Sodium in PDB 6xya: Cap-Binding Domain of Sftsv L Protein

The structure of Cap-Binding Domain of Sftsv L Protein, PDB code: 6xya was solved by N.Gogrefe, S.Guenther, M.Rosenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.22 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.974, 44.715, 63.515, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 17.7

The binding sites of Sodium atom in the Cap-Binding Domain of Sftsv L Protein (pdb code 6xya). 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 Cap-Binding Domain of Sftsv L Protein, PDB code: 6xya:

Sodium binding site 1 out of 1 in the Cap-Binding Domain of Sftsv L Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cap-Binding Domain of Sftsv L Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1902 b:33.3 occ:1.00 OG1 B:THR1743 2.5 56.0 1.0 OD2 B:ASP1741 2.6 23.0 1.0 OG B:SER1744 2.8 20.0 1.0 HG B:SER1744 2.8 24.0 1.0 OD1 B:ASP1741 3.2 16.3 1.0 CG B:ASP1741 3.3 17.1 1.0 H B:SER1744 3.5 20.0 1.0 HB3 B:SER1744 3.6 18.3 1.0 O B:HOH2151 3.6 42.2 1.0 CB B:SER1744 3.7 15.3 1.0 HZ3 B:TRP1746 3.7 19.1 1.0 N B:SER1744 3.8 16.6 1.0 CB B:THR1743 3.9 27.7 1.0 O B:HOH2055 4.1 25.0 1.0 HB B:THR1743 4.2 33.2 1.0 CA B:SER1744 4.3 16.0 1.0 C B:THR1743 4.4 18.2 1.0 O B:HOH2092 4.4 38.2 1.0 H B:THR1743 4.4 20.6 1.0 CZ3 B:TRP1746 4.5 15.9 1.0 HB2 B:SER1744 4.5 18.3 1.0 CA B:THR1743 4.6 18.5 1.0 HG23 B:THR1743 4.7 21.5 1.0 CB B:ASP1741 4.8 18.7 1.0 CG2 B:THR1743 4.8 17.9 1.0 HG21 B:THR1743 4.8 21.5 1.0 HE3 B:TRP1746 4.9 17.0 1.0 N B:THR1743 5.0 17.2 1.0 HB3 B:ASP1741 5.0 22.5 1.0

D.Vogel, S.R.Thorkelsson, E.Quemin, K.Meier, T.Kouba, N.Gogrefe, S.Guenther, S.Cusack, K.Grunewald, M.Rosenthal. Structural and Functional Characterization of the Severe Fever with Thrombocytopenia Syndrome Virus L Protein Biorxiv 2020.
DOI: DOI.ORG/10.1101/2020.03.02.973065