Chlorine in PDB 7b4v: Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)

The structure of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505), PDB code: 7b4v was solved by N.Friedrich, E.Stiegeler, M.Glogl, T.Lemmin, S.Hansen, C.Kadelka, Y.Wu, P.Ernst, L.Maliqi, C.Foulkes, M.Morin, M.Eroglu, T.Liechti, B.Ivan, T.Reinberg, J.Schaefer, U.Karakus, S.Ursprung, A.Mann, P.Rusert, R.D.Kouyos, J.A.Robinson, H.F.Gunthard, A.Pluckthun, A.Trkola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.24 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.63, 69.34, 69.92, 90, 90, 90
R / Rfree (%)	16.5 / 19.6

The structure of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Chlorine atom in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) (pdb code 7b4v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505), PDB code: 7b4v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:20.9 occ:1.00 HH21 C:ARG23 2.4 18.4 1.0 HZ2 C:LYS16 2.4 51.2 0.6 HE C:ARG23 2.5 18.7 1.0 HZ3 C:LYS16 2.7 52.0 0.4 O C:HOH304 2.8 46.6 1.0 HG2 C:GLU20 3.0 19.0 1.0 HB3 C:LEU19 3.1 21.1 1.0 NZ C:LYS16 3.1 42.7 0.6 NH2 C:ARG23 3.2 15.3 1.0 HZ1 C:LYS16 3.2 51.2 0.6 HD11 C:LEU54 3.2 23.7 1.0 NE C:ARG23 3.2 15.6 1.0 HD13 C:LEU54 3.4 23.7 1.0 HE3 C:LYS16 3.4 50.2 0.6 HZ D:PHE11 3.5 17.5 1.0 NZ C:LYS16 3.5 43.4 0.4 HG3 C:GLU20 3.6 19.0 1.0 HA C:GLU20 3.6 19.5 1.0 CZ C:ARG23 3.6 16.1 1.0 HZ1 C:LYS16 3.7 52.0 0.4 CG C:GLU20 3.7 15.8 1.0 CD1 C:LEU54 3.7 19.8 1.0 HE2 C:LYS16 3.8 43.6 0.4 HB2 C:LEU19 3.8 21.1 1.0 CE C:LYS16 3.8 41.8 0.6 HZ3 C:LYS16 3.8 51.2 0.6 HH22 C:ARG23 3.8 18.4 1.0 CB C:LEU19 3.8 17.6 1.0 HD2 C:LYS16 3.9 42.8 0.4 HD2 C:LYS16 3.9 42.3 0.6 CZ D:PHE11 4.0 14.6 1.0 HG3 B:PRO15 4.0 21.3 1.0 HE1 D:PHE11 4.1 21.9 1.0 C C:LEU19 4.1 15.8 1.0 N C:GLU20 4.1 15.6 1.0 CE C:LYS16 4.1 36.4 0.4 HZ2 C:LYS16 4.2 52.0 0.4 HB2 C:ARG23 4.2 16.3 1.0 CA C:GLU20 4.2 16.2 1.0 O C:LEU19 4.2 15.5 1.0 HD12 C:LEU54 4.2 23.7 1.0 CE1 D:PHE11 4.3 18.3 1.0 H C:GLU20 4.4 18.7 1.0 HD13 C:LEU19 4.4 34.9 1.0 HD2 C:ARG23 4.4 18.0 1.0 HD21 C:LEU54 4.4 16.0 1.0 CD C:LYS16 4.4 35.3 0.6 CD C:ARG23 4.4 15.0 1.0 CD C:LYS16 4.5 35.6 0.4 HD22 C:LEU54 4.6 16.0 1.0 CB C:GLU20 4.6 18.0 1.0 CA C:LEU19 4.6 14.2 1.0 HE2 C:LYS16 4.6 50.2 0.6 HB3 C:ARG23 4.7 16.3 1.0 HD22 C:LEU19 4.7 23.8 1.0 O B:HOH220 4.7 26.1 1.0 OE2 C:GLU20 4.8 28.4 1.0 CD C:GLU20 4.8 23.2 1.0 CB C:ARG23 4.8 13.6 1.0 CD2 C:LEU54 4.9 13.4 1.0 CE2 D:PHE11 4.9 12.7 1.0 CG C:LEU54 4.9 15.5 1.0 CG B:PRO15 4.9 17.8 1.0 CG C:LEU19 4.9 19.5 1.0 NH1 C:ARG23 5.0 15.9 1.0 HE3 C:LYS16 5.0 43.6 0.4

