Sodium in PDB 6wea: Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA

The structure of Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA, PDB code: 6wea was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.59 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.936, 42.641, 119.869, 90.00, 101.79, 90.00
R / Rfree (%)	21 / 23.8

The binding sites of Sodium atom in the Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA (pdb code 6wea). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA, PDB code: 6wea:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na612 b:5.1 occ:0.50 NA A:NA612 0.0 5.1 0.5 NA A:NA612 0.0 5.1 0.5 OG B:SER369 3.0 10.7 1.0 O A:HOH795 3.1 15.5 1.0 OG A:SER369 3.2 10.1 1.0 O B:HOH776 3.3 14.3 1.0 C1 B:EDO601 3.6 11.5 1.0 C2 A:EDO601 3.7 10.4 1.0 CB B:SER369 3.7 10.8 1.0 CB A:SER369 3.8 9.4 1.0 CA B:SER369 4.0 10.1 1.0 CD A:LYS372 4.0 7.8 1.0 CA A:SER369 4.0 8.5 1.0 CD B:LYS372 4.2 10.7 1.0 O1 B:EDO601 4.4 12.2 1.0 O2 A:EDO601 4.4 11.0 1.0 O B:HOH760 4.7 19.2 1.0 O B:HOH748 4.8 15.3 1.0 NZ A:LYS372 4.8 7.9 1.0 C2 B:EDO601 4.8 9.9 1.0 CB A:LYS372 4.8 7.9 1.0 C1 A:EDO601 4.9 10.9 1.0 NZ B:LYS372 4.9 10.7 1.0 O A:SER369 4.9 8.5 1.0 N B:SER369 5.0 9.2 1.0 O A:HOH773 5.0 18.3 1.0 O A:HOH752 5.0 15.8 1.0 O B:SER369 5.0 11.2 1.0 N A:SER369 5.0 8.6 1.0

Sodium binding site 2 out of 2 in the Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Yth Domain of Human YTHDC1 with A 10MER Oligo Containing N6MA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na612 b:5.1 occ:0.50 NA A:NA612 0.0 5.1 0.5 NA A:NA612 0.0 5.1 0.5 OG B:SER369 3.0 10.7 1.0 O A:HOH795 3.1 15.5 1.0 OG A:SER369 3.2 10.1 1.0 O B:HOH776 3.3 14.3 1.0 C1 B:EDO601 3.6 11.5 1.0 C2 A:EDO601 3.7 10.4 1.0 CB B:SER369 3.7 10.8 1.0 CB A:SER369 3.8 9.4 1.0 CA B:SER369 4.0 10.1 1.0 CD A:LYS372 4.0 7.8 1.0 CA A:SER369 4.0 8.5 1.0 CD B:LYS372 4.2 10.7 1.0 O1 B:EDO601 4.4 12.2 1.0 O2 A:EDO601 4.4 11.0 1.0 O B:HOH760 4.7 19.2 1.0 O B:HOH748 4.8 15.3 1.0 NZ A:LYS372 4.8 7.9 1.0 C2 B:EDO601 4.8 9.9 1.0 CB A:LYS372 4.8 7.9 1.0 C1 A:EDO601 4.9 10.9 1.0 NZ B:LYS372 4.9 10.7 1.0 O A:SER369 4.9 8.5 1.0 N B:SER369 5.0 9.2 1.0 O A:HOH773 5.0 18.3 1.0 O A:HOH752 5.0 15.8 1.0 O B:SER369 5.0 11.2 1.0 N A:SER369 5.0 8.6 1.0

C.B.Woodcock, J.R.Horton, J.Zhou, M.T.Bedford, R.M.Blumenthal, X.Zhang, X.Cheng. Biochemical and Structural Basis For Yth Domain of Human YTHDC1 Binding to Methylated Adenine in Dna. Nucleic Acids Res. V. 48 10329 2020.
ISSN: ESSN 1362-4962
PubMed: 32663306
DOI: 10.1093/NAR/GKAA604