Sodium 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
Chlorine	(Cl)	3 atoms

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

Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na514 b:51.2 occ:1.00 O H:TYR59 2.5 38.6 1.0 O H:HOH1038 2.5 40.0 1.0 OD2 G:ASP457 2.5 37.8 1.0 O G:HOH649 2.6 35.2 1.0 HB2 H:TYR59 2.8 38.0 1.0 HH21 G:ARG469 3.1 34.7 1.0 H H:TYR59 3.1 34.0 1.0 CG G:ASP457 3.2 40.4 1.0 HA H:TRP61 3.4 70.5 1.0 C H:TYR59 3.4 35.0 1.0 HG G:SER365 3.6 49.7 1.0 NH2 G:ARG469 3.7 28.9 1.0 CB H:TYR59 3.7 31.7 1.0 HB3 G:ASP457 3.7 44.2 1.0 OD1 G:ASP457 3.8 35.4 1.0 N H:TYR59 3.8 28.3 1.0 HE G:ARG469 3.8 37.2 1.0 CA H:TYR59 3.8 35.1 1.0 CB G:ASP457 4.0 36.8 1.0 HH22 G:ARG469 4.0 34.7 1.0 HD2 H:TYR59 4.1 40.7 1.0 O H:HOH1046 4.1 31.5 1.0 CA H:TRP61 4.2 58.7 1.0 HB3 H:TYR59 4.2 38.0 1.0 N H:TRP61 4.2 50.2 1.0 OG G:SER365 4.3 41.4 1.0 C H:ALA60 4.3 35.4 1.0 NE G:ARG469 4.3 31.0 1.0 CZ G:ARG469 4.3 32.3 1.0 O H:ALA60 4.4 32.4 1.0 HA G:ASP457 4.4 40.6 1.0 HB3 H:TRP61 4.6 72.5 1.0 H H:TRP61 4.6 60.2 1.0 N H:ALA60 4.6 32.1 1.0 CG H:TYR59 4.7 35.9 1.0 CD2 H:TYR59 4.7 33.9 1.0 OD1 H:ASN58 4.7 38.0 1.0 HB2 G:ASP457 4.8 44.2 1.0 HA H:TYR59 4.8 42.1 1.0 CA G:ASP457 4.8 33.8 1.0 CB H:TRP61 4.9 60.4 1.0 H G:GLY458 4.9 42.7 1.0 HA H:ASN58 4.9 34.8 1.0 O G:HOH817 5.0 50.6 1.0 CA H:ALA60 5.0 33.4 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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:Na515 b:77.2 occ:1.00 O G:HOH809 2.4 59.4 1.0 O H:THR53 2.5 28.7 1.0 HE3 H:MET75 3.0 53.8 1.0 HO5 G:BU3512 3.1 62.4 1.0 HB3 G:ASN425 3.2 34.4 1.0 O H:HOH1020 3.2 50.2 1.0 O G:HOH751 3.2 53.3 1.0 O5 G:BU3512 3.3 52.0 1.0 O G:HOH674 3.4 36.2 1.0 HA H:ASN54 3.4 35.0 1.0 OD2 G:ASP368 3.4 38.3 1.0 HH11 H:ARG71 3.6 36.7 1.0 C H:THR53 3.7 34.5 1.0 HH12 H:ARG71 3.7 36.7 1.0 CE H:MET75 3.8 44.8 1.0 HE1 H:MET75 3.9 53.8 1.0 NH1 H:ARG71 4.0 30.6 1.0 CB G:ASN425 4.0 28.7 1.0 O G:HOH810 4.1 52.2 1.0 HG22 H:THR53 4.1 40.4 1.0 HE2 H:MET75 4.1 53.8 1.0 HB2 G:ASN425 4.2 34.4 1.0 HB3 H:ASN54 4.2 31.9 1.0 CA H:ASN54 4.2 29.2 1.0 H13 G:BU3512 4.3 57.8 1.0 CG G:ASN425 4.4 29.6 1.0 HG23 H:THR53 4.4 40.4 1.0 N H:ASN54 4.5 30.1 1.0 HA2 G:GLY429 4.6 72.9 1.0 C2 G:BU3512 4.6 52.7 1.0 HA H:THR53 4.6 38.1 1.0 CG G:ASP368 4.7 38.2 1.0 CG2 H:THR53 4.7 33.7 1.0 CB H:ASN54 4.7 26.6 1.0 OD1 G:ASN425 4.8 29.2 1.0 CA H:THR53 4.8 31.8 1.0 ND2 G:ASN425 4.8 26.0 1.0 C1 G:BU3512 4.9 48.2 1.0 HD21 G:ASN425 4.9 31.2 1.0

Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na 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 G:Na516 b:53.7 occ:1.00 O G:HOH784 2.5 46.9 1.0 O G:HOH665 2.5 32.0 1.0 O G:HOH605 2.5 36.8 1.0 OG1 G:THR388 2.5 41.7 1.0 HB3 G:PRO363 3.0 39.2 1.0 H G:THR388 3.2 38.2 1.0 HD2 G:PRO364 3.2 33.3 1.0 HA G:THR388 3.4 43.0 1.0 OD1 G:ASN386 3.4 28.1 1.0 HB2 G:PRO363 3.4 39.2 1.0 N G:THR388 3.5 31.8 1.0 H G:THR387 3.6 33.1 1.0 CB G:THR388 3.7 38.8 1.0 CB G:PRO363 3.7 32.6 1.0 CA G:THR388 3.7 35.8 1.0 HD3 G:PRO364 3.9 33.3 1.0 CD G:PRO364 4.0 27.8 1.0 N2 G:NAG508 4.0 48.1 1.0 HA G:PRO363 4.2 43.5 1.0 HB G:THR388 4.2 46.5 1.0 C1 G:NAG508 4.2 44.3 1.0 CG G:ASN386 4.2 35.8 1.0 N G:THR387 4.2 27.6 1.0 C G:THR387 4.2 32.4 1.0 O G:THR372 4.2 31.4 1.0 OG1 G:THR387 4.4 28.7 1.0 CA G:PRO363 4.5 36.3 1.0 O G:HOH633 4.5 36.9 1.0 ND2 G:ASN386 4.6 44.5 1.0 HG23 G:THR388 4.6 48.9 1.0 C2 G:NAG508 4.6 51.3 1.0 HA G:ASN386 4.7 35.1 1.0 CG2 G:THR388 4.7 40.7 1.0 CA G:THR387 4.8 30.9 1.0 HG2 G:PRO364 4.8 34.7 1.0 HG3 G:PRO363 4.9 52.0 1.0 CG G:PRO363 4.9 43.3 1.0 C8 G:NAG508 5.0 54.6 1.0 O G:THR387 5.0 31.5 1.0 N G:PRO364 5.0 26.5 1.0 C7 G:NAG508 5.0 53.5 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na 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 G:Na517 b:64.4 occ:1.00 O G:HOH639 2.5 37.9 1.0 O G:HOH631 2.5 33.9 1.0 O G:ARG379 2.6 36.4 1.0 HE3 G:LYS207 3.0 61.1 1.0 HA3 G:GLY380 3.0 33.8 1.0 HB3 G:LYS207 3.2 54.6 1.0 OE2 G:GLU381 3.4 38.2 1.0 HD13 G:ILE439 3.4 55.4 1.0 HG2 G:GLU381 3.5 37.2 1.0 HG23 G:ILE439 3.5 54.6 1.0 H G:ILE208 3.6 39.7 1.0 C G:ARG379 3.7 34.4 1.0 CA G:GLY380 3.7 28.1 1.0 O G:ILE208 3.7 32.0 1.0 HG21 G:ILE439 3.8 54.6 1.0 C G:GLY380 3.9 27.8 1.0 CE G:LYS207 3.9 50.9 1.0 CD G:GLU381 4.0 38.1 1.0 CG2 G:ILE439 4.1 45.5 1.0 CB G:LYS207 4.1 45.5 1.0 O G:GLY380 4.2 28.1 1.0 CG G:GLU381 4.2 31.0 1.0 N G:GLY380 4.2 26.1 1.0 N G:GLU381 4.3 20.5 1.0 CD1 G:ILE439 4.3 46.2 1.0 HA G:LYS207 4.3 48.2 1.0 N G:ILE208 4.3 33.1 1.0 HG12 G:ILE439 4.4 53.2 1.0 HZ2 G:LYS207 4.4 55.2 1.0 HE2 G:LYS207 4.4 61.1 1.0 H G:GLU381 4.4 24.6 1.0 HZ1 G:LYS207 4.4 55.2 1.0 HD2 G:LYS207 4.5 59.0 1.0 HD11 G:ILE439 4.5 55.4 1.0 NZ G:LYS207 4.5 46.0 1.0 HG13 G:ILE208 4.5 39.0 1.0 HA2 G:GLY380 4.5 33.8 1.0 O G:HOH697 4.6 44.9 1.0 CD G:LYS207 4.6 49.2 1.0 CA G:LYS207 4.7 40.2 1.0 HB2 G:LYS207 4.7 54.6 1.0 H G:ILE439 4.7 47.2 1.0 HB3 G:ARG379 4.7 53.4 1.0 HG12 G:ILE208 4.7 39.0 1.0 HG22 G:ILE439 4.7 54.6 1.0 HG3 G:GLU381 4.8 37.2 1.0 CG1 G:ILE439 4.8 44.3 1.0 HB2 G:ARG379 4.8 53.4 1.0 CG G:LYS207 4.8 44.6 1.0 C G:ILE208 4.8 31.7 1.0 HG3 G:LYS207 4.8 53.5 1.0 C G:LYS207 4.9 40.5 1.0 HA G:GLU381 5.0 35.7 1.0 OE1 G:GLU381 5.0 37.7 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