Magnesium in PDB 7rxv: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3:
2.5.1.6;

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3, PDB code: 7rxv was solved by E.Fedorov, C.N.Niland, V.L.Schramm, A.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 1.07
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.981, 94.122, 117.315, 90, 90, 90
R / Rfree (%)	13 / 13.9

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Potassium	(K)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 (pdb code 7rxv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3, PDB code: 7rxv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:31.8 occ:1.00 MG A:MGF504 0.0 31.8 1.0 F3 A:MGF504 1.8 25.9 0.4 F2 A:MGF504 1.8 21.7 0.7 F1 A:MGF504 1.8 15.6 0.8 O A:HOH785 2.3 12.9 1.0 HH21 A:ARG264 2.8 14.3 1.0 MG A:MG506 3.1 8.8 1.0 HC22 A:MLA503 3.2 17.6 1.0 HE A:ARG264 3.2 13.3 1.0 O3B A:MLA503 3.3 11.4 1.0 HZ1 A:LYS265 3.3 13.5 1.0 HZ2 A:LYS265 3.3 13.5 1.0 C3 A:MLA503 3.4 10.7 1.0 O1A A:MLA503 3.5 9.2 1.0 NH2 A:ARG264 3.6 11.9 1.0 NZ A:LYS265 3.6 11.3 1.0 C2 A:MLA503 3.6 14.7 1.0 HZ3 A:LYS265 3.7 13.5 1.0 HB3 A:ARG264 3.8 8.9 1.0 C1 A:MLA503 3.9 9.7 1.0 NE A:ARG264 3.9 11.1 1.0 O A:ARG264 4.1 8.3 1.0 O3A A:MLA503 4.1 14.8 1.0 O A:HOH701 4.2 22.6 1.0 OD2 A:ASP31 4.2 7.9 1.0 HH22 A:ARG264 4.2 14.3 1.0 O A:HOH637 4.2 10.1 1.0 O A:HOH807 4.2 17.1 1.0 CZ A:ARG264 4.2 10.2 1.0 HC21 A:MLA503 4.6 17.6 1.0 CB A:ARG264 4.8 7.4 1.0 O1B A:MLA503 5.0 10.3 1.0 O A:HOH748 5.0 17.2 0.5

Magnesium binding site 2 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:8.8 occ:1.00 F1 A:MGF504 1.8 15.6 0.8 O1A A:MLA503 2.0 9.2 1.0 O3B A:MLA503 2.0 11.4 1.0 OD2 A:ASP31 2.1 7.9 1.0 O A:HOH637 2.1 10.1 1.0 O A:HOH631 2.1 9.8 1.0 C3 A:MLA503 3.0 10.7 1.0 CG A:ASP31 3.0 7.1 1.0 C1 A:MLA503 3.0 9.7 1.0 HZ1 A:LYS265 3.0 13.5 1.0 MG A:MGF504 3.1 31.8 1.0 OD1 A:ASP31 3.3 7.9 1.0 HE1 A:HIS29 3.3 10.3 1.0 HZ3 A:LYS265 3.4 13.5 1.0 C2 A:MLA503 3.4 14.7 1.0 NZ A:LYS265 3.6 11.3 1.0 HH21 A:ARG264 3.6 14.3 1.0 HB3 A:ARG264 3.7 8.9 1.0 K A:K507 3.8 10.2 0.5 HC22 A:MLA503 3.9 17.6 1.0 F3 A:MGF504 4.0 25.9 0.4 NH2 A:ARG264 4.0 11.9 1.0 HZ2 A:LYS265 4.1 13.5 1.0 O3A A:MLA503 4.1 14.8 1.0 O1B A:MLA503 4.1 10.3 1.0 OD2 A:ASP258 4.2 9.3 0.7 CE1 A:HIS29 4.2 8.6 1.0 HC21 A:MLA503 4.2 17.6 1.0 F2 A:MGF504 4.3 21.7 0.7 CB A:ASP31 4.3 7.8 1.0 HH22 A:ARG264 4.3 14.3 1.0 HB2 A:ARG264 4.4 8.9 1.0 HB2 A:ASP31 4.4 9.4 1.0 O A:ALA259 4.4 9.7 1.0 HE A:ARG264 4.5 13.3 1.0 CB A:ARG264 4.5 7.4 1.0 O A:HOH785 4.5 12.9 1.0 HE2 A:HIS29 4.5 9.9 1.0 CZ A:ARG264 4.6 10.2 1.0 HE2 A:LYS265 4.6 13.1 1.0 NE A:ARG264 4.7 11.1 1.0 HA2 A:GLY260 4.7 10.4 1.0 HG3 A:ARG264 4.7 10.4 1.0 CE A:LYS265 4.7 10.9 1.0 NE2 A:HIS29 4.8 8.2 1.0 HB3 A:ASP31 4.8 9.4 1.0 O A:ARG264 4.9 8.3 1.0 H A:ASP31 4.9 9.2 1.0 HD12 A:LEU261 4.9 13.3 0.4

A.Ghosh, C.N.Niland, S.M.Cahill, N.M.Karadkhelkar, V.L.Schramm. Mechanism of Triphosphate Hydrolysis By Human MAT2A at 1.07 Angstrom Resolution. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 34668717
DOI: 10.1021/JACS.1C09328