Sodium in PDB 7ndk: Crystal Structure of ZC3H12C Pin Catalytic Mutant

The structure of Crystal Structure of ZC3H12C Pin Catalytic Mutant, PDB code: 7ndk 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)	38.75 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.753, 61.475, 111.62, 90, 90.06, 90
R / Rfree (%)	22.9 / 27.5

The binding sites of Sodium atom in the Crystal Structure of ZC3H12C Pin Catalytic Mutant (pdb code 7ndk). 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 Catalytic Mutant, PDB code: 7ndk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of ZC3H12C Pin Catalytic Mutant


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 Catalytic Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:43.0 occ:1.00 O B:ASN281 2.2 47.6 1.0 O B:VAL284 2.2 54.9 1.0 O B:HIS279 2.5 54.9 1.0 O B:ALA276 2.9 43.6 1.0 O B:MET277 2.9 45.0 1.0 C B:MET277 3.3 45.3 1.0 C B:ASN281 3.4 56.0 1.0 C B:VAL284 3.4 57.4 1.0 C B:HIS279 3.5 54.9 1.0 CA B:MET277 3.7 42.2 1.0 CB B:SER286 3.8 54.9 1.0 N B:HIS279 3.9 52.4 1.0 C B:ALA276 3.9 41.3 1.0 CG2 B:VAL284 4.0 55.2 1.0 N B:SER286 4.0 56.8 1.0 N B:ASN281 4.0 57.0 1.0 C B:GLY280 4.2 58.2 1.0 N B:SER278 4.2 45.5 1.0 CA B:ASN281 4.2 57.5 1.0 C B:SER278 4.2 48.9 1.0 N B:VAL284 4.2 56.2 1.0 N B:MET277 4.2 43.2 1.0 CA B:HIS279 4.3 55.1 1.0 N B:LYS282 4.3 57.7 1.0 CA B:VAL284 4.3 56.7 1.0 CA B:LYS282 4.3 59.5 1.0 N B:PHE285 4.4 55.5 1.0 N B:GLY280 4.4 54.0 1.0 O B:GLY280 4.5 56.7 1.0 CA B:SER286 4.6 53.9 1.0 CA B:PHE285 4.6 56.4 1.0 CA B:GLY280 4.6 57.4 1.0 C B:PHE285 4.7 57.2 1.0 C B:LYS282 4.7 62.5 1.0 CA B:SER278 4.7 46.8 1.0 O B:SER278 4.7 50.3 1.0 CB B:ASN281 4.7 58.5 1.0 CB B:VAL284 4.8 54.9 1.0 CB B:HIS279 4.9 57.8 1.0 CE B:MET277 4.9 39.8 1.0 CB B:MET277 5.0 42.3 1.0 OG B:SER286 5.0 56.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of ZC3H12C Pin Catalytic Mutant


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 Catalytic Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:39.5 occ:1.00 O D:ASN281 2.2 53.9 1.0 O D:VAL284 2.3 53.3 1.0 O D:HIS279 2.4 64.3 1.0 O D:MET277 2.6 52.4 1.0 O D:ALA276 2.7 54.4 1.0 C D:MET277 3.1 51.2 1.0 C D:ASN281 3.4 60.5 1.0 C D:VAL284 3.4 52.2 1.0 CA D:MET277 3.5 50.3 1.0 C D:HIS279 3.5 64.4 1.0 CG2 D:VAL284 3.6 51.0 1.0 C D:ALA276 3.8 52.9 1.0 N D:VAL284 3.8 53.9 1.0 N D:ASN281 3.9 62.5 1.0 N D:HIS279 4.0 54.2 1.0 CA D:VAL284 4.0 51.2 1.0 N D:SER278 4.0 52.8 1.0 C D:GLY280 4.1 62.0 1.0 N D:MET277 4.1 53.1 1.0 N D:SER286 4.2 57.2 1.0 CB D:SER286 4.2 55.9 1.0 CA D:ASN281 4.2 60.9 1.0 C D:LYS282 4.3 65.3 1.0 N D:LYS282 4.3 64.3 1.0 C D:SER278 4.4 52.5 1.0 CA D:HIS279 4.4 62.0 1.0 N D:GLY280 4.4 64.4 1.0 CB D:VAL284 4.4 50.8 1.0 CA D:GLY280 4.4 61.9 1.0 CA D:LYS282 4.5 66.8 1.0 N D:PHE285 4.5 52.3 1.0 N D:GLU283 4.5 62.6 1.0 CA D:SER278 4.6 49.9 1.0 O D:LYS282 4.6 68.6 1.0 O D:GLY280 4.6 59.0 1.0 CB D:MET277 4.7 49.8 1.0 C D:GLU283 4.8 58.5 1.0 CA D:SER286 4.8 56.6 1.0 CA D:PHE285 4.8 54.0 1.0 CE D:MET277 4.9 53.7 1.0 CB D:ASN281 5.0 61.3 1.0 SD D:MET277 5.0 53.5 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