Sodium in PDB 5kvd: Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii

The structure of Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii, PDB code: 5kvd was solved by H.Zhao, C.A.Nelson, D.H.Fremont, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.65 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.020, 113.440, 132.970, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.1

The binding sites of Sodium atom in the Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii (pdb code 5kvd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii, PDB code: 5kvd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:48.6 occ:1.00 O L:LYS199 2.4 20.8 1.0 O L:HOH616 2.4 36.3 1.0 O L:HOH576 2.5 52.2 1.0 C L:LYS199 3.6 21.0 1.0 CA L:LYS199 4.4 22.9 1.0 CB L:LYS199 4.5 25.0 1.0 O L:HOH523 4.5 36.1 1.0 CE L:LYS199 4.5 36.3 1.0 N L:THR200 4.5 16.2 1.0 CA L:THR200 4.6 17.8 1.0 O L:HOH540 4.8 41.1 1.0 C L:THR200 4.9 18.0 1.0

Sodium binding site 2 out of 2 in the Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Zika Specific Antibody, Zv-2, Bound to Zika Envelope Diii within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:73.3 occ:1.00 O H:HOH526 2.5 44.2 1.0 O H:HOH608 2.5 36.4 1.0 O H:VAL171 2.5 27.4 1.0 O H:HOH592 2.9 48.9 1.0 O H:HOH585 3.7 35.7 1.0 C H:VAL171 3.7 25.1 1.0 N H:VAL171 4.3 23.3 1.0 O L:HOH424 4.4 37.3 1.0 NZ L:LYS169 4.4 58.6 1.0 CA H:VAL171 4.4 24.4 1.0 O H:HOH581 4.4 46.5 1.0 OD1 L:ASP167 4.5 31.7 1.0 O H:HOH458 4.5 36.0 1.0 CB H:VAL171 4.6 24.7 1.0 ND1 H:HIS172 4.7 37.1 1.0 N H:HIS172 4.7 22.5 1.0 O H:SER167 4.8 38.5 1.0 CA H:HIS172 4.9 24.4 1.0 CE1 H:HIS172 5.0 35.6 1.0

H.Zhao, E.Fernandez, K.A.Dowd, S.D.Speer, D.J.Platt, M.J.Gorman, J.Govero, C.A.Nelson, T.C.Pierson, M.S.Diamond, D.H.Fremont. Structural Basis of Zika Virus-Specific Antibody Protection. Cell V. 166 1016 2016.
ISSN: ISSN 1097-4172
PubMed: 27475895
DOI: 10.1016/J.CELL.2016.07.020