Sodium in PDB 7ndh: Crystal Structure of ZC3H12C Pin Domain

The structure of Crystal Structure of ZC3H12C Pin Domain, PDB code: 7ndh was solved by A.Garg, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 1.94
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.331, 80.331, 143.202, 90, 90, 90
R / Rfree (%)	17.2 / 21.3

The binding sites of Sodium atom in the Crystal Structure of ZC3H12C Pin Domain (pdb code 7ndh). 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 ZC3H12C Pin Domain, PDB code: 7ndh:

Sodium binding site 1 out of 1 in the Crystal Structure of ZC3H12C Pin Domain


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 ZC3H12C Pin Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:49.3 occ:1.00 O B:HIS279 2.2 37.4 1.0 O B:ASN281 2.3 41.4 1.0 O B:VAL284 2.3 38.7 1.0 O B:MET277 2.4 34.0 1.0 O B:ALA276 2.8 33.9 1.0 C B:MET277 3.0 37.0 1.0 CA B:MET277 3.4 35.5 1.0 C B:HIS279 3.4 34.8 1.0 C B:ASN281 3.4 47.4 1.0 C B:VAL284 3.5 41.3 1.0 C B:ALA276 3.8 30.4 1.0 N B:HIS279 3.9 33.4 1.0 N B:VAL284 3.9 45.2 1.0 CB B:SER286 4.0 39.6 1.0 CA B:LYS282 4.0 41.9 1.0 N B:SER278 4.0 30.0 1.0 C B:GLY280 4.0 48.6 1.0 N B:MET277 4.1 36.0 1.0 N B:SER286 4.1 41.0 1.0 N B:LYS282 4.1 44.2 1.0 C B:SER278 4.1 32.2 1.0 N B:ASN281 4.2 48.5 1.0 O B:GLY280 4.2 47.0 1.0 CA B:VAL284 4.2 45.1 1.0 CA B:HIS279 4.2 34.4 1.0 N B:GLY280 4.3 36.9 1.0 C B:LYS282 4.3 47.1 1.0 CA B:ASN281 4.4 49.2 1.0 CA B:GLY280 4.5 45.9 1.0 CB B:VAL284 4.5 50.6 1.0 O B:SER278 4.6 37.0 1.0 N B:GLU283 4.6 46.2 1.0 CA B:SER278 4.6 30.2 1.0 N B:PHE285 4.6 41.4 1.0 CB B:MET277 4.6 34.7 1.0 CA B:SER286 4.7 41.8 1.0 CE B:MET277 4.8 39.8 1.0 O B:LYS282 4.8 46.8 1.0 CA B:PHE285 4.8 38.5 1.0 C B:PHE285 4.9 38.9 1.0

A.Garg, Y.Roske, S.Yamada, T.Uehata, O.Takeuchi, U.Heinemann. Pin and Ccch Zn-Finger Domains Coordinate Rna Targeting in ZC3H12 Family Endoribonucleases. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33950203
DOI: 10.1093/NAR/GKAB316