Chlorine in PDB 4lsq: Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1, PDB code: 4lsq was solved by T.Zhou, S.Moquin, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.38 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.514, 67.621, 221.088, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.9

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1 also contains other interesting chemical elements:

Cadmium	(Cd)	5 atoms
Sodium	(Na)	4 atoms

The binding sites of Chlorine atom in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1 (pdb code 4lsq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1, PDB code: 4lsq:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1


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 Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl513 b:37.0 occ:1.00 H G:ILE423 2.5 34.0 1.0 H G:GLN422 2.5 33.2 1.0 HZ3 G:LYS421 2.5 36.0 1.0 HH11 G:ARG327 3.0 61.3 1.0 HG2 G:LYS421 3.2 32.3 1.0 N G:GLN422 3.2 27.7 1.0 HA G:LYS421 3.2 37.4 1.0 HB G:ILE423 3.3 41.0 1.0 HB3 G:LYS421 3.3 31.0 1.0 N G:ILE423 3.3 28.4 1.0 NH1 G:ARG327 3.3 51.1 1.0 NZ G:LYS421 3.4 30.0 1.0 HH12 G:ARG327 3.5 61.3 1.0 HB2 G:GLN422 3.5 37.4 0.5 HZ2 G:LYS421 3.5 36.0 1.0 HG13 G:ILE423 3.6 33.8 1.0 HB2 G:GLN422 3.6 37.4 0.5 HZ1 G:LYS421 3.8 36.0 1.0 CB G:LYS421 3.8 25.8 1.0 CA G:LYS421 3.8 31.2 1.0 OE1 G:GLN422 3.8 36.0 0.5 CG G:LYS421 3.9 26.9 1.0 C G:LYS421 4.0 28.0 1.0 CB G:ILE423 4.0 34.2 1.0 CA G:GLN422 4.1 31.3 0.5 CA G:GLN422 4.1 31.3 0.5 CZ G:ARG327 4.1 54.0 1.0 CA G:ILE423 4.1 30.3 1.0 C G:GLN422 4.2 32.5 1.0 CG1 G:ILE423 4.2 28.2 1.0 O G:ILE423 4.2 33.6 1.0 CB G:GLN422 4.2 31.1 0.5 HE G:ARG327 4.2 65.6 1.0 HD12 G:ILE423 4.2 40.6 1.0 HE3 G:LYS421 4.3 31.4 1.0 CB G:GLN422 4.3 31.2 0.5 CE G:LYS421 4.3 26.2 1.0 NE G:ARG327 4.5 54.7 1.0 CD G:GLN422 4.6 31.4 0.5 HG3 G:LYS421 4.6 32.3 1.0 C G:ILE423 4.6 30.5 1.0 HG3 G:GLN422 4.7 37.5 0.5 CD G:LYS421 4.7 30.2 1.0 HB2 G:LYS421 4.7 31.0 1.0 CD1 G:ILE423 4.8 33.9 1.0 HB3 G:GLN422 4.9 37.4 0.5 HA G:GLN422 5.0 37.6 1.0 NH2 G:ARG327 5.0 56.3 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1


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 Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl903 b:80.5 occ:1.00 CL H:CL904 2.3 72.7 1.0 CD H:CD901 2.5 50.0 1.0 O H:HOH1076 2.7 59.3 1.0 O G:HOH825 3.1 42.7 1.0 HA H:HIS33 3.4 45.0 1.0 O H:GLU32 3.5 38.5 1.0 O G:HOH824 3.7 49.4 1.0 HB2 H:PRO31 3.7 1.0 1.0 C H:GLU32 3.9 46.0 1.0 ND1 H:HIS33 3.9 38.3 1.0 N H:HIS33 4.1 43.2 1.0 CA H:HIS33 4.2 37.5 1.0 O H:HOH1032 4.2 21.7 1.0 H H:GLU32 4.3 74.0 1.0 HE1 H:HIS33 4.4 41.9 1.0 CE1 H:HIS33 4.4 34.9 1.0 N H:GLU32 4.4 61.7 1.0 OE1 H:GLU100B 4.6 42.6 1.0 CB H:PRO31 4.6 0.8 1.0 H H:HIS33 4.6 51.9 1.0 CG H:HIS33 4.7 38.0 1.0 HH11 H:ARG100 4.7 93.5 1.0 CA H:GLU32 4.8 52.2 1.0 C H:PRO31 4.8 0.6 1.0 O G:HOH785 4.8 44.3 1.0 HE1 H:PHE34 4.8 37.5 1.0 HH12 H:ARG100 4.9 93.5 1.0 HB3 H:PRO31 4.9 1.0 1.0 O H:HOH1064 5.0 45.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1


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 Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057 with Loop D and Loop V5 From Clade A Strain 3415_V1_C1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl904 b:72.7 occ:1.00 CL H:CL903 2.3 80.5 1.0 O G:HOH825 2.4 42.7 1.0 CD H:CD901 2.5 50.0 1.0 O G:HOH824 2.7 49.4 1.0 O G:HOH823 3.3 43.4 1.0 O H:HOH1032 3.7 21.7 1.0 HZ H:PHE34 3.9 37.4 1.0 OE1 H:GLU100B 3.9 42.6 1.0 O G:HOH776 3.9 46.9 1.0 CZ H:PHE34 4.0 31.2 1.0 CE1 H:PHE34 4.2 31.3 1.0 HE1 H:PHE34 4.2 37.5 1.0 HA H:HIS33 4.3 45.0 1.0 CE2 H:PHE34 4.5 35.3 1.0 HE2 H:PHE34 4.7 42.3 1.0 HB2 H:GLU100B 4.7 58.3 1.0 O H:GLU32 4.7 38.5 1.0 O H:HOH1076 4.8 59.3 1.0 CD1 H:PHE34 4.9 31.7 1.0 ND1 H:HIS33 4.9 38.3 1.0 O G:HOH763 4.9 47.3 1.0

T.Zhou, J.Zhu, X.Wu, S.Moquin, B.Zhang, P.Acharya, I.S.Georgiev, H.R.Altae-Tran, G.Y.Chuang, M.G.Joyce, Y.Do Kwon, N.S.Longo, M.K.Louder, T.Luongo, K.Mckee, C.A.Schramm, J.Skinner, Y.Yang, Z.Yang, Z.Zhang, A.Zheng, M.Bonsignori, B.F.Haynes, J.F.Scheid, M.C.Nussenzweig, M.Simek, D.R.Burton, W.C.Koff, J.C.Mullikin, M.Connors, L.Shapiro, G.J.Nabel, J.R.Mascola, P.D.Kwong. Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway For Hiv-1 Neutralization By VRC01-Class Antibodies. Immunity V. 39 245 2013.
ISSN: ISSN 1074-7613
PubMed: 23911655
DOI: 10.1016/J.IMMUNI.2013.04.012