Chlorine binding site 2 out of 5 in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:23.9 occ:1.00 H C:ILE129 2.4 20.6 1.0 HB2 C:ASP128 2.6 30.2 1.0 HB3 C:ASN126 2.7 15.3 1.0 O C:HOH432 2.8 24.7 1.0 H C:ASP128 2.9 20.3 1.0 HG13 C:ILE129 2.9 21.6 1.0 O C:HOH372 3.1 33.4 1.0 HA C:ASN126 3.1 15.2 1.0 N C:ILE129 3.2 17.2 1.0 HD12 C:ILE129 3.3 21.7 1.0 N C:ASP128 3.4 16.9 1.0 C C:ASN126 3.4 12.9 1.0 CA C:ASN126 3.5 12.7 1.0 CB C:ASN126 3.5 12.7 1.0 HB C:ILE129 3.5 19.4 1.0 CB C:ASP128 3.5 25.2 1.0 CG1 C:ILE129 3.6 18.0 1.0 O C:ASN126 3.7 14.7 1.0 CA C:ASP128 3.8 19.9 1.0 N C:GLU127 3.8 18.2 1.0 CD1 C:ILE129 3.9 18.1 1.0 H C:GLU127 3.9 21.9 1.0 CB C:ILE129 3.9 16.2 1.0 C C:ASP128 3.9 17.3 1.0 HD11 C:ILE129 4.1 21.7 1.0 HB3 C:ASP128 4.1 30.2 1.0 HB2 C:ASN126 4.1 15.3 1.0 CA C:ILE129 4.2 15.4 1.0 CG C:ASP128 4.3 35.3 1.0 C C:GLU127 4.3 16.1 1.0 HB2 C:LEU94 4.3 23.3 1.0 CG C:ASN126 4.4 14.7 1.0 HG12 C:ILE129 4.4 21.6 1.0 O C:HOH329 4.5 44.1 1.0 OD2 C:ASP128 4.5 42.3 1.0 OD1 C:ASN126 4.5 14.6 1.0 O C:HOH330 4.5 27.9 1.0 HD13 C:LEU94 4.6 29.3 1.0 CA C:GLU127 4.7 16.1 1.0 HA2 C:GLY92 4.7 16.8 1.0 HA C:ILE129 4.7 18.5 1.0 HA C:ASP128 4.7 23.9 1.0 HD13 C:ILE129 4.7 21.7 1.0 H C:ALA130 4.8 18.4 1.0 HG2 C:GLU127 4.8 30.7 1.0 HD22 C:LEU94 4.8 34.1 1.0 N C:ASN126 4.9 12.8 1.0

