Sodium in PDB 7yxe: Crystal Structure of YTHDF2 with Compound ZA_143

The structure of Crystal Structure of YTHDF2 with Compound ZA_143, PDB code: 7yxe was solved by F.Nai, F.Zalesak, Y.Li, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.06 / 1.85
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.16, 80.16, 114.04, 90, 90, 120
R / Rfree (%)	21 / 23.3

The binding sites of Sodium atom in the Crystal Structure of YTHDF2 with Compound ZA_143 (pdb code 7yxe). 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 YTHDF2 with Compound ZA_143, PDB code: 7yxe:

Sodium binding site 1 out of 1 in the Crystal Structure of YTHDF2 with Compound ZA_143


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 YTHDF2 with Compound ZA_143 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:35.0 occ:1.00 O B:HOH723 3.2 24.6 1.0 NH1 B:ARG494 3.3 38.5 1.0 O B:HOH747 3.5 25.6 1.0 CB B:CYS482 3.9 23.6 1.0 CG1 B:VAL485 4.3 26.2 1.0 CD B:ARG494 4.3 38.1 1.0 N B:CYS482 4.4 28.2 1.0 CZ B:ARG494 4.5 42.7 1.0 CB B:THR481 4.7 31.3 1.0 O B:HOH721 4.7 36.9 1.0 CA B:CYS482 4.7 25.4 1.0 NH2 B:ARG425 4.7 31.9 1.0 O B:CYS482 4.8 31.5 1.0 CG2 B:VAL485 4.8 26.6 1.0 NE B:ARG494 4.9 34.7 1.0

F.Nai, R.Nachawati, F.Zalesak, X.Wang, Y.Li, A.Caflisch. Fragment Ligands of the M 6 A-Rna Reader YTHDF2. Acs Med.Chem.Lett. V. 13 1500 2022.
ISSN: ISSN 1948-5875
PubMed: 36110386
DOI: 10.1021/ACSMEDCHEMLETT.2C00303