Cadmium 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:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	4 atoms

The binding sites of Cadmium 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 Cadmium atom.
In total 5 binding sites of Cadmium 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 Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 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 Cadmium with other atoms in the Cd 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:Cd510 b:0.2 occ:1.00 NE2 G:HIS216 2.5 33.9 1.0 O G:HOH636 2.5 32.5 1.0 O G:HOH601 2.5 35.7 1.0 HE1 G:HIS216 3.1 41.5 1.0 CE1 G:HIS216 3.2 34.6 1.0 O G:HOH721 3.4 47.2 1.0 H G:GLY250 3.4 38.7 1.0 O G:HOH777 3.6 46.8 1.0 O G:HOH778 3.6 69.0 1.0 CD2 G:HIS216 3.7 32.1 1.0 HA3 G:GLY250 3.7 38.5 1.0 O G:HOH752 3.9 70.8 1.0 HD2 G:HIS216 4.0 38.6 1.0 N G:GLY250 4.0 32.2 1.0 CA G:GLY250 4.3 32.1 1.0 ND1 G:HIS216 4.4 35.7 1.0 HA G:HIS249 4.6 41.0 1.0 HA2 G:GLY250 4.6 38.5 1.0 CG G:HIS216 4.7 36.1 1.0 HG21 G:THR77 4.8 53.5 1.0 HB2 G:PRO214 4.9 35.6 1.0 HG1 G:THR77 4.9 53.3 1.0 C G:HIS249 4.9 31.3 1.0 OD2 G:ASP57 5.0 48.1 1.0

Cadmium binding site 2 out of 5 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 Cadmium with other atoms in the Cd 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 G:Cd511 b:0.2 occ:1.00 O G:HOH780 2.5 72.7 1.0 OD1 G:ASP107 2.5 30.1 1.0 O G:HOH779 2.5 40.8 1.0 CG G:ASP107 3.3 30.2 1.0 OD2 G:ASP107 3.4 28.8 1.0 O G:GLN103 4.3 26.9 1.0 HB3 G:GLN103 4.4 36.8 1.0 HE1 G:TYR217 4.4 39.8 1.0 HB2 G:GLU106 4.4 40.1 1.0 CB G:ASP107 4.6 18.8 1.0 HA G:ASP107 4.6 29.5 1.0 OE2 G:GLU106 4.6 47.7 1.0 O G:HOH739 4.8 64.0 1.0 H G:ASP107 4.9 22.9 1.0 O G:LEU52 4.9 34.3 1.0 O G:HOH669 5.0 33.4 1.0 HB2 G:ASP107 5.0 22.5 1.0 O G:HOH797 5.0 30.1 1.0 N G:ASP107 5.0 19.1 1.0 CA G:ASP107 5.0 24.6 1.0

Cadmium binding site 3 out of 5 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 Cadmium with other atoms in the Cd 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:Cd901 b:50.0 occ:1.00 ND1 H:HIS33 2.5 38.3 1.0 OE1 H:GLU100B 2.5 42.6 1.0 O H:HOH1032 2.5 21.7 1.0 CL H:CL903 2.5 80.5 1.0 CL H:CL904 2.5 72.7 1.0 HA H:HIS33 2.8 45.0 1.0 HE1 H:HIS33 3.2 41.9 1.0 CE1 H:HIS33 3.2 34.9 1.0 CG H:HIS33 3.6 38.0 1.0 HB2 H:GLU100B 3.7 58.3 1.0 CD H:GLU100B 3.7 49.9 1.0 O G:HOH825 3.7 42.7 1.0 CA H:HIS33 3.8 37.5 1.0 HA H:GLU100B 3.8 59.5 1.0 H H:PHE34 3.9 45.2 1.0 O H:HOH1076 3.9 59.3 1.0 CB H:HIS33 4.1 34.1 1.0 HB3 H:HIS33 4.2 41.0 1.0 O G:HOH776 4.2 46.9 1.0 CB H:GLU100B 4.4 48.6 1.0 NE2 H:HIS33 4.4 37.8 1.0 CA H:GLU100B 4.5 49.6 1.0 N H:HIS33 4.5 43.2 1.0 OE2 H:GLU100B 4.5 52.1 1.0 N H:PHE34 4.6 37.6 1.0 CG H:GLU100B 4.6 51.7 1.0 O H:GLU32 4.6 38.5 1.0 CD2 H:HIS33 4.7 38.6 1.0 C H:HIS33 4.7 35.7 1.0 N H:GLU100B 4.8 50.2 1.0 C H:GLU32 4.9 46.0 1.0 HG2 H:GLU100B 4.9 62.0 1.0 O G:HOH823 4.9 43.4 1.0 H H:HIS33 5.0 51.9 1.0

Cadmium binding site 4 out of 5 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 Cadmium with other atoms in the Cd binding site number 4 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:Cd902 b:0.7 occ:1.00 HE2 H:HIS164 1.8 84.1 1.0 O L:HOH441 2.5 74.5 1.0 O L:HOH440 2.5 77.0 1.0 NE2 H:HIS164 2.5 70.1 1.0 OD1 L:ASN138 2.5 62.7 1.0 HD22 L:ASN138 2.8 84.0 1.0 CG L:ASN138 3.3 68.6 1.0 CD2 H:HIS164 3.3 64.9 1.0 ND2 L:ASN138 3.3 70.0 1.0 HD2 H:HIS164 3.4 77.9 1.0 CE1 H:HIS164 3.5 70.8 1.0 O L:HOH439 3.5 56.4 1.0 HE1 H:HIS164 3.7 85.0 1.0 HA2 H:GLY162 4.0 81.0 1.0 HD21 L:ASN138 4.2 84.0 1.0 HD22 L:ASN137 4.3 70.7 1.0 OD2 L:ASP170 4.4 73.6 1.0 CG H:HIS164 4.5 65.7 1.0 ND1 H:HIS164 4.5 70.5 1.0 OD1 L:ASN137 4.7 60.3 1.0 CB L:ASN138 4.7 67.9 1.0 OG L:SER174 4.8 60.2 1.0 CA H:GLY162 4.8 67.5 1.0 ND2 L:ASN137 4.9 58.9 1.0 HB3 L:ASN138 4.9 81.5 1.0 HG L:SER174 5.0 72.2 1.0

Cadmium binding site 5 out of 5 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 Cadmium with other atoms in the Cd binding site number 5 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 L:Cd301 b:0.3 occ:1.00 NE2 L:HIS189 2.5 82.2 1.0 O L:HOH444 2.5 99.6 1.0 O L:HOH448 2.5 65.0 1.0 O L:HOH442 2.5 79.7 1.0 O L:HOH401 2.5 53.9 1.0 HE1 L:HIS189 3.1 94.2 1.0 CE1 L:HIS189 3.1 78.5 1.0 O L:HOH447 3.4 63.0 1.0 O L:HOH443 3.5 72.9 1.0 CD2 L:HIS189 3.7 80.8 1.0 O L:HOH446 3.8 64.4 1.0 HD2 L:HIS189 4.0 97.0 1.0 ND1 L:HIS189 4.4 76.2 1.0 O L:HOH450 4.6 59.9 1.0 OD1 L:ASP185 4.6 92.2 1.0 HE3 L:LYS188 4.7 1.0 1.0 CG L:HIS189 4.7 76.9 1.0 O L:HOH438 4.7 65.9 1.0 HE22 L:GLN155 4.9 85.0 1.0 HG2 L:LYS188 5.0 0.1 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