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Chlorine in PDB 6v2f: Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207

Protein crystallography data

The structure of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207, PDB code: 6v2f was solved by T.C.Appleby, J.O.Link, S.R.Yant, A.G.Villasenor, J.R.Somoza, E.Y.Hu, S.D.Schroeder, T.Cihlar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 2.00
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 158.301, 158.301, 55.648, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 25.1

Other elements in 6v2f:

The structure of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 also contains other interesting chemical elements:

Fluorine (F) 60 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 (pdb code 6v2f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207, PDB code: 6v2f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6v2f

Go back to Chlorine Binding Sites List in 6v2f
Chlorine binding site 1 out of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl300

b:29.1
occ:1.00
CL47 A:QNG300 0.0 29.1 1.0
C10 A:QNG300 1.7 24.9 1.0
C09 A:QNG300 2.7 24.5 1.0
C11 A:QNG300 2.7 22.2 1.0
N17 A:QNG300 3.1 28.6 1.0
C16 A:QNG300 3.3 25.1 1.0
CG2 A:ILE73 3.6 20.3 1.0
CG A:LYS70 3.7 34.2 1.0
OD1 A:ASN74 3.7 34.3 1.0
O A:LYS70 3.9 25.2 1.0
CB A:ILE73 3.9 21.1 1.0
ND2 A:ASN74 4.0 36.1 1.0
C12 A:QNG300 4.0 22.0 1.0
CG A:ASN74 4.0 30.1 1.0
C08 A:QNG300 4.0 22.9 1.0
N A:ASN74 4.4 21.3 1.0
CA A:LYS70 4.5 23.4 1.0
CD1 A:ILE73 4.5 19.9 1.0
C07 A:QNG300 4.5 19.6 1.0
N15 A:QNG300 4.6 24.3 1.0
C A:LYS70 4.6 26.7 1.0
S48 A:QNG300 4.7 36.0 1.0
CD A:LYS70 4.7 30.0 1.0
CB A:ALA105 4.7 23.0 1.0
CB A:LYS70 4.7 24.0 1.0
C A:ILE73 4.8 20.6 1.0
CG1 A:ILE73 4.8 20.1 1.0
CG2 A:THR107 4.9 24.5 1.0
N14 A:QNG300 4.9 23.6 1.0
O51 A:QNG300 4.9 38.9 1.0
CA A:ILE73 4.9 22.6 1.0
CA A:ASN74 4.9 25.1 1.0
CB A:ASN74 5.0 28.4 1.0

Chlorine binding site 2 out of 6 in 6v2f

Go back to Chlorine Binding Sites List in 6v2f
Chlorine binding site 2 out of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl300

b:25.4
occ:1.00
CL47 B:QNG300 0.0 25.4 1.0
C10 B:QNG300 1.7 21.3 1.0
C09 B:QNG300 2.7 24.8 1.0
C11 B:QNG300 2.7 19.3 1.0
N17 B:QNG300 3.2 25.6 1.0
C16 B:QNG300 3.3 23.8 1.0
CG2 B:ILE73 3.5 19.8 1.0
OD1 B:ASN74 3.7 36.0 1.0
ND2 B:ASN74 3.8 31.2 1.0
O B:LYS70 3.8 19.6 1.0
CG B:LYS70 3.9 30.1 1.0
CB B:ILE73 3.9 20.8 1.0
CG B:ASN74 3.9 30.5 1.0
C12 B:QNG300 4.0 19.6 1.0
C08 B:QNG300 4.0 20.9 1.0
O B:HOH492 4.1 35.6 1.0
O B:HOH407 4.4 33.7 1.0
N B:ASN74 4.5 20.6 1.0
C07 B:QNG300 4.5 20.1 1.0
CA B:LYS70 4.5 21.4 1.0
CD B:LYS70 4.6 29.3 1.0
N15 B:QNG300 4.6 23.5 1.0
C B:LYS70 4.6 23.8 1.0
CD1 B:ILE73 4.6 18.0 1.0
CB B:ALA105 4.6 19.2 1.0
CB B:LYS70 4.7 26.9 1.0
CG2 B:THR107 4.8 22.9 1.0
S48 B:QNG300 4.8 29.3 1.0
C B:ILE73 4.8 21.5 1.0
CG1 B:ILE73 4.9 23.4 1.0
N14 B:QNG300 4.9 24.2 1.0
CA B:ILE73 4.9 20.6 1.0
CB B:ASN74 4.9 24.6 1.0
CA B:ASN74 5.0 25.1 1.0

