Chlorine in PDB 6u3z: Structure of VD20_5A4 Fab

Protein crystallography data

The structure of Structure of VD20_5A4 Fab, PDB code: 6u3z was solved by G.Dionne, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.30 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.207, 108.733, 55.418, 90.00, 105.78, 90.00
R / Rfree (%) 19.9 / 23.6

Other elements in 6u3z:

The structure of Structure of VD20_5A4 Fab also contains other interesting chemical elements:

Praseodymium (Pr) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of VD20_5A4 Fab (pdb code 6u3z). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of VD20_5A4 Fab, PDB code: 6u3z:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6u3z

Go back to Chlorine Binding Sites List in 6u3z
Chlorine binding site 1 out of 4 in the Structure of VD20_5A4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of VD20_5A4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:71.8
occ:1.00
N C:VAL129 3.4 37.9 1.0
O C:VAL129 3.7 38.8 1.0
OE2 D:GLU123 3.8 73.2 1.0
CA C:SER128 4.1 37.6 1.0
CA C:VAL129 4.2 39.9 1.0
C C:SER128 4.3 40.6 1.0
CB C:VAL129 4.3 41.7 1.0
C C:VAL129 4.4 41.2 1.0
CG1 C:VAL215 4.5 51.1 1.0
CB C:SER128 4.6 45.1 1.0
CG2 C:VAL129 4.8 38.1 1.0
O C:PRO127 4.8 42.2 1.0
CG2 C:VAL215 4.9 47.6 1.0
CD D:GLU123 4.9 65.9 1.0

Chlorine binding site 2 out of 4 in 6u3z

Go back to Chlorine Binding Sites List in 6u3z
Chlorine binding site 2 out of 4 in the Structure of VD20_5A4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of VD20_5A4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:75.4
occ:1.00
NH1 C:ARG98 2.9 39.1 1.0
NH2 C:ARG98 3.7 32.5 1.0
CZ C:ARG98 3.7 40.1 1.0
O C:HOH460 3.7 43.7 1.0
CB C:ALA27 4.2 42.0 1.0
O C:GLY26 4.3 46.8 1.0
CG2 C:VAL2 4.5 33.5 1.0
O C:HOH421 4.6 40.3 1.0
CA C:ALA27 4.8 40.4 1.0
NE C:ARG98 5.0 34.3 1.0

Chlorine binding site 3 out of 4 in 6u3z

Go back to Chlorine Binding Sites List in 6u3z
Chlorine binding site 3 out of 4 in the Structure of VD20_5A4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of VD20_5A4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:66.5
occ:1.00
OG D:SER14 3.6 45.7 1.0
O D:LYS107 3.9 34.4 1.0
C D:ARG108 4.0 32.7 1.0
CA D:ARG108 4.1 32.1 1.0
O D:HOH423 4.1 34.2 1.0
O D:ARG108 4.3 31.8 1.0
N D:THR109 4.3 33.3 1.0
C D:LYS107 4.3 33.5 1.0
CB D:SER14 4.4 37.2 1.0
CG D:LYS107 4.4 39.5 1.0
N D:ARG108 4.4 32.5 1.0
CD D:LYS107 4.7 49.1 1.0
CG2 D:THR109 4.7 37.0 1.0
CA D:THR109 4.9 34.3 1.0
O D:HOH499 5.0 42.1 1.0
CB D:LYS107 5.0 34.8 1.0

Chlorine binding site 4 out of 4 in 6u3z

Go back to Chlorine Binding Sites List in 6u3z
Chlorine binding site 4 out of 4 in the Structure of VD20_5A4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of VD20_5A4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:48.7
occ:1.00
N D:GLY68 3.1 35.9 1.0
O D:HOH407 3.4 34.6 1.0
CA D:ASP30 3.6 40.5 1.0
CB D:SER67 3.8 42.1 1.0
CA D:GLY68 3.9 37.1 1.0
CA D:SER67 3.9 36.4 1.0
OD1 D:ASP30 4.0 64.2 1.0
C D:SER67 4.0 36.1 1.0
C D:ASP30 4.1 38.5 1.0
N D:ASP30 4.1 37.1 1.0
CG D:LYS31 4.1 38.2 1.0
N D:LYS31 4.1 32.9 1.0
OH D:TYR71 4.2 31.8 1.0
CD D:LYS31 4.6 39.8 1.0
CB D:ASP30 4.6 41.6 1.0
CG D:ASP30 4.7 53.2 1.0
OG D:SER67 4.8 44.4 1.0
CE D:LYS31 4.8 49.9 1.0
O D:ASP30 5.0 33.1 1.0
O D:GLY68 5.0 31.8 1.0
CB D:LYS31 5.0 31.0 1.0
C D:GLY68 5.0 35.9 1.0

Reference:

G.E.Phad, P.Pushparaj, K.Tran, V.Dubrovskaya, M.Adori, P.Martinez-Murillo, N.Vazquez Bernat, S.Singh, G.Dionne, S.O'dell, K.Bhullar, S.Narang, C.Sorini, E.J.Villablanca, C.Sundling, B.Murrell, J.R.Mascola, L.Shapiro, M.Pancera, M.Martin, M.Corcoran, R.T.Wyatt, G.B.Karlsson Hedestam. Extensive Dissemination and Intraclonal Maturation of Hiv Env Vaccine-Induced B Cell Responses. J.Exp.Med. 2019.
ISSN: ESSN 1540-9538
PubMed: 31704807
DOI: 10.1084/JEM.20191155
Page generated: Sat Dec 12 13:47:33 2020

Last articles

Cl in 3TEE
Cl in 3TCT
Cl in 3TDJ
Cl in 3TDQ
Cl in 3TD5
Cl in 3TCS
Cl in 3TCP
Cl in 3TC9
Cl in 3TBD
Cl in 3TBE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy