Sodium in PDB 7v9e: Crystal Structure of A Methyl Transferase Ribozyme

The structure of Crystal Structure of A Methyl Transferase Ribozyme, PDB code: 7v9e was solved by J.Deng, D.M.J.Lilley, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.43 / 2.30
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	50.381, 52.507, 99.939, 90, 90, 90
R / Rfree (%)	24.4 / 27.1

The structure of Crystal Structure of A Methyl Transferase Ribozyme also contains other interesting chemical elements:

Barium

(Ba)

9 atoms

The binding sites of Sodium atom in the Crystal Structure of A Methyl Transferase Ribozyme (pdb code 7v9e). 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 A Methyl Transferase Ribozyme, PDB code: 7v9e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Methyl Transferase Ribozyme


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 A Methyl Transferase Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na111 b:34.3 occ:1.00 H5'' A:A36 3.9 52.9 1.0 OP2 A:G3 4.0 84.2 1.0 H5' A:C38 4.2 61.1 1.0 OP1 A:C2 4.3 89.8 1.0 OP2 A:A36 4.6 45.8 1.0 H5'' A:C38 4.7 61.1 1.0 C5' A:A36 4.8 44.0 1.0 H5' A:A36 4.9 52.9 1.0 OP1 A:A37 4.9 42.6 1.0 C5' A:C38 4.9 50.9 1.0 OP1 A:C38 5.0 54.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Methyl Transferase Ribozyme


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 A Methyl Transferase Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na112 b:50.9 occ:1.00 O2 A:C35 2.5 47.0 1.0 O A:HOH224 2.5 44.7 1.0 C2 A:C35 3.3 43.0 1.0 H62 A:A36 3.4 46.1 1.0 N3 A:C35 3.5 40.0 1.0 H41 A:C14 3.7 62.0 1.0 O A:HOH209 4.0 39.5 1.0 N6 A:A36 4.2 38.3 1.0 N7 A:A13 4.3 43.8 1.0 H62 A:A13 4.4 57.0 1.0 H2' A:C35 4.4 56.8 1.0 H2' A:G12 4.4 47.4 1.0 HO2' A:G12 4.4 51.0 1.0 OP2 A:A13 4.4 33.9 1.0 N4 A:C14 4.4 51.6 1.0 N7 A:A36 4.4 37.8 1.0 N1 A:C35 4.5 42.8 1.0 H61 A:A36 4.6 46.1 1.0 H61 A:A34 4.7 50.6 1.0 H42 A:C14 4.7 62.0 1.0 C4 A:C35 4.7 40.7 1.0 H1' A:C35 4.8 51.2 1.0 H5 A:C14 4.8 65.0 1.0 H8 A:A13 4.9 54.4 1.0 O2' A:G12 4.9 42.5 1.0 N6 A:A34 4.9 42.1 1.0 C8 A:A13 5.0 45.2 1.0 C1' A:C35 5.0 42.6 1.0 C2' A:C35 5.0 47.3 1.0

J.Deng, T.J.Wilson, J.Wang, X.Peng, M.Li, X.Lin, W.Liao, D.M.J.Lilley, L.Huang. Structure and Mechanism of A Methyltransferase Ribozyme. Nat.Chem.Biol. V. 18 556 2022.
ISSN: ESSN 1552-4469
PubMed: 35301479
DOI: 10.1038/S41589-022-00982-Z