Sodium in PDB 9ls8: Crystal Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A

All present enzymatic activity of Crystal Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A:
3.1.1.29;

The structure of Crystal Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A, PDB code: 9ls8 was solved by R.Pandey, M.Zohib, A.Arora, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.06 / 1.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.765, 47.584, 69.168, 90, 90, 90
R / Rfree (%)	15.8 / 19.8

The binding sites of Sodium atom in the Crystal Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A (pdb code 9ls8). 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 Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A, PDB code: 9ls8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A


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 Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:52.0 occ:1.00 N A:LYS39 3.7 22.2 1.0 CA A:LYS38 4.0 20.8 1.0 CB A:LYS38 4.3 24.9 1.0 CB A:LYS39 4.4 26.8 1.0 C A:LYS38 4.4 20.9 1.0 CA A:LYS39 4.7 24.0 1.0 CG A:LYS38 4.9 28.7 1.0 O A:PHE37 4.9 24.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A


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 Peptidyl-Trna Hydrolase From Enterococcus Faecium at 1.22 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:35.1 occ:1.00 OG A:SER116 2.7 14.5 1.0 O A:HOH421 3.3 30.7 1.0 OE1 A:GLU67 3.3 31.5 1.0 NE2 A:HIS120 3.3 20.7 1.0 CB A:SER116 3.4 14.5 1.0 CD2 A:HIS120 3.5 18.2 1.0 O A:ASN66 3.7 17.2 1.0 CA A:SER116 3.7 13.4 1.0 O A:HOH373 3.8 38.1 1.0 CD A:GLU67 4.0 29.4 1.0 O A:SER116 4.2 15.0 1.0 CA A:GLU67 4.3 14.3 1.0 C A:SER116 4.4 14.7 1.0 CB A:SER119 4.6 23.0 1.0 OG A:SER119 4.6 27.4 1.0 CE1 A:HIS120 4.6 20.6 1.0 C A:ASN66 4.7 15.8 1.0 C A:GLU67 4.7 14.0 1.0 NE A:ARG70 4.8 31.5 1.0 O A:HOH349 4.9 24.9 1.0 CG A:ARG70 4.9 21.5 1.0 CG A:HIS120 4.9 18.2 1.0 O A:GLU67 4.9 14.5 1.0 N A:SER116 4.9 13.4 1.0 N A:GLU67 5.0 14.1 1.0

R.Pandey, M.Zohib, A.Arora. Characterization of Structure of Peptidyl-Trna Hydrolase From Enterococcus Faecium and Its Inhibition By A Pyrrolinone Compound. Int J Biol Macromol V. 275 33445 2024.
ISSN: ISSN 1879-0003
PubMed: 38945334
DOI: 10.1016/J.IJBIOMAC.2024.133445