Sodium in PDB 4zke: Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp.

The structure of Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp., PDB code: 4zke was solved by E.Kowalinski, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.58 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.150, 123.106, 104.967, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.9

The structure of Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp. (pdb code 4zke). 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 the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp., PDB code: 4zke:

Sodium binding site 1 out of 1 in the Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp.


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 the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gtp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:48.7 occ:0.64 HB3 A:PHE332 2.9 60.6 1.0 O3B A:GTP802 2.9 44.8 1.0 O2A A:GTP802 3.0 44.6 1.0 O2G A:GTP802 3.0 45.2 1.0 H A:ASN277 3.1 56.5 1.0 HB2 A:PHE332 3.2 60.6 1.0 HA A:PHE332 3.3 58.7 1.0 HG1 A:THR276 3.4 56.7 1.0 CB A:PHE332 3.4 50.5 1.0 PG A:GTP802 3.5 44.5 1.0 HA A:ASN277 3.5 56.7 1.0 O A:GLY331 3.6 55.2 1.0 HZ2 A:LYS318 3.7 60.8 1.0 OG1 A:THR276 3.7 47.2 1.0 N A:ASN277 3.8 47.0 1.0 HZ1 A:LYS318 3.8 60.8 1.0 CA A:PHE332 3.9 48.9 1.0 O1G A:GTP802 4.0 43.2 1.0 C5' A:GTP802 4.0 46.8 1.0 PA A:GTP802 4.0 43.5 1.0 O3A A:GTP802 4.1 42.5 1.0 CA A:ASN277 4.1 47.3 1.0 PB A:GTP802 4.2 43.5 1.0 NZ A:LYS318 4.2 50.6 1.0 O A:HOH951 4.3 37.4 1.0 H A:SER333 4.3 58.9 1.0 HB2 A:ASN277 4.5 59.0 1.0 O5' A:GTP802 4.5 46.1 1.0 C A:GLY331 4.6 53.8 1.0 HZ3 A:LYS318 4.7 60.8 1.0 N A:PHE332 4.7 53.6 1.0 HA A:THR276 4.7 54.2 1.0 OD1 A:ASN277 4.8 58.1 1.0 CG A:PHE332 4.8 51.2 1.0 O1B A:GTP802 4.8 43.1 1.0 CB A:ASN277 4.8 49.1 1.0 O3G A:GTP802 4.8 42.4 1.0 C A:THR276 4.9 49.2 1.0 N A:SER333 4.9 49.1 1.0 CB A:THR276 5.0 45.8 1.0 C A:PHE332 5.0 52.9 1.0

E.Kowalinski, A.Schuller, R.Green, E.Conti. Saccharomyces Cerevisiae SKI7 Is A Gtp-Binding Protein Adopting the Characteristic Conformation of Active Translational Gtpases. Structure V. 23 1336 2015.
ISSN: ISSN 0969-2126
PubMed: 26051716
DOI: 10.1016/J.STR.2015.04.018