Sodium in PDB 8pha: O(S)-Methyltransferase From Pleurotus Sapidus

The structure of O(S)-Methyltransferase From Pleurotus Sapidus, PDB code: 8pha was solved by L.Korf, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.363, 109.116, 192.925, 90, 90, 90
R / Rfree (%)	17.1 / 21.2

The binding sites of Sodium atom in the O(S)-Methyltransferase From Pleurotus Sapidus (pdb code 8pha). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the O(S)-Methyltransferase From Pleurotus Sapidus, PDB code: 8pha:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the O(S)-Methyltransferase From Pleurotus Sapidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of O(S)-Methyltransferase From Pleurotus Sapidus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:47.5 occ:1.00 OE1 C:GLN101 2.2 44.3 1.0 O A:HOH816 2.6 35.7 1.0 O A:HOH618 2.9 31.7 1.0 O C:HOH798 3.0 29.9 1.0 CD C:GLN101 3.2 42.7 1.0 O C:HOH610 3.2 25.1 1.0 NH2 C:ARG180 3.3 23.6 1.0 O A:HOH748 3.7 45.6 1.0 NE2 C:GLN101 3.7 41.0 1.0 CB C:GLU177 3.9 35.2 1.0 OD2 A:ASP188 3.9 27.1 1.0 CG C:GLN101 4.3 35.2 1.0 CZ C:ARG180 4.5 25.1 1.0 CG C:GLU177 4.6 46.3 1.0 CG A:ASP188 4.7 32.2 1.0 N C:GLU177 4.7 30.5 1.0 CA C:GLU177 4.8 32.4 1.0 O C:HOH727 4.8 20.9 1.0 OD1 A:ASP188 4.8 29.8 1.0 OG C:SER97 4.9 23.7 1.0 NH1 C:ARG180 4.9 23.1 1.0 CB A:TYR187 4.9 24.6 1.0

Sodium binding site 2 out of 4 in the O(S)-Methyltransferase From Pleurotus Sapidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of O(S)-Methyltransferase From Pleurotus Sapidus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:53.7 occ:1.00 O A:HOH805 2.1 35.6 1.0 O C:HOH800 2.2 46.3 1.0 O A:HOH672 2.3 46.9 1.0 O C:HOH787 2.7 51.6 1.0 OE1 C:GLN12 3.7 40.8 1.0 O A:PRO39 3.7 30.3 1.0 CG2 C:THR75 4.3 24.5 1.0 CD C:GLN12 4.3 34.5 1.0 CA A:SER40 4.4 32.6 1.0 N A:LEU41 4.6 31.4 1.0 CB C:GLN12 4.7 29.0 1.0 OG1 C:THR75 4.7 27.9 1.0 O A:HOH727 4.8 41.5 1.0 C A:PRO39 4.8 36.6 1.0 NE2 C:GLN12 4.9 44.9 1.0 CA C:GLY9 4.9 34.2 1.0 O C:HOH829 5.0 49.0 1.0

Sodium binding site 3 out of 4 in the O(S)-Methyltransferase From Pleurotus Sapidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of O(S)-Methyltransferase From Pleurotus Sapidus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:47.4 occ:1.00 OE1 D:GLN101 2.2 38.6 1.0 O B:HOH801 2.7 37.5 1.0 O D:HOH795 2.8 30.3 1.0 O B:HOH629 2.9 29.6 1.0 O D:HOH648 3.1 25.8 1.0 CD D:GLN101 3.2 35.6 1.0 NH2 D:ARG180 3.3 25.8 1.0 O B:HOH724 3.5 41.9 1.0 NE2 D:GLN101 3.8 39.8 1.0 CB D:GLU177 3.9 35.6 1.0 OD2 B:ASP188 4.1 31.8 1.0 CG D:GLN101 4.2 36.2 1.0 O D:HOH819 4.3 48.2 1.0 CZ D:ARG180 4.4 25.8 1.0 NH1 D:ARG180 4.7 19.9 1.0 CG D:GLU177 4.7 42.8 1.0 N D:GLU177 4.7 23.4 1.0 OG D:SER97 4.8 20.6 1.0 CA D:GLU177 4.8 27.5 1.0 O D:HOH703 4.9 22.0 1.0 CG B:ASP188 4.9 30.6 1.0 CB B:TYR187 4.9 22.7 1.0

Sodium binding site 4 out of 4 in the O(S)-Methyltransferase From Pleurotus Sapidus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of O(S)-Methyltransferase From Pleurotus Sapidus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na504 b:59.8 occ:1.00 O B:HOH852 2.1 39.0 1.0 O D:HOH809 2.3 53.4 1.0 O B:HOH783 2.4 55.3 1.0 O D:HOH774 2.6 42.0 1.0 O B:PRO39 3.7 35.5 1.0 OE1 D:GLN12 3.7 38.9 1.0 O B:HOH843 3.8 53.5 1.0 CG2 D:THR75 4.2 29.1 1.0 CD D:GLN12 4.3 40.6 1.0 CA B:SER40 4.4 34.4 1.0 OG1 D:THR75 4.6 30.9 1.0 N B:LEU41 4.7 34.9 1.0 O B:HOH780 4.7 50.5 1.0 CB D:GLN12 4.7 29.4 1.0 C B:PRO39 4.7 38.3 1.0 O D:HOH855 4.8 56.1 1.0 NE2 D:GLN12 4.9 45.8 1.0 O D:HOH638 5.0 41.8 1.0

F.F.Brescia, L.Korf, L.O.Essen, H.Zorn, M.Ruehl. A Novel O - and S -Methyltransferase From Pleurotus Sapidus Is Involved in Flavor Formation. J.Agric.Food Chem. 2024.
ISSN: ESSN 1520-5118
PubMed: 38462720
DOI: 10.1021/ACS.JAFC.3C08849