Sodium in PDB 8ydw: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Xbb.1.5 Variant Spike Protein in Complex with Cespiace

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Xbb.1.5 Variant Spike Protein in Complex with Cespiace, PDB code: 8ydw was solved by S.Nakamura, N.Numoto, Y.Fujiyoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.62 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.76, 74.76, 100.07, 90, 90, 120
R / Rfree (%)	22.3 / 25.4

The binding sites of Sodium atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Xbb.1.5 Variant Spike Protein in Complex with Cespiace (pdb code 8ydw). 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 Receptor Binding Domain of Sars-Cov-2 Omicron Xbb.1.5 Variant Spike Protein in Complex with Cespiace, PDB code: 8ydw:

Sodium binding site 1 out of 1 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Omicron Xbb.1.5 Variant Spike Protein in Complex with Cespiace


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 Receptor Binding Domain of Sars-Cov-2 Omicron Xbb.1.5 Variant Spike Protein in Complex with Cespiace within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:65.3 occ:1.00 O B:ASN405 2.4 46.1 1.0 O B:HOH750 2.5 63.4 1.0 OG B:SER408 2.5 56.0 1.0 O B:HOH704 2.5 57.5 1.0 O B:HOH759 2.6 63.4 1.0 O B:HOH738 2.7 64.8 1.0 C B:ASN405 3.2 53.5 1.0 CB B:SER408 3.5 55.3 1.0 CA B:ASN405 3.7 45.5 1.0 O B:HOH719 3.9 51.9 1.0 N B:SER408 4.2 48.4 1.0 CB B:ASN405 4.3 57.5 1.0 N B:GLU406 4.3 51.2 1.0 CA B:SER408 4.5 48.7 1.0 O B:HOH736 4.5 61.2 1.0 O B:GLY404 4.5 45.7 1.0 O B:HOH710 4.6 61.4 1.0 N B:VAL407 4.8 47.8 1.0 CA B:GLU406 4.8 51.5 1.0 C B:GLU406 4.9 46.2 1.0 O B:HOH761 4.9 75.9 1.0 N B:ASN405 5.0 45.8 1.0

S.Nakamura, Y.Tanimura, R.Nomura, H.Suzuki, K.Nishikawa, A.Kamegawa, N.Numoto, A.Tanaka, S.Kawabata, S.Sakaguchi, A.Emi, Y.Suzuki, Y.Fujiyoshi. Development of A Short-Peptide Inhibiting Any Sars-Cov-2 Variants Based on Structural Biology To Be Published.