Magnesium in PDB 7rxx: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site:
2.5.1.6;

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site, PDB code: 7rxx 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)	19.88 / 1.25
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.224, 94.121, 117.159, 90, 90, 90
R / Rfree (%)	12.9 / 14.1

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site also contains other interesting chemical elements:

Sodium	(Na)	4 atoms
Potassium	(K)	1 atom

The binding sites of Magnesium atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site (pdb code 7rxx). 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 Two Sulfate in the Active Site, PDB code: 7rxx:
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 Two Sulfate in the Active Site


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 Two Sulfate in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:6.7 occ:0.72 O4 A:SO4405 2.0 8.6 0.9 O A:HOH531 2.0 14.5 1.0 O3 A:SO4406 2.1 9.0 0.8 O A:HOH548 2.1 11.7 1.0 O A:HOH538 2.1 10.4 0.5 OD2 A:ASP31 2.2 7.6 1.0 O A:HOH538 2.9 10.4 0.5 CG A:ASP31 3.1 6.2 1.0 HZ1 A:LYS265 3.1 10.2 1.0 O A:HOH501 3.2 12.9 0.6 S A:SO4405 3.3 3.9 0.7 OD1 A:ASP31 3.3 6.4 1.0 S A:SO4406 3.3 7.5 0.5 HE1 A:HIS29 3.4 7.4 1.0 O4 A:SO4406 3.4 14.6 0.6 HZ3 A:LYS265 3.4 10.2 1.0 O3 A:SO4405 3.5 10.8 0.9 NZ A:LYS265 3.7 8.4 1.0 HH21 A:ARG264 3.8 13.7 1.0 HB3 A:ARG264 3.8 6.2 1.0 K A:K409 3.9 10.0 0.7 O2 A:SO4405 4.0 10.7 1.0 HZ2 A:LYS265 4.1 10.2 1.0 NH2 A:ARG264 4.1 11.4 1.0 O2 A:SO4406 4.2 11.4 0.7 OD2 A:ASP258 4.2 9.0 0.5 CE1 A:HIS29 4.3 6.2 1.0 O1 A:SO4405 4.3 7.5 0.9 O1 A:SO4406 4.3 15.0 0.6 O A:ALA259 4.4 8.3 1.0 HB2 A:ARG264 4.4 6.2 1.0 CB A:ASP31 4.4 5.5 1.0 HH22 A:ARG264 4.4 13.7 1.0 HB2 A:ASP31 4.5 6.7 1.0 HE A:ARG264 4.5 10.6 1.0 CB A:ARG264 4.5 5.1 1.0 HE2 A:HIS29 4.6 7.4 1.0 HA2 A:GLY260 4.6 8.0 1.0 CZ A:ARG264 4.7 9.6 1.0 HE2 A:LYS265 4.7 11.1 1.0 NE A:ARG264 4.7 8.8 1.0 NE2 A:HIS29 4.8 6.1 1.0 CE A:LYS265 4.8 9.3 1.0 HG3 A:ARG264 4.8 7.8 1.0 O A:HOH502 4.8 11.8 0.6 HD12 A:LEU261 4.9 14.1 0.4 HB3 A:ASP31 4.9 6.7 1.0 O A:ARG264 4.9 5.6 1.0 OD1 A:ASP258 5.0 14.5 0.8 CG A:ASP258 5.0 9.7 0.7 H5'1 A:MTA402 5.0 12.1 1.0 H A:ASP31 5.0 5.8 1.0

Magnesium binding site 2 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site


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 Two Sulfate in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:11.6 occ:0.52 O A:HOH502 1.7 11.8 0.6 O2 A:SO4405 1.9 10.7 1.0 O A:HOH599 2.0 10.7 0.6 O2 A:SO4406 2.2 11.4 0.7 O A:HOH581 2.6 11.9 1.0 S A:SO4405 3.3 3.9 0.7 HZ1 A:LYS181 3.4 6.2 1.0 HZ2 A:LYS265 3.5 10.2 1.0 HZ1 A:LYS265 3.5 10.2 1.0 S A:SO4406 3.5 7.5 0.5 O4 A:SO4406 3.7 14.6 0.6 O3 A:SO4405 3.7 10.8 0.9 NZ A:LYS265 3.9 8.4 1.0 HE3 A:LYS265 4.0 11.1 1.0 O A:HOH601 4.0 13.8 1.0 OE2 A:GLU23 4.0 6.9 0.8 HZ2 A:LYS181 4.1 6.2 1.0 O4 A:SO4405 4.1 8.6 0.9 O1 A:SO4405 4.1 7.5 0.9 NZ A:LYS181 4.1 5.2 0.7 O3 A:SO4406 4.2 9.0 0.8 O A:HOH610 4.3 7.7 1.0 O A:HOH501 4.4 12.9 0.6 CE A:LYS265 4.5 9.3 1.0 O1 A:SO4406 4.5 15.0 0.6 HZ3 A:LYS265 4.6 10.2 1.0 HZ3 A:LYS181 4.6 6.2 1.0 OE1 A:GLU23 4.7 9.2 0.9 CD A:GLU23 4.8 6.3 0.7 HE3 A:LYS181 4.9 8.1 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