Sodium in PDB 7b4w: Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)

The structure of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505), PDB code: 7b4w was solved by N.Friedrich, E.Stiegeler, M.Glogl, T.Lemmin, S.Hansen, C.Kadelka, Y.Wu, P.Ernst, L.Maliqi, C.Foulkes, M.Morin, M.Eroglu, T.Liechti, B.Ivan, T.Reinberg, J.Schaefer, U.Karakus, S.Ursprung, A.Mann, P.Rusert, R.D.Kouyos, J.A.Robinson, H.F.Gunthard, A.Pluckthun, A.Trkola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.60 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.4, 67.06, 93.11, 90, 90, 90
R / Rfree (%)	18.1 / 22.7

The structure of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) (pdb code 7b4w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505), PDB code: 7b4w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:42.9 occ:1.00 OE1 A:GLU159 2.4 34.8 1.0 O A:GLY157 2.7 28.8 1.0 O A:HOH404 2.8 54.1 1.0 CD A:GLU159 3.6 35.5 1.0 C A:GLY157 3.6 28.6 1.0 O A:HOH340 4.0 43.4 1.0 OE2 A:GLU159 4.1 37.8 1.0 CA A:GLY157 4.3 27.5 1.0 N A:GLU159 4.4 27.9 1.0 N A:ASN158 4.5 25.9 1.0 CA A:ASN158 4.7 26.0 1.0 CG A:GLU159 4.8 34.4 1.0 O A:HOH327 4.8 48.9 1.0 CB A:GLU159 4.8 32.9 1.0

Sodium binding site 2 out of 2 in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:33.5 occ:1.00 O A:HOH341 2.4 40.0 1.0 O A:GLY146 2.5 25.6 1.0 O A:HOH384 2.6 39.0 1.0 OE1 A:GLN142 2.6 34.2 1.0 O C:HOH275 2.6 51.9 1.0 O A:HOH432 2.6 49.6 1.0 CD A:GLN142 3.3 33.2 1.0 C A:GLY146 3.5 25.8 1.0 CA A:GLY146 3.9 26.1 1.0 CG A:GLN142 3.9 29.8 1.0 NE2 A:GLN142 4.1 34.7 1.0 N A:LYS147 4.7 25.1 1.0 O C:HOH203 4.7 36.6 1.0 CG2 A:THR148 4.8 22.5 1.0 CB A:GLN142 4.8 26.6 1.0 OD2 A:ASP151 4.9 26.8 1.0 O C:GLY157 4.9 30.6 1.0

N.Friedrich, E.Stiegeler, M.Glogl, T.Lemmin, S.Hansen, C.Kadelka, Y.Wu, P.Ernst, L.Maliqi, C.Foulkes, M.Morin, M.Eroglu, T.Liechti, B.Ivan, T.Reinberg, J.Schaefer, U.Karakus, S.Ursprung, A.Mann, P.Rusert, R.D.Kouyos, J.A.Robinson, H.F.Gunthard, A.Pluckthun, A.Trkola. Broadly Neutralizing Darpin in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) To Be Published.