Magnesium in PDB 6g6r: Human Methionine Adenosyltransferase II with Same and Ppnp

All present enzymatic activity of Human Methionine Adenosyltransferase II with Same and Ppnp:
2.5.1.6;

The structure of Human Methionine Adenosyltransferase II with Same and Ppnp, PDB code: 6g6r was solved by J.Panmanee, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.20 / 1.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.630, 94.000, 116.690, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 16.2

The structure of Human Methionine Adenosyltransferase II with Same and Ppnp also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Human Methionine Adenosyltransferase II with Same and Ppnp (pdb code 6g6r). 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 II with Same and Ppnp, PDB code: 6g6r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Methionine Adenosyltransferase II with Same and Ppnp


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 II with Same and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:11.3 occ:1.00 O2G A:PPK401 2.0 11.7 0.9 O1A A:PPK401 2.0 10.4 0.9 O1B A:PPK401 2.0 11.9 0.9 OD2 A:ASP31 2.1 9.7 1.0 O A:HOH552 2.1 11.6 1.0 O A:HOH538 2.2 12.8 1.0 CG A:ASP31 3.0 8.6 1.0 PB A:PPK401 3.1 11.6 0.9 OD1 A:ASP31 3.2 8.9 1.0 PG A:PPK401 3.3 12.8 0.8 PA A:PPK401 3.3 9.4 0.9 O3A A:PPK401 3.5 12.1 0.9 N3B A:PPK401 3.5 11.7 0.9 NZ A:LYS265 3.6 9.3 1.0 K A:K404 3.8 13.5 0.9 NH2 A:ARG264 4.0 12.1 1.0 O4A A:PPK401 4.2 11.0 0.9 O3G A:PPK401 4.2 13.0 0.9 OD2 A:ASP258 4.3 11.1 0.8 CE1 A:HIS29 4.3 8.4 1.0 O1G A:PPK401 4.3 14.4 0.9 CB A:ASP31 4.4 8.0 1.0 O2A A:PPK401 4.4 12.3 0.9 O A:ALA259 4.4 11.6 1.0 NE A:ARG264 4.4 11.3 1.0 CB A:ARG264 4.4 8.6 1.0 CZ A:ARG264 4.5 11.2 1.0 O2B A:PPK401 4.5 13.8 0.9 CE A:LYS265 4.7 9.5 1.0 O A:ARG264 4.8 7.9 1.0 NE2 A:HIS29 4.9 8.4 1.0 O A:HOH541 4.9 25.0 0.9

Magnesium binding site 2 out of 2 in the Human Methionine Adenosyltransferase II with Same and Ppnp


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 II with Same and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:10.6 occ:0.70 O4A A:PPK401 2.0 11.0 0.9 O A:HOH536 2.1 14.7 1.0 O3G A:PPK401 2.2 13.0 0.9 O A:HOH624 2.2 11.3 1.0 PA A:PPK401 3.4 9.4 0.9 PG A:PPK401 3.4 12.8 0.8 N3B A:PPK401 3.5 11.7 0.9 NZ A:LYS265 3.8 9.3 1.0 O3A A:PPK401 3.9 12.1 0.9 OE2 A:GLU23 4.0 11.3 1.0 NZ A:LYS181 4.1 9.9 1.0 O A:HOH598 4.1 14.5 1.0 O1A A:PPK401 4.2 10.4 0.9 O A:HOH632 4.2 9.9 1.0 O2A A:PPK401 4.4 12.3 0.9 O2G A:PPK401 4.4 11.7 0.9 O1G A:PPK401 4.5 14.4 0.9 CE A:LYS265 4.5 9.5 1.0 PB A:PPK401 4.5 11.6 0.9 OE1 A:GLU23 4.5 11.6 1.0 CD A:GLU23 4.7 11.5 1.0

J.Panmanee, J.Bradley-Clarke, J.M.Mato, P.M.O'neill, S.V.Antonyuk, S.S.Hasnain. Control and Regulation of S-Adenosylmethionine Biosynthesis By the Regulatory Beta Subunit and Quinolone-Based Compounds. Febs J. V. 286 2135 2019.
ISSN: ISSN 1742-464X
PubMed: 30776190
DOI: 10.1111/FEBS.14790