Magnesium in PDB 7rxw: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp):
2.5.1.6;

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp), PDB code: 7rxw 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)	19.89 / 1.07
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.322, 94.069, 117.344, 90, 90, 90
R / Rfree (%)	12.8 / 13.8

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp) also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp) (pdb code 7rxw). 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 and Inhibitor Imido-Diphosphate (Pnp), PDB code: 7rxw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)


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 and Inhibitor Imido-Diphosphate (Pnp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:11.6 occ:0.53 O A:HOH557 1.9 17.6 1.0 O3 A:2PN403 2.0 10.5 0.5 O6 A:2PN403 2.0 18.1 0.6 OD2 A:ASP31 2.1 9.7 1.0 O A:HOH526 2.1 16.9 1.0 O A:HOH520 2.1 19.4 1.0 HZ3 A:LYS265 2.9 14.7 1.0 CG A:ASP31 3.0 8.0 1.0 P2 A:2PN403 3.1 13.7 0.4 OD1 A:ASP31 3.2 8.6 1.0 P1 A:2PN403 3.3 13.3 0.7 HE1 A:HIS29 3.4 10.8 1.0 N1 A:2PN403 3.4 17.0 0.6 HZ2 A:LYS265 3.6 14.7 1.0 HH21 A:ARG264 3.6 16.2 1.0 NZ A:LYS265 3.6 12.2 1.0 O4 A:2PN403 3.6 18.3 0.4 HB3 A:ARG264 3.7 8.2 1.0 K A:K407 4.0 16.2 0.4 HZ1 A:LYS265 4.0 14.7 1.0 NH2 A:ARG264 4.0 13.5 1.0 O1 A:2PN403 4.0 14.7 0.5 O A:HOH552 4.1 28.7 1.0 HN1 A:2PN403 4.1 20.4 0.6 OD2 A:ASP258 4.1 10.2 0.6 CE1 A:HIS29 4.2 9.0 1.0 HH22 A:ARG264 4.3 16.2 1.0 O2 A:2PN403 4.3 15.3 0.9 O A:HOH506 4.3 22.9 1.0 CB A:ASP31 4.3 7.9 1.0 HB2 A:ARG264 4.4 8.2 1.0 HB2 A:ASP31 4.4 9.5 1.0 O5 A:2PN403 4.4 17.8 0.5 O A:ALA259 4.4 11.2 1.0 CB A:ARG264 4.5 6.9 1.0 HE A:ARG264 4.5 13.2 1.0 HE2 A:HIS29 4.6 10.4 1.0 CZ A:ARG264 4.6 10.4 1.0 HA2 A:GLY260 4.6 10.0 1.0 HE2 A:LYS265 4.7 14.1 1.0 NE A:ARG264 4.7 11.0 1.0 HG3 A:ARG264 4.7 10.0 1.0 O A:ARG264 4.8 7.6 1.0 HB3 A:ASP31 4.8 9.5 1.0 CE A:LYS265 4.8 11.8 1.0 O A:HOH656 4.8 14.2 1.0 MG A:MG406 4.8 13.3 0.4 NE2 A:HIS29 4.8 8.7 1.0 H A:ASP31 4.9 8.5 1.0 HD12 A:LEU261 5.0 14.5 0.4

Magnesium binding site 2 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)


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 and Inhibitor Imido-Diphosphate (Pnp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:13.3 occ:0.40 O A:HOH552 2.0 28.7 1.0 O4 A:2PN403 2.0 18.3 0.4 O1 A:2PN403 2.2 14.7 0.5 O A:HOH506 3.0 22.9 1.0 P2 A:2PN403 3.2 13.7 0.4 P1 A:2PN403 3.3 13.3 0.7 N1 A:2PN403 3.4 17.0 0.6 O A:HOH557 3.8 17.6 1.0 HZ1 A:LYS265 3.8 14.7 1.0 O A:HOH546 3.8 22.9 1.0 O A:HOH570 3.9 11.3 1.0 HN1 A:2PN403 4.0 20.4 0.6 O3 A:2PN403 4.0 10.5 0.5 O5 A:2PN403 4.2 17.8 0.5 HZ3 A:LYS265 4.2 14.7 1.0 O6 A:2PN403 4.3 18.1 0.6 HZ1 A:LYS181 4.4 12.0 1.0 O2 A:2PN403 4.4 15.3 0.9 NZ A:LYS265 4.5 12.2 1.0 O A:HOH732 4.5 18.4 1.0 O A:HOH656 4.7 14.2 1.0 HZ2 A:LYS181 4.7 12.0 1.0 MG A:MG405 4.8 11.6 0.5 HH21 A:ARG264 4.8 16.2 1.0 NZ A:LYS181 5.0 10.0 1.0 HZ2 A:LYS265 5.0 14.7 1.0

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