Sodium in PDB 4lsp: Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- CH31 in Complex with Hiv-1 Clade A/E GP120 93TH057, PDB code: 4lsp 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)	48.04 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.392, 83.958, 175.734, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.4

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 (pdb code 4lsp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 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, PDB code: 4lsp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na522 b:69.7 occ:1.00 O G:HOH651 2.4 59.5 1.0 HB3 G:ASN99 2.6 60.4 1.0 O G:HOH650 2.8 37.0 1.0 HB G:VAL488 2.9 53.2 1.0 OD1 G:ASP49 2.9 77.1 1.0 HA G:ASP49 3.0 68.7 1.0 HG3 G:MET100 3.2 56.3 1.0 HG21 G:VAL488 3.5 44.8 1.0 HG23 G:VAL488 3.5 44.8 1.0 O G:ALA48 3.5 70.1 1.0 H G:MET100 3.6 47.4 1.0 CB G:ASN99 3.6 50.4 1.0 H G:ASN99 3.7 58.7 1.0 CB G:VAL488 3.7 44.3 1.0 CG2 G:VAL488 3.8 37.3 1.0 H G:VAL488 3.8 66.4 1.0 O G:HOH678 3.8 52.9 1.0 N G:MET100 3.9 39.5 1.0 CG G:ASP49 3.9 77.5 1.0 CA G:ASP49 3.9 57.2 1.0 HB2 G:ASN99 4.0 60.4 1.0 HG2 G:MET100 4.0 56.3 1.0 CG G:MET100 4.0 46.9 1.0 H G:THR50 4.1 60.1 1.0 N G:ASN99 4.1 49.0 1.0 CA G:ASN99 4.1 39.8 1.0 C G:ASN99 4.2 42.5 1.0 HB3 G:ASP49 4.3 78.2 1.0 CB G:ASP49 4.3 65.1 1.0 OD1 G:ASN98 4.3 46.8 1.0 HG11 G:VAL488 4.4 52.6 1.0 C G:ALA48 4.4 63.1 1.0 OD1 G:ASN99 4.5 72.7 1.0 CG G:ASN99 4.5 78.0 1.0 N G:VAL488 4.5 55.3 1.0 HA G:MET100 4.6 53.9 1.0 N G:ASP49 4.6 55.1 1.0 CG1 G:VAL488 4.6 43.8 1.0 CA G:MET100 4.7 44.9 1.0 CA G:VAL488 4.7 41.4 1.0 HG22 G:VAL488 4.7 44.8 1.0 N G:THR50 4.8 50.1 1.0 HD11 G:LEU52 4.9 51.4 1.0 HE21 G:GLN103 4.9 63.4 1.0 OD2 G:ASP49 4.9 89.0 1.0 HG12 G:VAL488 4.9 52.6 1.0 C G:ASP49 4.9 54.7 1.0 O G:ASN99 5.0 49.2 1.0 CB G:MET100 5.0 36.9 1.0

Sodium 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na523 b:83.9 occ:1.00 HO2 G:EDO517 2.6 72.3 1.0 HA2 G:GLY429 2.6 81.3 1.0 O2 G:EDO517 2.6 60.2 1.0 O H:HOH426 2.9 46.7 1.0 HG22 H:THR53 3.1 59.1 1.0 HG23 H:THR53 3.3 59.1 1.0 O G:MET426 3.4 50.5 1.0 O G:HOH666 3.4 66.4 1.0 H22 G:EDO517 3.5 66.6 1.0 O G:HOH633 3.5 50.0 1.0 CA G:GLY429 3.5 67.8 1.0 O H:THR53 3.5 36.0 1.0 C2 G:EDO517 3.6 55.5 1.0 CG2 H:THR53 3.6 49.2 1.0 H G:GLY429 3.8 72.2 1.0 O1 G:EDO517 3.8 61.1 1.0 HA G:TRP427 3.9 56.1 1.0 HA3 G:GLY429 3.9 81.3 1.0 HG21 H:THR53 3.9 59.1 1.0 HB3 H:ASN54 4.0 44.6 1.0 N G:GLY429 4.0 60.2 1.0 C1 G:EDO517 4.2 48.3 1.0 HO1 G:PEG520 4.3 72.9 1.0 O G:TRP427 4.4 54.2 1.0 C H:THR53 4.4 33.7 1.0 H21 G:EDO517 4.4 66.6 1.0 C G:GLY429 4.4 70.7 1.0 C G:MET426 4.5 46.6 1.0 H11 G:EDO517 4.5 58.0 1.0 HA H:ASN54 4.5 44.7 1.0 C G:TRP427 4.6 46.2 1.0 CA G:TRP427 4.6 46.8 1.0 HO1 G:EDO517 4.6 73.3 1.0 HB3 G:ASN425 4.7 41.1 1.0 CB H:ASN54 4.8 37.1 1.0 HE1 H:MET75 4.9 55.5 1.0 O G:GLY429 4.9 81.5 1.0 CB H:THR53 5.0 45.4 1.0 O1 G:PEG520 5.0 60.8 1.0

Sodium 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:81.8 occ:1.00 O H:HOH419 2.9 42.4 1.0 O H:HOH471 3.0 85.2 1.0 O H:HOH477 3.1 88.8 1.0 HG21 H:THR87 3.2 62.8 1.0 OG1 H:THR87 3.2 49.8 1.0 O H:HOH466 3.3 62.1 1.0 O H:VAL111 3.4 57.0 1.0 HG1 H:THR87 3.5 59.7 1.0 HD21 H:LEU170 3.5 65.7 1.0 HD22 H:LEU170 3.5 65.7 1.0 HB H:THR87 3.6 51.7 1.0 CB H:THR87 3.8 43.0 1.0 HB2 H:SER84 3.9 75.3 1.0 HG13 H:VAL110 3.9 62.6 1.0 CG2 H:THR87 3.9 52.4 1.0 CD2 H:LEU170 3.9 54.7 1.0 HB2 H:SER112 3.9 59.0 1.0 O H:SER84 4.1 50.2 1.0 H H:VAL111 4.2 56.0 1.0 HD23 H:LEU170 4.2 65.7 1.0 HG23 H:THR87 4.4 62.8 1.0 O H:HOH410 4.4 45.5 1.0 C H:VAL111 4.5 43.1 1.0 HH H:TYR176 4.5 66.7 1.0 HA H:SER84 4.5 70.5 1.0 OH H:TYR176 4.6 55.6 1.0 HG22 H:THR87 4.6 62.8 1.0 O H:HOH431 4.6 55.0 1.0 HG12 H:VAL110 4.7 62.6 1.0 CG1 H:VAL110 4.7 52.1 1.0 CB H:SER84 4.8 62.7 1.0 N H:VAL111 4.8 46.7 1.0 CB H:SER112 4.9 49.2 1.0 C H:SER84 4.9 53.4 1.0 CA H:SER84 4.9 58.7 1.0 HA H:SER112 4.9 57.9 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