Chlorine in PDB 4nx4: Re-Refinement of Cap-1 Hiv-Ca Complex

The structure of Re-Refinement of Cap-1 Hiv-Ca Complex, PDB code: 4nx4 was solved by P.T.Lang, J.M.Holton, J.S.Fraser, T.Alber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.15 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	42.187, 62.777, 106.286, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 19.1

The structure of Re-Refinement of Cap-1 Hiv-Ca Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine atom in the Re-Refinement of Cap-1 Hiv-Ca Complex (pdb code 4nx4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Re-Refinement of Cap-1 Hiv-Ca Complex, PDB code: 4nx4:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Re-Refinement of Cap-1 Hiv-Ca Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Re-Refinement of Cap-1 Hiv-Ca Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:23.0 occ:0.57 H C:LEU111 2.3 20.2 1.0 HE22 C:GLN50 2.4 34.6 1.0 O C:HOH363 3.0 51.5 1.0 HA C:THR110 3.1 20.3 1.0 N C:LEU111 3.1 16.8 1.0 NE2 C:GLN50 3.2 28.8 1.0 HB2 C:LEU111 3.3 22.5 1.0 HB3 C:LEU111 3.5 22.5 1.0 HB C:THR110 3.5 23.1 1.0 O C:HOH382 3.5 27.8 1.0 HE21 C:GLN50 3.6 34.6 1.0 CB C:LEU111 3.8 18.8 1.0 CA C:THR110 3.8 16.9 1.0 C C:THR110 3.9 15.5 1.0 CA C:LEU111 4.0 16.6 1.0 CB C:THR110 4.1 19.2 1.0 CD C:GLN50 4.2 26.9 1.0 HG22 C:THR110 4.3 24.9 1.0 OE1 C:GLN50 4.3 30.6 1.0 HA C:LEU111 4.5 20.0 1.0 H C:GLN112 4.6 21.7 1.0 CG2 C:THR110 4.8 20.8 1.0 O C:SER109 4.9 17.8 1.0

Chlorine binding site 2 out of 3 in the Re-Refinement of Cap-1 Hiv-Ca Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Re-Refinement of Cap-1 Hiv-Ca Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl204 b:61.3 occ:0.42 CL1 C:JPR204 0.0 61.3 0.4 C4 C:JPR204 1.7 61.0 0.4 CL1 C:JPR204 1.8 59.6 0.5 H11 C:JPR204 2.0 73.3 0.5 C4 C:JPR204 2.2 60.3 0.5 C2 C:JPR204 2.5 60.7 0.5 C1 C:JPR204 2.6 61.1 0.5 C6 C:JPR204 2.6 61.1 0.4 H6 C:JPR204 2.7 73.3 0.4 C2 C:JPR204 2.8 60.9 0.4 H13A C:JPR204 2.8 73.3 0.5 H12 C:JPR204 2.9 73.5 0.4 C1 C:JPR204 3.2 61.3 0.4 H11 C:JPR204 3.2 73.5 0.4 C6 C:JPR204 3.2 60.9 0.5 HD21 C:LEU138 3.3 27.1 1.0 HG21 C:VAL59 3.4 36.4 1.0 H12 C:JPR204 3.5 73.3 0.5 HD22 C:LEU69 3.5 30.8 1.0 H6 C:JPR204 3.6 73.1 0.5 HG23 C:VAL59 3.6 36.4 1.0 C3 C:JPR204 3.7 60.9 0.5 HD23 C:LEU138 3.8 27.1 1.0 HZ2 C:TRP23 3.8 25.8 1.0 CD2 C:LEU138 3.8 22.6 1.0 HD22 C:LEU138 3.8 27.1 1.0 HD23 C:LEU69 3.9 30.8 1.0 CG2 C:VAL59 3.9 30.4 1.0 C7 C:JPR204 4.0 61.3 0.4 C3 C:JPR204 4.1 60.9 0.4 HE2 C:MET66 4.1 50.4 1.0 CD2 C:LEU69 4.1 25.7 1.0 H13A C:JPR204 4.1 73.5 0.4 HE1 C:MET66 4.2 50.4 1.0 HD22 C:LEU56 4.2 29.2 1.0 C7 C:JPR204 4.2 61.2 0.5 H3 C:JPR204 4.3 73.1 0.5 HD21 C:LEU69 4.4 30.8 1.0 HB C:VAL59 4.4 38.3 1.0 C5 C:JPR204 4.4 61.2 0.5 CZ2 C:TRP23 4.5 21.4 1.0 C5 C:JPR204 4.5 61.2 0.4 HG11 C:VAL27 4.6 36.2 1.0 CE C:MET66 4.6 42.0 1.0 HD23 C:LEU56 4.7 29.2 1.0 HH2 C:TRP23 4.7 27.7 1.0 HG22 C:VAL59 4.7 36.4 1.0 HG21 C:VAL27 4.7 35.1 1.0 HG13 C:VAL27 4.8 36.2 1.0 CB C:VAL59 4.8 31.9 1.0 HD13 C:ILE141 4.8 43.2 1.0 CD2 C:LEU56 4.8 24.3 1.0 H3 C:JPR204 4.9 73.0 0.4 HD12 C:ILE141 4.9 43.2 1.0 HG22 C:VAL27 4.9 35.1 1.0 CH2 C:TRP23 5.0 23.1 1.0

