Sodium in PDB 6sjn: Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Methyl-Tetrahydrofolate (P212121)

All present enzymatic activity of Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Methyl-Tetrahydrofolate (P212121):
2.1.1.86;

The structure of Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Methyl-Tetrahydrofolate (P212121), PDB code: 6sjn 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 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.910, 83.790, 86.550, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 17.3

The binding sites of Sodium atom in the Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Methyl-Tetrahydrofolate (P212121) (pdb code 6sjn). 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 Methyl-Tetrahydrofolate (P212121), PDB code: 6sjn:
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 Methyl-Tetrahydrofolate (P212121)


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 Methyl-Tetrahydrofolate (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:43.7 occ:1.00 O A:HOH527 2.3 23.5 1.0 O A:HOH623 2.3 24.9 1.0 O A:TYR25 2.3 19.5 1.0 O A:HOH567 3.0 22.0 1.0 O A:HOH588 3.2 31.1 1.0 C A:TYR25 3.5 17.9 1.0 O A:HOH534 3.8 27.6 1.0 C A:PRO26 3.9 16.5 1.0 O A:HOH574 4.0 34.4 1.0 N A:THR27 4.1 17.9 1.0 O A:PRO26 4.1 16.0 1.0 O A:ALA259 4.1 20.4 1.0 O A:HOH604 4.1 24.6 1.0 OD1 A:ASP260 4.3 24.1 1.0 N A:TYR25 4.3 19.0 1.0 CA A:PRO26 4.3 17.7 1.0 N A:PRO26 4.4 18.6 1.0 CA A:TYR25 4.4 18.2 1.0 OG1 A:THR27 4.5 17.6 1.0 CA A:THR27 4.5 17.5 1.0 CA A:ASP260 4.6 18.7 1.0 N A:GLY23 4.6 23.1 1.0 O A:HOH556 4.6 30.1 1.0 CB A:TYR25 4.7 18.0 1.0 O A:ASP260 4.9 18.4 1.0

Sodium binding site 2 out of 2 in the Methyltransferase Mtga From Desulfitobacterium Hafniense in Complex with Methyl-Tetrahydrofolate (P212121)


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 Methyl-Tetrahydrofolate (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:32.1 occ:1.00 OE1 B:GLU61 2.7 21.9 1.0 OE1 B:GLN60 2.9 26.1 1.0 O B:LEU57 3.1 17.9 1.0 O B:MET267 3.3 18.4 1.0 CD B:GLN60 3.6 21.8 1.0 CG B:GLN60 3.6 21.3 1.0 CB B:ALA270 3.7 16.9 1.0 N B:GLU61 3.7 18.6 1.0 CE B:MET267 3.7 21.6 1.0 CB B:GLN60 3.7 19.1 1.0 C B:LEU57 3.9 17.4 1.0 CD B:GLU61 3.9 19.4 1.0 CB B:MET267 4.0 19.4 1.0 C B:MET267 4.0 18.0 1.0 CA B:GLU61 4.1 17.9 1.0 CD2 B:LEU57 4.1 21.0 1.0 CB B:GLU61 4.1 18.0 1.0 CA B:LEU57 4.1 18.2 1.0 C B:GLN60 4.2 18.8 1.0 CA B:MET267 4.4 17.9 1.0 CB B:LEU57 4.5 20.1 1.0 CA B:GLN60 4.6 19.7 1.0 CG B:MET267 4.6 20.9 1.0 CG B:GLU61 4.6 17.5 1.0 OH B:TYR264 4.7 18.4 1.0 O B:GLN60 4.9 17.8 1.0 SD B:MET267 4.9 23.0 1.0 OE2 B:GLU61 4.9 20.1 1.0 CD1 B:LEU64 4.9 18.3 1.0 NE2 B:GLN60 4.9 20.8 1.0 CG B:LEU57 4.9 20.8 1.0 N B:MET268 5.0 17.6 1.0 CA B:ALA270 5.0 16.6 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