1.0 CB A:VAL27 4.9 53.8 1.0

Chlorine binding site 2 out of 6 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl314 b:65.7 occ:0.89 O A:HOH445 2.7 52.2 1.0 N A:ARG162 3.5 53.1 1.0 N A:PHE161 3.6 52.6 1.0 O A:HOH416 3.7 60.4 1.0 O A:GLN219 3.9 91.2 1.0 CB A:ARG162 4.0 61.1 1.0 CB A:PRO160 4.0 61.9 1.0 O A:CYS218 4.1 69.4 1.0 CB A:PHE161 4.2 50.0 1.0 CA A:PHE161 4.2 51.6 1.0 C A:PRO160 4.2 54.8 1.0 CA A:GLN219 4.3 85.0 1.0 C A:PHE161 4.3 51.4 1.0 CA A:ARG162 4.4 52.4 1.0 CA A:PRO160 4.4 60.2 1.0 I A:IOD303 4.4 57.9 0.6 C A:GLN219 4.6 92.2 1.0 CG A:GLN219 4.8 93.4 1.0 C A:CYS218 4.9 72.2 1.0 O A:HOH513 5.0 68.7 1.0

Chlorine binding site 3 out of 6 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl315 b:82.5 occ:1.00 OE2 A:GLU98 3.1 87.0 1.0 CD A:GLU98 3.9 85.5 1.0 I A:IOD308 4.0 0.2 0.6 CZ2 A:TRP80 4.1 63.1 1.0 CD A:PRO99 4.3 64.5 1.0 OE1 A:GLU98 4.3 86.0 1.0 CD1 A:ILE124 4.4 79.1 1.0 CD2 A:HIS84 4.4 68.7 1.0 CG2 A:ILE124 4.4 69.5 1.0 CH2 A:TRP80 4.5 63.7 1.0 CG A:PRO99 4.7 60.7 1.0 CG1 A:ILE124 4.8 78.2 1.0 O A:HOH511 4.8 72.8 1.0 CG A:GLU98 4.9 82.5 1.0 NE2 A:HIS84 4.9 66.8 1.0

Chlorine binding site 4 out of 6 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl316 b:71.6 occ:1.00 O A:HOH471 3.0 60.6 1.0 NH1 A:ARG167 3.4 52.6 1.0 CD A:ARG167 3.6 48.0 1.0 I A:IOD310 3.7 78.6 0.3 O A:HOH484 3.9 68.9 1.0 CD1 A:ILE153 3.9 47.5 1.0 CB A:ARG167 4.2 45.0 1.0 CG A:ARG167 4.2 51.8 1.0 CZ A:ARG167 4.4 55.5 1.0 NE A:ARG167 4.5 48.6 1.0 CG2 A:THR148 4.5 73.3 1.0 OG1 A:THR171 4.9 50.3 1.0

Chlorine binding site 5 out of 6 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl317 b:0.0 occ:1.00 O A:HOH509 3.2 77.3 1.0 I A:IOD308 3.6 0.2 0.6 CD1 A:ILE129 3.8 58.5 1.0 CZ3 A:TRP80 4.0 62.7 1.0 CH2 A:TRP80 4.1 63.7 1.0 CG1 A:ILE129 4.4 59.2 1.0

Chlorine binding site 6 out of 6 in the Structure of the 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 E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl318 b:90.0 occ:0.93 N A:ARG97 3.2 70.0 1.0 CG A:ARG97 3.6 67.3 1.0 CA A:MET96 3.7 75.8 1.0 CB A:ARG97 3.9 70.0 1.0 CG2 A:ILE91 3.9 76.7 1.0 C A:MET96 3.9 71.2 1.0 CD A:ARG97 4.0 67.6 1.0 CB A:MET96 4.1 81.3 1.0 CA A:ARG97 4.1 70.2 1.0 CG1 A:ILE91 4.2 73.6 1.0 CB A:ILE91 4.5 77.0 1.0 NE A:ARG97 4.6 65.2 1.0 OE2 A:GLU113 4.7 66.6 1.0 O A:GLN95 4.8 79.5 1.0 N A:MET96 4.9 76.2 1.0 CD1 A:ILE91 5.0 72.8 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