Chlorine binding site 3 out of 5 in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:23.6 occ:1.00 O D:HOH101 2.4 31.2 1.0 HH11 A:ARG23 2.6 25.5 1.0 HD3 A:ARG23 2.9 24.3 1.0 O A:HOH320 3.1 28.9 1.0 HG2 A:GLU20 3.2 28.3 1.0 HA D:PRO15 3.2 15.6 1.0 N D:LYS1 3.2 12.5 1.0 O A:HOH435 3.3 27.2 1.0 HB2 D:LYS1 3.4 16.5 1.0 NH1 A:ARG23 3.4 21.2 1.0 H D:SER2 3.4 19.3 1.0 HD2 A:ARG23 3.4 24.3 1.0 H1 D:LYS1 3.6 15.0 1.0 CD A:ARG23 3.6 20.3 1.0 O A:HOH335 3.7 30.5 1.0 HG2 D:LYS1 3.7 19.1 1.0 HH12 A:ARG23 3.8 25.5 1.0 HA A:GLU20 3.8 21.7 1.0 CA D:PRO15 4.0 13.0 1.0 CB D:LYS1 4.0 13.8 1.0 N D:SER2 4.0 16.1 1.0 HB3 D:SER2 4.1 18.5 1.0 CA D:LYS1 4.1 14.5 1.0 C D:PRO15 4.1 11.3 1.0 CG A:GLU20 4.2 23.6 1.0 HB3 A:ARG23 4.2 20.4 1.0 HB3 D:PRO15 4.3 19.7 1.0 O A:HOH422 4.3 27.2 1.0 CG D:LYS1 4.3 15.9 1.0 CZ A:ARG23 4.4 20.1 1.0 NE A:ARG23 4.4 19.0 1.0 HG3 A:GLU20 4.5 28.3 1.0 C D:LYS1 4.5 15.8 1.0 CB D:PRO15 4.5 16.4 1.0 HB2 D:PRO15 4.5 19.7 1.0 O A:HOH386 4.5 25.2 1.0 HG3 D:LYS1 4.7 19.1 1.0 CA A:GLU20 4.7 18.1 1.0 CG A:ARG23 4.7 16.4 1.0 HB3 A:GLU20 4.7 26.5 1.0 CB D:SER2 4.7 15.4 1.0 OG D:SER2 4.7 22.2 1.0 CB A:GLU20 4.8 22.1 1.0 CB A:ARG23 4.8 17.0 1.0 HB2 A:ARG23 4.8 20.4 1.0 HB3 D:LYS1 4.9 16.5 1.0 HG D:SER2 4.9 26.6 1.0 HG2 A:ARG23 4.9 19.6 1.0 OE2 A:GLU20 4.9 30.4 1.0 HA D:LYS1 5.0 17.4 1.0

Chlorine binding site 4 out of 5 in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:16.5 occ:1.00 HE1 A:TRP57 2.5 15.1 1.0 HA B:DPR14 2.8 16.2 1.0 O D:HOH109 3.1 15.3 1.0 HD2 D:DPR14 3.1 18.3 1.0 O A:HOH429 3.1 18.0 1.0 HD3 B:PRO15 3.2 18.7 1.0 HD3 C:ARG23 3.2 18.0 1.0 O C:HOH462 3.2 14.4 1.0 HB3 B:DPR14 3.2 16.5 1.0 HB3 D:DPR14 3.3 17.7 1.0 HG3 D:DPR14 3.3 20.7 1.0 NE1 A:TRP57 3.4 12.5 1.0 HD2 B:PRO15 3.5 18.7 1.0 CA B:DPR14 3.6 13.5 1.0 HA B:ALA13 3.7 17.8 1.0 CD B:PRO15 3.8 15.6 1.0 CB B:DPR14 3.8 13.7 1.0 CG D:DPR14 3.9 17.2 1.0 CD D:DPR14 3.9 15.3 1.0 HZ2 A:TRP57 3.9 17.2 1.0 CB D:DPR14 4.0 14.8 1.0 CD C:ARG23 4.0 15.0 1.0 HG2 C:ARG23 4.1 17.7 1.0 HB2 B:DPR14 4.1 16.5 1.0 O B:TYR12 4.1 11.8 1.0 HH11 C:ARG23 4.1 19.1 1.0 HD2 C:ARG23 4.1 18.0 1.0 CE2 A:TRP57 4.2 14.8 1.0 CD1 A:TRP57 4.3 14.8 1.0 HD1 A:TRP57 4.4 17.7 1.0 O A:HOH381 4.4 16.0 1.0 CZ2 A:TRP57 4.4 14.4 1.0 N B:DPR14 4.4 13.9 1.0 CG C:ARG23 4.5 14.7 1.0 HD3 D:DPR14 4.6 18.3 1.0 CA B:ALA13 4.6 14.8 1.0 HB2 D:DPR14 4.6 17.7 1.0 N B:PRO15 4.7 15.5 1.0 N D:DPR14 4.7 14.8 1.0 C B:DPR14 4.7 14.8 1.0 HG2 D:DPR14 4.8 20.7 1.0 HG3 C:ARG23 4.8 17.7 1.0 NH1 C:ARG23 4.8 15.9 1.0 C B:ALA13 4.9 13.6 1.0 CA D:DPR14 5.0 13.9 1.0 O C:HOH409 5.0 20.5 1.0 CG B:PRO15 5.0 17.8 1.0

