Sodium in PDB 7nto: The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution

The structure of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution, PDB code: 7nto was solved by M.Witzenberger, R.Janowski, E.Davydova, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.14 / 1.23
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.88, 36.3, 39.1, 90, 119.18, 90
R / Rfree (%)	12.7 / 17.2

The structure of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution (pdb code 7nto). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution, PDB code: 7nto:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:41.1 occ:1.00 NE A:ARG90 2.8 14.3 0.5 NH2 A:ARG90 3.2 14.1 0.5 CB A:ARG90 3.4 13.4 1.0 CZ A:ARG90 3.4 13.4 0.5 CG A:ARG90 3.8 14.1 0.5 O A:HOH333 3.8 24.5 1.0 CD A:ARG90 3.9 15.2 0.5 O A:HOH353 4.2 27.7 1.0 O A:HOH359 4.4 32.0 1.0 CA A:ARG90 4.6 11.9 1.0 NH1 A:ARG90 4.7 16.0 0.5 C A:ARG90 4.7 11.4 1.0 O A:HOH327 4.8 15.0 1.0 O A:ARG90 4.9 11.2 1.0

Sodium binding site 2 out of 6 in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:21.7 occ:1.00 O A:HOH368 2.9 48.1 1.0 N A:ALA119 3.1 12.8 1.0 CL A:CL213 3.5 27.6 0.8 CA A:SER118 3.5 12.0 1.0 CB A:SER118 3.7 11.4 1.0 C A:SER118 3.9 11.7 1.0 CB A:ALA119 3.9 15.4 1.0 CA A:ALA119 4.1 12.3 1.0 CZ A:PHE73 4.3 22.3 1.0 CE2 A:PHE73 4.4 20.7 1.0 O A:ARG117 4.6 17.8 1.0 N A:ALA120 4.8 11.5 1.0 N A:SER118 4.8 11.2 1.0 OG A:SER118 4.9 10.7 1.0

Sodium binding site 3 out of 6 in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:68.6 occ:1.00 O A:HOH338 2.2 52.3 1.0 NZ A:LYS74 3.5 41.4 1.0 O A:HOH311 3.7 41.6 1.0 O A:HOH343 3.7 46.5 1.0 O A:HOH355 3.8 31.1 1.0 OE1 A:GLU71 4.0 51.2 1.0 O A:HOH339 4.4 44.7 1.0 CE A:LYS74 4.5 36.8 1.0 NZ A:LYS102 4.7 26.6 0.1 CD A:GLU71 4.9 46.8 1.0

Sodium binding site 4 out of 6 in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:58.6 occ:1.00 O A:LEU126 3.0 16.3 1.0 CB A:HIS130 3.3 29.7 1.0 C A:LEU126 3.7 13.2 1.0 CG A:HIS130 3.8 32.9 1.0 CB A:LEU126 4.0 14.0 1.0 ND1 A:HIS130 4.1 36.1 1.0 CA A:LEU126 4.2 11.9 1.0 CD2 A:LEU126 4.3 16.8 1.0 CG1 A:VAL141 4.4 23.4 1.0 CA A:HIS130 4.5 22.8 1.0 CD2 A:HIS130 4.6 43.6 1.0 N A:ARG127 4.7 11.3 1.0 CG A:LEU126 4.8 15.5 1.0 N A:HIS130 5.0 17.2 1.0

Sodium binding site 5 out of 6 in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:49.6 occ:0.50 NH1 A:ARG127 3.8 19.3 1.0 CZ A:ARG127 3.9 16.9 1.0 NE A:ARG127 4.0 17.5 1.0 NH2 A:ARG127 4.4 18.0 1.0 CL A:CL212 4.5 24.5 1.0 CD A:ARG127 4.7 17.7 1.0 O A:HOH337 5.0 46.7 1.0

Sodium binding site 6 out of 6 in the The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Rrm Domain of Human TRMT2A at 1.23 A Resolution within 5.0Å range:

M.A.Margreiter, M.Witzenberger, Y.Wasser, E.Davydova, R.Janowski, J.Metz, P.Habib, S.E.M.Sahnoun, C.Sobisch, B.Poma, O.Palomino-Hernandez, M.Wagner, T.Carell, N.Jon Shah, J.B.Schulz, D.Niessing, A.Voigt, G.Rossetti. Small-Molecule Modulators of TRMT2A Decrease Polyq Aggregation and Polyq-Induced Cell Death. Comput Struct Biotechnol J V. 20 443 2022.
ISSN: ESSN 2001-0370
PubMed: 35070167
DOI: 10.1016/J.CSBJ.2021.12.029