Sodium in PDB 4ydj: Crystal Structure of Broadly and Potently Neutralizing Antibody 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120, PDB code: 4ydj 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)	38.30 / 2.31
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	293.796, 67.053, 93.638, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Broadly and Potently Neutralizing Antibody 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120 (pdb code 4ydj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Broadly and Potently Neutralizing Antibody 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120, PDB code: 4ydj:

Sodium binding site 1 out of 1 in the Crystal Structure of Broadly and Potently Neutralizing Antibody 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120


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 44- VRC13.01 in Complex with Hiv-1 Clade Ae Strain 93TH057 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na303 b:59.1 occ:1.00 HG23 L:VAL133 2.7 50.4 1.0 O L:THR131 2.7 47.5 1.0 HA L:PRO120 2.9 54.1 1.0 O L:HOH423 3.0 46.9 1.0 HD21 H:LEU124 3.1 54.4 1.0 O L:PRO119 3.1 41.3 1.0 HD22 H:LEU141 3.2 42.1 1.0 HD23 H:LEU124 3.3 54.4 1.0 HD22 H:LEU124 3.3 54.4 1.0 HG21 L:VAL133 3.4 50.4 1.0 CD2 H:LEU124 3.4 45.3 1.0 H L:SER121 3.5 53.8 1.0 CG2 L:VAL133 3.5 42.0 1.0 CA L:PRO120 3.7 45.1 1.0 C L:PRO119 3.8 43.0 1.0 HB L:THR131 3.9 59.4 1.0 C L:THR131 3.9 46.6 1.0 HB3 L:PHE118 3.9 50.4 1.0 OE1 L:GLU124 4.0 52.6 1.0 N L:PRO120 4.0 45.4 1.0 CD2 H:LEU141 4.0 35.1 1.0 H L:VAL133 4.1 46.1 1.0 HD23 H:LEU141 4.1 42.1 1.0 N L:SER121 4.1 44.8 1.0 O L:PHE118 4.1 40.4 1.0 HB L:VAL133 4.2 49.0 1.0 HG22 L:VAL133 4.2 50.4 1.0 HA L:LEU132 4.2 51.9 1.0 HB2 L:PHE118 4.3 50.4 1.0 C L:PRO120 4.3 44.6 1.0 HB2 H:LEU141 4.4 43.7 1.0 CB L:VAL133 4.4 40.8 1.0 N L:VAL133 4.5 38.4 1.0 H L:THR131 4.5 56.9 1.0 HD21 H:LEU141 4.5 42.1 1.0 CB L:PHE118 4.6 42.0 1.0 C L:PHE118 4.6 41.6 1.0 HB3 L:SER121 4.7 59.2 1.0 CB L:THR131 4.7 49.5 1.0 HG22 L:THR131 4.7 58.7 1.0 O L:HOH453 4.7 50.0 1.0 CA L:THR131 4.8 48.2 1.0 HB3 L:PRO120 4.8 57.6 1.0 N L:LEU132 4.8 45.5 1.0 CA L:LEU132 4.8 43.2 1.0 CB L:PRO120 4.9 48.0 1.0 CA L:PRO119 4.9 43.6 1.0 HB3 H:LEU141 5.0 43.7 1.0 CG H:LEU124 5.0 43.8 1.0 C L:LEU132 5.0 40.4 1.0

T.Zhou, R.M.Lynch, L.Chen, P.Acharya, X.Wu, N.A.Doria-Rose, M.G.Joyce, D.Lingwood, C.Soto, R.T.Bailer, M.J.Ernandes, R.Kong, N.S.Longo, M.K.Louder, K.Mckee, S.O'dell, S.D.Schmidt, L.Tran, Z.Yang, A.Druz, T.S.Luongo, S.Moquin, S.Srivatsan, Y.Yang, B.Zhang, A.Zheng, M.Pancera, T.Kirys, I.S.Georgiev, T.Gindin, H.P.Peng, A.S.Yang, J.C.Mullikin, M.D.Gray, L.Stamatatos, D.R.Burton, W.C.Koff, M.S.Cohen, B.F.Haynes, J.P.Casazza, M.Connors, D.Corti, A.Lanzavecchia, Q.J.Sattentau, R.A.Weiss, A.P.West, P.J.Bjorkman, J.F.Scheid, M.C.Nussenzweig, L.Shapiro, J.R.Mascola, P.D.Kwong. Structural Repertoire of Hiv-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell V. 161 1280 2015.
ISSN: ISSN 1097-4172
PubMed: 26004070
DOI: 10.1016/J.CELL.2015.05.007