Sodium in PDB 5kve: Zika Specific Antibody, Zv-48, Bound to Zika Envelope Diii

The structure of Zika Specific Antibody, Zv-48, Bound to Zika Envelope Diii, PDB code: 5kve 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)	48.50 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.240, 87.980, 147.520, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The binding sites of Sodium atom in the Zika Specific Antibody, Zv-48, Bound to Zika Envelope Diii (pdb code 5kve). 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-48, Bound to Zika Envelope Diii, PDB code: 5kve:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Zika Specific Antibody, Zv-48, 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-48, Bound to Zika Envelope Diii within 5.0Å range: probe atom residue distance (Å) B Occ E:Na501 b:43.8 occ:1.00 O E:HOH633 2.3 26.8 1.0 O E:ASP336 2.4 27.4 1.0 O E:HOH667 2.6 26.9 1.0 C E:ASP336 3.5 28.3 1.0 O E:HOH762 3.7 59.4 1.0 O E:HOH725 3.8 31.5 1.0 O E:PRO338 3.8 22.5 1.0 O E:HOH634 4.0 30.1 1.0 CA E:ASP336 4.1 30.9 1.0 CB E:ASP336 4.3 31.9 1.0 O E:GLY337 4.3 30.4 1.0 C E:GLY337 4.3 27.9 1.0 O E:HOH763 4.3 54.7 1.0 O E:HOH644 4.4 25.9 1.0 N E:GLY337 4.5 26.3 1.0 N E:PRO338 4.7 27.7 1.0 CA E:GLY337 4.7 22.8 1.0 C E:PRO338 4.8 21.4 1.0

Sodium binding site 2 out of 2 in the Zika Specific Antibody, Zv-48, 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-48, Bound to Zika Envelope Diii within 5.0Å range: probe atom residue distance (Å) B Occ H:Na201 b:45.9 occ:1.00 OG H:SER82A 2.4 31.5 1.0 O1 H:EDO203 2.4 51.2 1.0 OG H:SER82B 2.9 42.7 1.0 O H:ASN65 3.2 29.6 1.0 CB H:SER82A 3.2 29.9 1.0 CB H:SER82B 3.4 38.2 1.0 C1 H:EDO203 3.5 49.9 1.0 C H:SER82A 3.7 27.7 1.0 O H:SER82A 3.8 26.8 1.0 O H:HOH301 3.9 60.8 1.0 N H:SER82B 3.9 29.4 1.0 CA H:SER82A 4.0 26.5 1.0 O H:HOH451 4.2 30.5 1.0 C H:ASN65 4.3 25.8 1.0 CA H:SER82B 4.3 34.9 1.0 C2 H:EDO203 4.5 50.0 1.0 CA H:LYS66 4.7 24.4 1.0 N H:SER82A 4.8 26.2 1.0 O H:HOH365 4.9 29.3 1.0 N H:LYS66 4.9 24.4 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