Chlorine binding site 3 out of 6 in 6v2f

Go back to Chlorine Binding Sites List in 6v2f
Chlorine binding site 3 out of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl300

b:26.2
occ:1.00
CL47 C:QNG300 0.0 26.2 1.0
C10 C:QNG300 1.7 18.6 1.0
C09 C:QNG300 2.7 24.9 1.0
C11 C:QNG300 2.7 18.9 1.0
N17 C:QNG300 3.2 23.9 1.0
C16 C:QNG300 3.3 23.3 1.0
CG2 C:ILE73 3.5 18.7 1.0
CG C:LYS70 3.6 36.0 1.0
ND2 C:ASN74 3.6 31.5 1.0
OD1 C:ASN74 3.8 42.1 1.0
O C:LYS70 3.8 22.1 1.0
CB C:ILE73 3.9 19.2 1.0
CG C:ASN74 3.9 34.8 1.0
C12 C:QNG300 4.0 19.5 1.0
C08 C:QNG300 4.0 20.2 1.0
O C:HOH490 4.1 34.4 1.0
CD C:LYS70 4.2 36.1 1.0
O C:HOH437 4.4 34.4 1.0
CA C:LYS70 4.5 22.0 1.0
N C:ASN74 4.5 20.8 1.0
C07 C:QNG300 4.5 19.6 1.0
CD1 C:ILE73 4.6 19.8 1.0
C C:LYS70 4.6 21.4 1.0
N15 C:QNG300 4.6 23.4 1.0
CB C:ALA105 4.6 19.7 1.0
CB C:LYS70 4.6 28.7 1.0
CG2 C:THR107 4.8 23.2 1.0
C C:ILE73 4.8 21.4 1.0
S48 C:QNG300 4.8 26.9 1.0
CG1 C:ILE73 4.8 22.0 1.0
N14 C:QNG300 4.9 24.2 1.0
CA C:ILE73 4.9 20.0 1.0
CA C:ASN74 5.0 23.0 1.0

Chlorine binding site 4 out of 6 in 6v2f

Go back to Chlorine Binding Sites List in 6v2f
Chlorine binding site 4 out of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl300

b:30.5
occ:1.00
CL47 D:QNG300 0.0 30.5 1.0
C10 D:QNG300 1.7 24.9 1.0
C09 D:QNG300 2.7 23.7 1.0
C11 D:QNG300 2.7 22.5 1.0
N17 D:QNG300 3.1 28.4 1.0
C16 D:QNG300 3.3 26.6 1.0
CG2 D:ILE73 3.5 21.0 1.0
ND2 D:ASN74 3.7 31.0 1.0
OD1 D:ASN74 3.8 38.0 1.0
O D:LYS70 3.9 25.2 1.0
CG D:LYS70 3.9 34.5 1.0
CB D:ILE73 3.9 21.4 1.0
CG D:ASN74 3.9 31.6 1.0
C12 D:QNG300 4.0 23.0 1.0
C08 D:QNG300 4.0 24.3 1.0
O D:HOH462 4.3 34.4 1.0
N D:ASN74 4.4 23.8 1.0
CA D:LYS70 4.5 26.8 1.0
C07 D:QNG300 4.5 21.2 1.0
N15 D:QNG300 4.6 27.4 1.0
CD1 D:ILE73 4.6 19.4 1.0
CB D:LYS70 4.6 26.6 1.0
C D:LYS70 4.6 27.1 1.0
CB D:ALA105 4.7 21.8 1.0
S48 D:QNG300 4.7 35.3 1.0
C D:ILE73 4.8 23.8 1.0
CG2 D:THR107 4.8 25.2 1.0
CG1 D:ILE73 4.9 19.7 1.0
N14 D:QNG300 4.9 25.1 1.0
CB D:ASN74 4.9 29.1 1.0
CA D:ASN74 4.9 26.5 1.0
O51 D:QNG300 4.9 34.5 1.0
CD D:LYS70 4.9 30.9 1.0
CA D:ILE73 4.9 21.0 1.0
CE D:LYS70 5.0 29.4 1.0

Chlorine binding site 5 out of 6 in 6v2f

Go back to Chlorine Binding Sites List in 6v2f
Chlorine binding site 5 out of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl300

