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)

Protein crystallography data

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

Other elements in 7b4v:

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

Chlorine Binding Sites:

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 7b4v

Go back to Chlorine Binding Sites List in 7b4v
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 7b4v

Go back to Chlorine Binding Sites List in 7b4v
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 7b4v

Go back to Chlorine Binding Sites List in 7b4v
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 7b4v

Go back to Chlorine Binding Sites List in 7b4v
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 7b4v

Go back to Chlorine Binding Sites List in 7b4v
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

Reference:

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.
Page generated: Thu Nov 25 08:52:48 2021

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