Sodium in PDB 5cd1: Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS

All present enzymatic activity of Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS:
2.1.1.220;

The structure of Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS, PDB code: 5cd1 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)	59.39 / 3.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.240, 137.440, 157.590, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.3

The binding sites of Sodium atom in the Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS (pdb code 5cd1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS, PDB code: 5cd1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS within 5.0Å range: probe atom residue distance (Å) B Occ M:Na101 b:51.0 occ:1.00 OP1 M:U8 2.5 0.8 1.0 OP2 M:A9 2.6 0.3 1.0 H5 M:U12 2.6 0.9 1.0 OP2 M:U12 3.1 0.0 1.0 OP1 M:A9 3.2 0.0 1.0 P M:A9 3.4 1.0 1.0 C5 M:U12 3.6 0.6 1.0 H5'' M:U8 3.8 0.4 1.0 P M:U8 3.8 0.1 1.0 OP2 M:C11 3.9 0.6 1.0 H6 M:U12 4.2 0.8 1.0 H3' M:C11 4.3 90.5 1.0 O5' M:U8 4.3 91.8 1.0 O5' M:C11 4.3 84.3 1.0 C6 M:U12 4.3 0.3 1.0 O3' M:U8 4.5 82.4 1.0 C4 M:U12 4.5 0.5 1.0 P M:C11 4.5 83.2 1.0 O4 M:U12 4.5 97.4 1.0 C5' M:U8 4.5 0.1 1.0 P M:U12 4.5 76.2 1.0 O5' M:A9 4.6 88.9 1.0 OP1 M:C11 4.6 81.0 1.0 H3' M:U8 4.6 0.8 1.0 OP2 M:U8 4.7 95.8 1.0 O3' M:A7 4.9 0.0 1.0 O5' M:U12 4.9 71.7 1.0

Sodium binding site 2 out of 2 in the Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Asymmetric Tetramer of Human Trna M1A58 Methyltransferase in A Complex with Sah and TRNA3LYS within 5.0Å range: probe atom residue distance (Å) B Occ N:Na101 b:69.9 occ:1.00 OP1 N:U8 3.0 98.5 1.0 OP1 N:A9 3.1 0.9 1.0 OP2 N:U12 3.3 0.3 1.0 H5'' N:C11 3.5 98.6 1.0 OP2 N:A9 3.6 78.3 1.0 P N:A9 3.8 0.3 1.0 OP2 N:C11 4.2 0.1 1.0 OP1 N:C11 4.2 93.0 1.0 H5'' N:U8 4.2 0.9 1.0 H5 N:U12 4.3 0.7 1.0 C5' N:C11 4.4 82.1 1.0 H5' N:C11 4.4 98.6 1.0 P N:U8 4.5 0.3 1.0 H3' N:C11 4.6 98.0 1.0 P N:C11 4.6 90.6 1.0 P N:U12 4.7 0.2 1.0 O3' N:U8 4.8 0.5 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