Sodium in PDB 6sj8: Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate

All present enzymatic activity of Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate:
2.1.1.86;

The structure of Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate, PDB code: 6sj8 was solved by T.Badmann, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.760, 83.850, 86.490, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 15.7

The binding sites of Sodium atom in the Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate (pdb code 6sj8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate, PDB code: 6sj8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:26.9 occ:1.00 O A:HOH1130 2.1 20.3 1.0 O A:HOH1169 2.2 23.7 1.0 O A:HOH1054 2.2 15.9 1.0 O A:TYR25 2.3 13.9 1.0 O A:HOH1095 2.9 21.3 1.0 O A:HOH1057 3.3 17.8 1.0 C A:TYR25 3.5 12.3 1.0 O A:HOH1090 3.8 18.2 1.0 C A:PRO26 3.9 12.4 1.0 O A:HOH1084 4.0 25.0 1.0 N A:THR27 4.0 11.7 1.0 O A:ALA259 4.2 13.6 1.0 O A:PRO26 4.2 13.6 1.0 O A:HOH1164 4.3 17.8 1.0 CA A:PRO26 4.3 14.3 1.0 N A:TYR25 4.3 13.8 1.0 N A:PRO26 4.3 13.0 1.0 OG1 A:THR27 4.4 12.9 1.0 N A:GLY23 4.4 17.4 1.0 O A:HOH1126 4.4 21.3 1.0 CA A:TYR25 4.4 14.7 1.0 CA A:THR27 4.5 11.4 1.0 OD1 A:ASP260 4.6 16.1 1.0 OD1 A:ASP281 4.7 12.5 1.0 CA A:ASP260 4.8 9.9 1.0 CB A:TYR25 4.9 14.8 1.0 O A:GLN21 4.9 17.0 1.0 CA A:GLY23 4.9 17.6 1.0

Sodium binding site 2 out of 2 in the Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Tetrahydrofolate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:31.6 occ:1.00 O11 B:44V901 2.5 23.5 1.0 CD1 B:PHE156 2.9 40.1 1.0 N B:VAL197 3.0 14.4 1.0 O B:HOH1231 3.2 35.1 1.0 CE1 B:PHE156 3.2 44.2 1.0 O B:HOH1019 3.3 23.9 1.0 O B:VAL197 3.4 18.4 1.0 N03 B:44V901 3.5 39.1 1.0 C10 B:44V901 3.5 20.8 1.0 CA B:GLY196 3.6 13.4 1.0 C B:GLY196 3.8 12.6 1.0 CG B:PHE156 3.8 32.1 1.0 O B:HOH1023 3.8 14.8 1.0 CA B:VAL197 3.9 13.7 1.0 C B:VAL197 3.9 15.7 1.0 C04 B:44V901 3.9 29.3 1.0 CB B:PHE156 4.3 22.6 1.0 CB B:VAL197 4.3 14.4 1.0 CZ B:PHE156 4.4 50.6 1.0 C02 B:44V901 4.5 39.8 1.0 N09 B:44V901 4.7 17.1 1.0 O B:ALA224 4.7 12.9 1.0 CD2 B:PHE156 4.8 42.6 1.0 O B:HOH1132 4.8 16.8 1.0 C13 B:44V901 4.8 60.6 1.0 N B:GLY196 4.9 12.3 1.0 CG2 B:VAL197 5.0 14.0 1.0 O B:GLY196 5.0 13.3 1.0

T.Badmann, M.Groll. Structures in Tetrahydrofolate Methylation in Desulfitobacterial Glycine Betaine Metabolism at Atomic Resolution. Chembiochem 2019.
ISSN: ESSN 1439-7633
PubMed: 31518049
DOI: 10.1002/CBIC.201900515