Sodium in PDB 7ndj: Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer

The structure of Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer, PDB code: 7ndj 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)	44.72 / 1.65
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	63.248, 63.248, 114.544, 90, 90, 90
R / Rfree (%)	17.5 / 20.8

The structure of Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer (pdb code 7ndj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer, PDB code: 7ndj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer


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-Ccch Zn Finger Domain with Rna Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:24.2 occ:1.00 O A:VAL154 2.2 24.6 1.0 O A:HIS149 2.2 29.3 1.0 O A:ASN151 2.3 27.3 1.0 O A:MET147 2.4 24.3 1.0 O A:ALA146 2.7 21.9 1.0 C A:MET147 3.0 21.3 1.0 CA A:MET147 3.4 20.2 1.0 C A:VAL154 3.4 23.5 1.0 C A:ASN151 3.4 30.0 1.0 C A:HIS149 3.4 24.3 1.0 C A:ALA146 3.7 22.6 1.0 N A:HIS149 3.9 20.8 1.0 N A:VAL154 3.9 32.4 1.0 CB A:SER156 3.9 22.7 1.0 N A:SER148 4.0 19.8 1.0 N A:MET147 4.0 20.8 1.0 N A:SER156 4.0 25.3 1.0 N A:ASN151 4.1 30.2 1.0 CA A:LYS152 4.1 27.4 1.0 C A:SER148 4.1 21.2 1.0 CA A:VAL154 4.1 25.9 1.0 C A:GLY150 4.1 34.7 1.0 C A:LYS152 4.2 32.5 1.0 N A:LYS152 4.2 31.5 1.0 CA A:HIS149 4.2 23.5 1.0 O A:LYS152 4.3 33.1 1.0 CA A:ASN151 4.3 30.0 1.0 N A:GLY150 4.4 28.8 1.0 O A:GLY150 4.4 33.4 1.0 N A:PHE155 4.5 24.1 1.0 CB A:VAL154 4.5 28.1 1.0 O A:SER148 4.5 24.6 1.0 CA A:SER148 4.6 22.0 1.0 CA A:GLY150 4.6 30.8 1.0 CA A:SER156 4.7 23.4 1.0 CB A:MET147 4.7 22.3 1.0 N A:GLU153 4.7 33.7 1.0 CA A:PHE155 4.7 24.4 1.0 C A:PHE155 4.8 25.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:27.4 occ:1.00 O B:HIS149 2.2 32.1 1.0 O B:VAL154 2.4 30.9 1.0 O B:ASN151 2.4 31.1 1.0 O B:MET147 2.5 25.9 1.0 O B:ALA146 2.6 26.7 1.0 C B:MET147 3.0 27.2 1.0 C B:HIS149 3.3 33.4 1.0 CA B:MET147 3.4 28.9 1.0 C B:ASN151 3.5 33.1 1.0 C B:VAL154 3.5 31.4 1.0 C B:ALA146 3.7 24.8 1.0 N B:HIS149 3.7 29.2 1.0 CB B:SER156 3.9 32.1 1.0 N B:SER148 4.0 26.4 1.0 C B:SER148 4.0 26.4 1.0 N B:SER156 4.1 31.2 1.0 N B:MET147 4.1 23.4 1.0 N B:VAL154 4.1 36.0 1.0 CA B:HIS149 4.1 30.2 1.0 N B:ASN151 4.2 33.5 1.0 C B:GLY150 4.2 36.3 1.0 CA B:LYS152 4.2 39.6 1.0 CA B:VAL154 4.2 33.5 1.0 N B:LYS152 4.3 39.4 1.0 N B:GLY150 4.4 27.9 1.0 C B:LYS152 4.4 40.0 1.0 CA B:ASN151 4.4 35.1 1.0 O B:GLY150 4.5 35.6 1.0 O B:SER148 4.5 27.5 1.0 CB B:VAL154 4.5 40.2 1.0 CA B:SER148 4.5 26.6 1.0 CA B:GLY150 4.5 30.5 1.0 N B:PHE155 4.6 30.5 1.0 O B:LYS152 4.6 41.9 1.0 CA B:SER156 4.6 29.5 1.0 CB B:MET147 4.7 30.1 1.0 CA B:PHE155 4.8 28.6 1.0 C B:PHE155 4.8 31.9 1.0 CB B:HIS149 4.8 23.6 1.0 O B:HOH599 4.9 29.3 1.0 N B:GLU153 4.9 39.5 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