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

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