Sodium in PDB 8z62: Crystal Structure of Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3

All present enzymatic activity of Crystal Structure of Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3:
2.1.1.189;

The structure of Crystal Structure of Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3, PDB code: 8z62 was solved by S.Saha, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.83 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.89, 96.61, 122.4, 90, 90, 90
R / Rfree (%)	16.9 / 23.7

The binding sites of Sodium atom in the Crystal Structure of Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3 (pdb code 8z62). 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 Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3, PDB code: 8z62:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3


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 Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:11.1 occ:1.00 OG1 A:THR146 3.0 23.6 1.0 O A:SER143 3.4 27.8 1.0 N A:SER143 3.5 26.6 1.0 N A:PHE142 3.5 27.4 1.0 CD1 A:ILE136 3.6 32.7 1.0 CB A:PHE142 3.6 26.7 1.0 CA A:PRO140 3.6 29.7 1.0 CB A:THR146 3.6 24.2 1.0 CG1 A:ILE136 3.8 32.7 1.0 C A:PRO140 3.9 30.6 1.0 CG2 A:THR146 3.9 24.4 1.0 CA A:PHE142 3.9 26.9 1.0 N A:ILE141 4.0 29.3 1.0 CB A:PRO140 4.0 29.7 1.0 O A:ILE136 4.1 26.9 1.0 C A:PHE142 4.2 26.6 1.0 C A:SER143 4.3 28.8 1.0 CA A:SER143 4.5 27.4 1.0 O A:PRO140 4.5 32.2 1.0 CG A:PHE142 4.6 25.7 1.0 C A:ILE141 4.7 27.5 1.0 CD2 A:PHE142 4.7 26.1 1.0 CG2 A:ILE136 4.8 31.1 1.0 O A:CYS139 4.8 27.3 1.0 CB A:ILE136 4.8 30.9 1.0 N A:PRO140 4.9 28.5 1.0 CA A:ILE141 5.0 27.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3


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 Rrna (Uracil-C5)-Methyltransferase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:17.4 occ:1.00 OG1 B:THR146 3.1 30.8 1.0 N B:PHE142 3.2 33.8 1.0 N B:SER143 3.2 32.7 1.0 O B:SER143 3.3 32.9 1.0 CB B:PHE142 3.5 30.6 1.0 CA B:PRO140 3.5 37.8 1.0 C B:PRO140 3.6 36.2 1.0 CA B:PHE142 3.6 32.3 1.0 N B:ILE141 3.7 34.7 1.0 CD1 B:ILE136 3.8 31.4 1.0 CB B:THR146 3.9 30.5 1.0 C B:PHE142 3.9 33.1 1.0 CB B:PRO140 3.9 40.4 1.0 CG1 B:ILE136 4.0 30.5 1.0 O B:PRO140 4.1 36.6 1.0 C B:SER143 4.1 30.9 1.0 CG2 B:THR146 4.2 30.1 1.0 CA B:SER143 4.3 30.8 1.0 O B:ILE136 4.3 30.4 1.0 C B:ILE141 4.3 35.3 1.0 CG B:PHE142 4.6 29.3 1.0 CA B:ILE141 4.6 34.1 1.0 CD1 B:TYR108 4.7 32.0 1.0 CD2 B:PHE142 4.7 29.6 1.0 N B:PRO140 4.8 36.0 1.0 O B:CYS139 4.8 34.1 1.0

S.Saha, S.P.Kanaujia. Decoding Substrate Selectivity of An Archaeal Rlmcd-Like Methyltransferase Through Its Salient Traits. Biochemistry V. 63 2477 2024.
ISSN: ISSN 0006-2960
PubMed: 39350642
DOI: 10.1021/ACS.BIOCHEM.4C00401