Sodium in PDB 7rey: Mycobacterium Abscessus Trna Methyltransferase in Apo Form

All present enzymatic activity of Mycobacterium Abscessus Trna Methyltransferase in Apo Form:
2.1.1.228;

The structure of Mycobacterium Abscessus Trna Methyltransferase in Apo Form, PDB code: 7rey was solved by G.R.Prucha, M.Ismail, A.Suske, B.Das, M.Oz, A.Perez, R.Bolen, S.Jayaraman, V.Stojanoff, J.Halloran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.26 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.785, 79.375, 86.604, 90, 90, 90
R / Rfree (%)	17.4 / 22.6

The binding sites of Sodium atom in the Mycobacterium Abscessus Trna Methyltransferase in Apo Form (pdb code 7rey). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mycobacterium Abscessus Trna Methyltransferase in Apo Form, PDB code: 7rey:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mycobacterium Abscessus Trna Methyltransferase in Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Abscessus Trna Methyltransferase in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:50.0 occ:1.00 NA B:NA302 2.7 53.2 1.0 OD2 B:ASP121 2.8 35.9 1.0 O B:VAL118 2.9 31.1 1.0 CB B:ASP121 3.6 34.2 1.0 CG B:ASP121 3.6 38.4 1.0 N B:ALA122 3.6 33.8 1.0 CH2 A:TRP190 3.7 33.9 1.0 C B:VAL118 3.8 30.3 1.0 CA B:VAL118 3.8 27.6 1.0 CG1 B:VAL118 3.8 29.7 1.0 NH1 B:ARG125 4.0 54.4 1.0 CB B:ALA122 4.1 34.1 1.0 NH1 A:ARG191 4.1 40.5 1.0 CA B:GLY67 4.1 34.6 1.0 CA B:ALA122 4.2 33.9 1.0 C B:ASP121 4.2 34.4 1.0 CB B:VAL118 4.3 30.3 1.0 CZ3 A:TRP190 4.4 32.7 1.0 CA B:ASP121 4.5 36.0 1.0 CD1 B:LEU70 4.5 37.4 1.0 O B:ARG117 4.7 29.9 1.0 CZ2 A:TRP190 4.7 32.2 1.0 N B:GLY67 4.8 34.5 1.0 OD1 B:ASP121 4.8 39.3 1.0 O B:GLY67 4.9 41.0 1.0 CB B:LEU70 4.9 35.9 1.0 CG2 B:VAL118 4.9 29.6 1.0 N B:ASP121 5.0 34.5 1.0 N B:VAL118 5.0 29.8 1.0

Sodium binding site 2 out of 2 in the Mycobacterium Abscessus Trna Methyltransferase in Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Abscessus Trna Methyltransferase in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:53.2 occ:1.00 NA B:NA301 2.7 50.0 1.0 NH1 B:ARG125 3.0 54.4 1.0 O B:GLY67 3.1 41.0 1.0 OD1 B:ASP71 3.2 48.2 1.0 NH1 A:ARG191 3.4 40.5 1.0 CB B:LEU70 3.5 35.9 1.0 OD2 B:ASP121 3.6 35.9 1.0 N B:ASP71 3.8 38.4 1.0 NH2 B:ARG125 3.8 59.8 1.0 CZ B:ARG125 3.8 64.4 1.0 CA B:GLY67 3.8 34.6 1.0 C B:GLY67 3.9 32.9 1.0 C B:LEU70 4.0 39.0 1.0 CG B:ASP71 4.1 50.4 1.0 CA B:LEU70 4.2 37.3 1.0 CA B:ASP71 4.5 42.6 1.0 CZ A:ARG191 4.5 38.4 1.0 CD1 B:LEU70 4.6 37.4 1.0 CG B:LEU70 4.6 33.7 1.0 O B:LEU70 4.6 38.0 1.0 O B:TRP66 4.7 32.9 1.0 N B:LEU70 4.7 35.0 1.0 CG B:ASP121 4.8 38.4 1.0 CB B:ASP71 4.8 44.1 1.0 NH2 A:ARG191 4.8 39.3 1.0 OD2 B:ASP71 4.9 49.0 1.0 CB B:ALA122 4.9 34.1 1.0 N B:GLY67 4.9 34.5 1.0 CA B:ALA122 4.9 33.9 1.0

G.R.Prucha, M.Ismail, A.Suske, A.Perez, R.Bolen, S.Jayaraman, V.Stojanoff, J.Halloran. Crystal Structure of Divalent MG2+ Dependent Mycobacterium Abscessus Trna (M1 G37) Methyltransferase (Trmd) To Be Published.