Sodium in PDB 9iqp: Crystal Structure of the Wuhan Sars-Cov-2 Spike Rbd (319-541) Complexed with 1P1B10 Nanobody

The structure of Crystal Structure of the Wuhan Sars-Cov-2 Spike Rbd (319-541) Complexed with 1P1B10 Nanobody, PDB code: 9iqp was solved by N.N.Sluchanko, I.O.Matyuta, E.A.Dronova, I.A.Favorskaya, I.B.Esmagambetov, D.V.Shcheblyakov, D.Y.Logunov, A.L.Gintsburg, V.O.Popov, K.M.Boyko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.33, 47.05, 60.15, 90, 102.99, 90
R / Rfree (%)	17.4 / 20.8

The binding sites of Sodium atom in the Crystal Structure of the Wuhan Sars-Cov-2 Spike Rbd (319-541) Complexed with 1P1B10 Nanobody (pdb code 9iqp). 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 the Wuhan Sars-Cov-2 Spike Rbd (319-541) Complexed with 1P1B10 Nanobody, PDB code: 9iqp:

Sodium binding site 1 out of 1 in the Crystal Structure of the Wuhan Sars-Cov-2 Spike Rbd (319-541) Complexed with 1P1B10 Nanobody


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 the Wuhan Sars-Cov-2 Spike Rbd (319-541) Complexed with 1P1B10 Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:27.4 occ:1.00 O B:HOH421 2.3 33.5 1.0 O B:VAL29 2.4 26.1 1.0 O B:SER32 2.4 24.6 1.0 O B:HOH374 2.5 23.0 1.0 O B:HOH332 2.7 37.9 1.0 HA B:ASP33 3.1 19.3 1.0 HA B:HIS30 3.4 26.6 1.0 C B:SER32 3.4 20.2 1.0 HE21 B:GLN71 3.4 27.0 1.0 HG2 B:MET34 3.5 18.4 1.0 C B:VAL29 3.6 24.4 1.0 H B:MET34 3.7 17.9 1.0 CA B:ASP33 3.8 19.1 1.0 NE2 B:GLN71 3.9 26.5 1.0 N B:ASP33 3.9 18.9 1.0 CA B:HIS30 4.0 27.3 1.0 C B:HIS30 4.1 23.4 1.0 H B:SER32 4.2 22.1 1.0 HE22 B:GLN71 4.2 27.1 1.0 OE1 B:GLN71 4.2 26.4 1.0 N B:MET34 4.2 17.2 1.0 N B:HIS30 4.3 24.0 1.0 O B:HIS30 4.3 24.6 1.0 HB B:VAL29 4.4 22.7 1.0 C B:ASP33 4.4 17.9 1.0 N B:SER32 4.4 22.6 1.0 CG B:MET34 4.4 17.6 1.0 CD B:GLN71 4.5 26.2 1.0 CA B:SER32 4.5 20.8 1.0 HA2 B:GLY53 4.5 38.3 1.0 OD1 B:ASP33 4.6 21.7 1.0 H B:ASP33 4.7 19.5 1.0 HG3 B:MET34 4.7 18.2 1.0 HA B:VAL29 4.8 21.1 1.0 CA B:VAL29 4.8 21.6 1.0 N B:ASP31 4.8 21.4 1.0 HA B:SER32 4.8 21.5 0.5 O B:LEU51 4.8 24.2 1.0 O B:HOH386 4.8 38.3 1.0 HA B:SER32 4.8 22.0 0.5 H B:ASP31 5.0 21.5 1.0 HB2 B:MET34 5.0 17.2 1.0

D.V.Shcheblyakov, I.A.Favorskaya, I.V.Dolzhikova, A.I.Korobkova, I.A.Alekseeva, I.B.Esmagambetov, O.L.Voronina, A.I.Tukhvatulin, O.V.Zubkova, A.A.Derkaev, E.I.Ryabova, A.A.Iliukhina, I.D.Zorkov, D.M.Grousova, D.A.Reshetnikov, N.N.Ryzhova, E.I.Ermolova, M.S.Kunda, I.O.Matyuta, K.M.Boyko, V.O.Popov, D.Y.Logunov, N.N.Sluchanko, A.L.Gintsburg. Ultra-Potent Rbm-Specific Single-Domain Antibody Broadly Neutralizes Multiple Sars-Cov-2 Variants with Picomolar Activity. Int.J.Biol.Macromol. V. 319 45386 2025.
ISSN: ISSN 0141-8130
PubMed: 40543774
DOI: 10.1016/J.IJBIOMAC.2025.145386