Sodium in PDB 5ccb: Crystal Structure of Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah

All present enzymatic activity of Crystal Structure of Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah:
2.1.1.220;

The structure of Crystal Structure of Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah, PDB code: 5ccb was solved by J.Finer-Moore, N.Czudnochowski, J.D.O'connell Iii, A.L.Wang, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.37 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.180, 137.180, 177.020, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.2

The binding sites of Sodium atom in the Crystal Structure of Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah (pdb code 5ccb). 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 Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah, PDB code: 5ccb:

Sodium binding site 1 out of 1 in the Crystal Structure of Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah


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 Human M1A58 Methyltransferase in A Complex with TRNA3LYS and Sah within 5.0Å range: probe atom residue distance (Å) B Occ N:Na101 b:42.8 occ:1.00 OP1 N:U8 2.1 45.9 1.0 OP2 N:A9 2.1 40.7 1.0 O N:HOH276 2.1 46.8 1.0 O N:HOH249 2.1 43.1 1.0 O N:HOH255 2.2 45.8 1.0 O N:HOH211 2.4 44.3 1.0 P N:A9 3.3 40.9 1.0 P N:U8 3.5 42.4 1.0 H5'' N:U8 3.7 54.3 1.0 OP1 N:A9 3.8 43.5 1.0 O N:HOH233 3.9 46.5 1.0 O N:HOH268 3.9 51.7 1.0 O N:HOH223 3.9 37.8 1.0 OP2 N:U12 3.9 48.1 1.0 H5 N:U12 4.0 51.2 1.0 O N:HOH304 4.1 63.9 1.0 H3' N:U8 4.1 43.8 1.0 O5' N:U8 4.2 46.1 1.0 O3' N:U8 4.2 44.3 1.0 O N:HOH278 4.3 48.7 1.0 OP2 N:U8 4.3 36.9 1.0 C5' N:U8 4.4 45.2 1.0 O N:HOH256 4.4 46.4 1.0 O5' N:A9 4.5 41.7 1.0 O3' N:A7 4.5 49.5 1.0 OP2 N:C11 4.5 47.1 1.0 O N:HOH301 4.6 51.9 1.0 C3' N:U8 4.6 36.5 1.0 C5 N:U12 4.8 42.6 1.0

J.Finer-Moore, N.Czudnochowski, J.D.O'connell, A.L.Wang, R.M.Stroud. Crystal Structure of the Human Trna M(1)A58 Methyltransferase-TRNA3(Lys) Complex: Refolding of Substrate Trna Allows Access to the Methylation Target. J.Mol.Biol. V. 427 3862 2015.
ISSN: ESSN 1089-8638
PubMed: 26470919
DOI: 10.1016/J.JMB.2015.10.005