Sodium in PDB 2xz2: Crystal Structure of Cstf-50 Homodimerization Domain

The structure of Crystal Structure of Cstf-50 Homodimerization Domain, PDB code: 2xz2 was solved by M.Moreno-Morcillo, S.Fribourg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.13 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.230, 52.230, 57.850, 90.00, 90.00, 90.00
R / Rfree (%)	19.89 / 24.52

The binding sites of Sodium atom in the Crystal Structure of Cstf-50 Homodimerization Domain (pdb code 2xz2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Cstf-50 Homodimerization Domain, PDB code: 2xz2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Cstf-50 Homodimerization 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 Cstf-50 Homodimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1066 b:15.1 occ:1.00 O A:LEU21 2.9 7.7 1.0 O A:SER50 2.9 9.9 1.0 N A:LEU53 3.0 9.6 1.0 N A:ARG52 3.4 9.8 1.0 CB A:LEU53 3.5 8.2 1.0 N A:GLN25 3.6 6.6 1.0 CB A:SER24 3.6 9.4 1.0 C A:SER50 3.7 11.0 1.0 C A:LEU21 3.8 8.1 1.0 CA A:LEU53 3.9 8.8 1.0 CB A:ARG52 3.9 10.8 1.0 C A:ARG52 3.9 12.4 1.0 CD2 A:LEU21 3.9 17.1 1.0 CA A:ARG52 3.9 10.5 1.0 CB A:GLN25 4.0 8.6 1.0 CA A:LEU21 4.0 7.7 1.0 CA A:GLN25 4.0 6.7 1.0 C A:GLU51 4.0 12.3 1.0 C A:SER24 4.1 7.9 1.0 OE1 A:GLN25 4.1 9.4 1.0 OG A:SER50 4.1 18.1 1.0 CA A:GLU51 4.2 10.7 1.0 CB A:SER50 4.3 13.4 1.0 CB A:LEU21 4.3 8.6 1.0 N A:GLU51 4.3 10.0 1.0 CA A:SER24 4.4 6.5 1.0 CA A:SER50 4.6 9.1 1.0 OG A:SER24 4.7 14.3 1.0 O A:SER24 4.7 8.1 1.0 CG A:LEU21 4.8 14.5 1.0 O A:GLU51 4.8 11.4 1.0 CD A:GLN25 4.9 9.0 1.0 CG A:LEU53 4.9 10.2 1.0 N A:SER24 5.0 7.1 1.0 N A:SER50 5.0 10.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Cstf-50 Homodimerization Domain


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 Cstf-50 Homodimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1067 b:24.1 occ:1.00 OD1 A:ASN14 2.8 14.5 1.0 O A:HOH2005 2.8 23.8 1.0 N A:ASP7 3.0 14.7 1.0 CD A:LYS13 3.6 29.9 1.0 O A:ASP7 3.6 12.4 1.0 CA A:LEU6 3.7 22.7 1.0 CB A:ASP7 3.8 13.2 1.0 CA A:ASP7 3.8 12.9 1.0 C A:LEU6 3.8 21.2 1.0 CG A:ASN14 3.9 13.5 1.0 CG A:LYS13 3.9 17.8 1.0 CD1 A:ILE17 4.0 16.9 1.0 CG A:LEU6 4.0 29.7 1.0 C A:ASP7 4.1 13.8 1.0 CD1 A:LEU6 4.1 29.5 1.0 CE A:LYS13 4.2 36.3 1.0 CB A:LYS13 4.2 13.3 1.0 O A:ILE5 4.3 30.1 1.0 CB A:LEU6 4.4 23.9 1.0 ND2 A:ASN14 4.4 13.9 1.0 CB A:ASN10 4.5 12.0 1.0 NZ A:LYS13 4.6 38.1 1.0 O A:ASN10 4.7 13.0 1.0 N A:ASN14 4.7 10.8 1.0 N A:LEU6 4.7 24.6 1.0 C A:ILE5 4.9 30.1 1.0 C A:LYS13 4.9 13.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Cstf-50 Homodimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Cstf-50 Homodimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1068 b:24.0 occ:1.00 OD2 A:ASP7 2.6 11.9 1.0 ND2 A:ASN10 3.0 15.4 1.0 CG A:ASP7 3.5 11.9 1.0 CB A:ASP7 3.6 13.2 1.0 CB A:ASN10 3.7 12.0 1.0 CG A:ASN10 3.8 13.4 1.0 OD1 A:ASP7 4.7 11.5 1.0 CD A:LYS13 4.8 29.9 1.0 CA A:ASN10 5.0 11.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Cstf-50 Homodimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Cstf-50 Homodimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1069 b:23.1 occ:1.00 OD1 A:ASP29 2.8 15.2 1.0 OE1 A:GLU51 2.9 18.4 1.0 NE2 A:GLN25 3.1 10.3 1.0 CG A:ASP29 3.7 12.3 1.0 OD2 A:ASP29 3.7 11.2 1.0 CB A:GLU51 3.9 13.2 1.0 CD2 A:TYR28 4.0 15.5 1.0 CD A:GLU51 4.0 25.6 1.0 CE2 A:TYR28 4.1 17.1 1.0 CD2 A:LEU54 4.1 14.4 1.0 CD A:GLN25 4.3 9.0 1.0 CG A:GLU51 4.5 18.0 1.0 OE1 A:GLN25 4.9 9.4 1.0

M.Moreno-Morcillo, L.Minvielle-Sebastia, C.Mackereth, S.Fribourg. Hexameric Architecture of Cstf Supported By Cstf- 50 Homodimerization Domain Structure. Rna V. 17 412 2011.
ISSN: ISSN 1355-8382
PubMed: 21233223
DOI: 10.1261/RNA.2481011