Chlorine binding site 3 out of 3 in the Re-Refinement of Cap-1 Hiv-Ca Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Re-Refinement of Cap-1 Hiv-Ca Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl204 b:59.6 occ:0.49 CL1 C:JPR204 0.0 59.6 0.5 C4 C:JPR204 1.7 60.3 0.5 CL1 C:JPR204 1.8 61.3 0.4 C4 C:JPR204 2.3 61.0 0.4 C6 C:JPR204 2.7 60.9 0.5 HE2 C:MET66 2.7 50.4 1.0 H6 C:JPR204 2.8 73.1 0.5 C2 C:JPR204 2.8 60.7 0.5 C6 C:JPR204 2.8 61.1 0.4 H6 C:JPR204 2.8 73.3 0.4 H13A C:JPR204 2.9 73.3 0.5 C1 C:JPR204 3.1 61.1 0.5 H11 C:JPR204 3.1 73.3 0.5 HE1 C:MET66 3.2 50.4 1.0 C2 C:JPR204 3.3 60.9 0.4 HD23 C:LEU69 3.3 30.8 1.0 CE C:MET66 3.3 42.0 1.0 H12 C:JPR204 3.3 73.5 0.4 HA C:MET66 3.4 43.6 1.0 HD22 C:LEU69 3.5 30.8 1.0 HG23 C:VAL59 3.6 36.4 1.0 HB2 C:MET66 3.7 45.6 1.0 C1 C:JPR204 3.8 61.3 0.4 CD2 C:LEU69 3.8 25.7 1.0 C7 C:JPR204 4.0 61.3 0.4 C7 C:JPR204 4.0 61.2 0.5 C3 C:JPR204 4.1 60.9 0.5 HG21 C:VAL59 4.1 36.4 1.0 H12 C:JPR204 4.1 73.3 0.5 SD C:MET66 4.1 40.5 1.0 CA C:MET66 4.1 36.4 1.0 HE3 C:MET66 4.2 50.4 1.0 O1 C:JPR204 4.2 60.1 0.4 H11 C:JPR204 4.2 73.5 0.4 CG2 C:VAL59 4.3 30.4 1.0 O C:VAL59 4.3 44.7 1.0 HB2 C:HIS62 4.3 42.7 0.1 HB1 C:ALA65 4.3 50.0 1.0 N C:MET66 4.3 35.8 1.0 HB2 C:LEU69 4.3 31.7 1.0 C3 C:JPR204 4.3 60.9 0.4 CB C:MET66 4.3 38.0 1.0 HB3 C:ALA65 4.3 50.0 1.0 HD22 C:LEU56 4.4 29.2 1.0 HD13 C:ILE141 4.4 43.2 1.0 HD21 C:LEU69 4.4 30.8 1.0 HB3 C:LEU69 4.5 31.7 1.0 C5 C:JPR204 4.5 61.2 0.5 C C:ALA65 4.6 37.7 1.0 H C:MET66 4.6 42.9 1.0 HD21 C:LEU138 4.6 27.1 1.0 C5 C:JPR204 4.6 61.2 0.4 H13A C:JPR204 4.6 73.5 0.4 HB C:VAL59 4.7 38.3 1.0 HD23 C:LEU138 4.7 27.1 1.0 O C:ALA65 4.7 34.3 1.0 CB C:ALA65 4.8 41.7 1.0 CB C:LEU69 4.8 26.4 1.0 HD11 C:ILE141 4.8 43.2 1.0 H3 C:JPR204 4.8 73.1 0.5 CG C:MET66 4.9 40.0 1.0 HD12 C:ILE141 4.9 43.2 1.0 CD1 C:ILE141 4.9 36.0 1.0 O C:HIS62 4.9 36.3 0.1 N1 C:JPR204 4.9 61.2 0.4 CG C:LEU69 5.0 26.1 1.0 HG22 C:VAL59 5.0 36.4 1.0

P.T.Lang, J.M.Holton, J.S.Fraser, T.Alber. Protein Structural Ensembles Are Revealed By Redefining X-Ray Electron Density Noise. Proc.Natl.Acad.Sci.Usa V. 111 237 2014.
ISSN: ISSN 0027-8424
PubMed: 24363322
DOI: 10.1073/PNAS.1302823110