b:29.6
occ:1.00
CL47 E:QNG300 0.0 29.6 1.0
C10 E:QNG300 1.7 24.5 1.0
C09 E:QNG300 2.7 24.7 1.0
C11 E:QNG300 2.7 22.1 1.0
N17 E:QNG300 3.1 26.4 1.0
C16 E:QNG300 3.3 25.4 1.0
CG2 E:ILE73 3.5 21.9 1.0
ND2 E:ASN74 3.6 30.4 1.0
OD1 E:ASN74 3.8 35.0 1.0
CG E:ASN74 3.8 28.8 1.0
C12 E:QNG300 4.0 20.2 1.0
C08 E:QNG300 4.0 25.0 1.0
O E:LYS70 4.0 23.1 1.0
CB E:ILE73 4.0 23.9 1.0
N E:ASN74 4.5 22.4 1.0
C07 E:QNG300 4.5 20.3 1.0
N15 E:QNG300 4.6 22.6 1.0
CA E:LYS70 4.6 20.2 1.0
S48 E:QNG300 4.6 29.3 1.0
CB E:LYS70 4.7 25.4 1.0
C E:LYS70 4.7 23.5 1.0
CB E:ALA105 4.7 22.4 1.0
CE E:LYS70 4.8 27.4 1.0
CD1 E:ILE73 4.8 21.7 1.0
CG2 E:THR107 4.8 26.8 1.0
CG E:LYS70 4.8 31.0 1.0
C E:ILE73 4.9 24.6 1.0
N14 E:QNG300 4.9 24.2 1.0
CB E:ASN74 4.9 28.0 1.0
CA E:ASN74 4.9 27.6 1.0
O50 E:QNG300 4.9 31.5 1.0

Chlorine binding site 6 out of 6 in 6v2f

Go back to Chlorine Binding Sites List in 6v2f
Chlorine binding site 6 out of 6 in the Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Hiv Capsid Hexamer Bound to the Small Molecule Long-Acting Inhibitor, Gs-6207 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl300

b:29.0
occ:1.00
CL47 F:QNG300 0.0 29.0 1.0
C10 F:QNG300 1.7 23.8 1.0
C09 F:QNG300 2.7 22.2 1.0
C11 F:QNG300 2.7 22.7 1.0
N17 F:QNG300 3.1 24.2 1.0
C16 F:QNG300 3.3 24.8 1.0
CG2 F:ILE73 3.5 20.4 1.0
OD1 F:ASN74 3.7 35.1 1.0
ND2 F:ASN74 3.8 31.4 1.0
CG F:ASN74 3.9 27.5 1.0
O F:LYS70 4.0 22.4 1.0
C12 F:QNG300 4.0 21.7 1.0
C08 F:QNG300 4.0 24.3 1.0
CB F:ILE73 4.0 20.6 1.0
N F:ASN74 4.5 20.5 1.0
C07 F:QNG300 4.5 21.4 1.0
N15 F:QNG300 4.6 23.0 1.0
CG F:LYS70 4.6 31.4 1.0
CA F:LYS70 4.6 20.6 1.0
S48 F:QNG300 4.7 27.0 1.0
C F:LYS70 4.7 23.7 1.0
CB F:ALA105 4.7 20.8 1.0
CB F:LYS70 4.8 25.6 1.0
CD1 F:ILE73 4.8 22.8 1.0
CE F:LYS70 4.8 27.8 1.0
C F:ILE73 4.8 22.8 1.0
CG2 F:THR107 4.8 26.3 1.0
N14 F:QNG300 4.9 22.9 1.0
CB F:ASN74 4.9 26.8 1.0
CA F:ASN74 4.9 25.0 1.0
O51 F:QNG300 4.9 31.9 1.0

Reference:

J.O.Link, M.S.Rhee, W.C.Tse, J.Zheng, J.R.Somoza, W.Rowe, R.Begley, A.Chiu, A.Mulato, D.Hansen, E.Singer, L.K.Tsai, R.A.Bam, C.H.Chou, E.Canales, G.Brizgys, J.R.Zhang, J.Li, M.Graupe, P.Morganelli, Q.Liu, Q.Wu, R.L.Halcomb, R.D.Saito, S.D.Schroeder, S.E.Lazerwith, S.Bondy, D.Jin, M.Hung, N.Novikov, X.Liu, A.G.Villasenor, C.E.Cannizzaro, E.Y.Hu, R.L.Anderson, T.C.Appleby, B.Lu, J.Mwangi, A.Liclican, A.Niedziela-Majka, G.A.Papalia, M.H.Wong, S.A.Leavitt, Y.Xu, D.Koditek, G.J.Stepan, H.Yu, N.Pagratis, S.Clancy, S.Ahmadyar, T.Z.Cai, S.Sellers, S.A.Wolckenhauer, J.Ling, C.Callebaut, N.Margot, R.R.Ram, Y.P.Liu, R.Hyland, G.I.Sinclair, P.J.Ruane, G.E.Crofoot, C.K.Mcdonald, D.M.Brainard, L.Lad, S.Swaminathan, W.I.Sundquist, R.Sakowicz, A.E.Chester, W.E.Lee, E.S.Daar, S.R.Yant, T.Cihlar. Clinical Targeting of Hiv Capsid Protein with A Long-Acting Small Molecule. Nature V. 584 614 2020.
ISSN: ESSN 1476-4687
PubMed: 32612233
DOI: 10.1038/S41586-020-2443-1
Page generated: Mon Jul 29 16:03:41 2024

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