Chlorine binding site 5 out of 5 in the Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Broadly Neutralizing Darpin Bnd.2 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:23.2 occ:1.00 H A:ILE129 2.5 18.4 1.0 HB2 A:ASP128 2.7 24.9 1.0 HB3 A:ASN126 2.7 18.5 1.0 H A:ASP128 2.8 19.8 1.0 O A:HOH410 2.8 38.6 1.0 O A:HOH444 2.9 38.4 1.0 HA A:ASN126 3.0 19.3 1.0 O A:HOH415 3.0 38.9 1.0 HG13 A:ILE129 3.0 24.2 1.0 N A:ILE129 3.3 15.3 1.0 HD12 A:ILE129 3.3 22.9 1.0 N A:ASP128 3.4 16.5 1.0 C A:ASN126 3.4 16.7 1.0 CA A:ASN126 3.4 16.1 1.0 CB A:ASN126 3.5 15.4 1.0 HB A:ILE129 3.5 20.8 1.0 CB A:ASP128 3.6 20.7 1.0 N A:GLU127 3.7 18.9 1.0 O A:ASN126 3.7 16.0 1.0 H A:GLU127 3.7 22.6 1.0 CG1 A:ILE129 3.7 20.2 1.0 CA A:ASP128 3.8 20.0 1.0 CD1 A:ILE129 3.9 19.1 1.0 CB A:ILE129 4.0 17.3 1.0 C A:ASP128 4.0 16.1 1.0 HB2 A:ASN126 4.2 18.5 1.0 HD11 A:ILE129 4.2 22.9 1.0 HB3 A:ASP128 4.2 24.9 1.0 CA A:ILE129 4.3 15.2 1.0 C A:GLU127 4.3 18.2 1.0 CG A:ASP128 4.3 32.6 1.0 CG A:ASN126 4.4 16.0 1.0 O A:HOH383 4.5 35.8 1.0 OD1 A:ASN126 4.5 18.4 1.0 OD2 A:ASP128 4.5 30.9 1.0 CA A:GLU127 4.6 17.9 1.0 HG12 A:ILE129 4.6 24.2 1.0 H A:ALA130 4.7 21.0 1.0 HA A:ASP128 4.8 24.1 1.0 HD13 A:ILE129 4.8 22.9 1.0 O A:HOH351 4.8 35.6 1.0 HA A:ILE129 4.8 18.3 1.0 N A:ASN126 4.8 15.1 1.0 HB2 A:LEU94 4.9 25.9 1.0

N.Friedrich, E.Stiegeler, M.Glogl, T.Lemmin, S.Hansen, C.Kadelka, Y.Wu, P.Ernst, L.Maliqi, C.Foulkes, M.Morin, M.Eroglu, T.Liechti, B.Ivan, T.Reinberg, J.Schaefer, U.Karakus, S.Ursprung, A.Mann, P.Rusert, R.D.Kouyos, J.A.Robinson, H.F.Gunthard, A.Pluckthun, A.Trkola. Broadly Neutralizing Darpin in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) To Be Published.