Sodium in PDB 7q80: Crystal Structure of the Methyltransferase-Ribozyme 1, No Magnesium Condition (with 1-Methyl-Adenosine)

The structure of Crystal Structure of the Methyltransferase-Ribozyme 1, No Magnesium Condition (with 1-Methyl-Adenosine), PDB code: 7q80 was solved by M.Mieczkowski, C.Hoebartner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.17 / 3.14
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.867, 120.867, 82.25, 90, 90, 90
R / Rfree (%)	17.6 / 20.5

The binding sites of Sodium atom in the Crystal Structure of the Methyltransferase-Ribozyme 1, No Magnesium Condition (with 1-Methyl-Adenosine) (pdb code 7q80). 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 Methyltransferase-Ribozyme 1, No Magnesium Condition (with 1-Methyl-Adenosine), PDB code: 7q80:

Sodium binding site 1 out of 1 in the Crystal Structure of the Methyltransferase-Ribozyme 1, No Magnesium Condition (with 1-Methyl-Adenosine)


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 Methyltransferase-Ribozyme 1, No Magnesium Condition (with 1-Methyl-Adenosine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:103.5 occ:1.00 O2' A:1MA7 2.5 148.1 1.0 O2' C:A34 2.6 124.9 1.0 OP2 A:G8 2.6 124.5 1.0 OP2 C:C35 2.6 134.5 1.0 O3' C:A34 3.5 116.0 1.0 P C:C35 3.7 117.5 1.0 C2' A:1MA7 3.7 129.6 1.0 P A:G8 3.8 117.8 1.0 O3' A:1MA7 3.8 123.0 1.0 C2' C:A34 3.8 122.6 1.0 C3' A:1MA7 4.0 147.2 1.0 C3' C:A34 4.1 123.8 1.0 OP1 A:G8 4.6 144.2 1.0 OP1 C:C35 4.7 115.9 1.0 C1' C:A34 4.7 118.1 1.0 O5' C:C35 4.8 120.9 1.0 C1' A:1MA7 4.9 120.3 1.0 O5' A:G8 4.9 99.3 1.0

C.P.M.Scheitl, M.Mieczkowski, H.Schindelin, C.Hobartner. Structure and Mechanism of the Methyltransferase Ribozyme MTR1. Nat.Chem.Biol. V. 18 547 2022.
ISSN: ESSN 1552-4469
PubMed: 35301481
DOI: 10.1038/S41589-022-00976-X