Magnesium in PDB 8swa: Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp

All present enzymatic activity of Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp:
2.5.1.6;

The structure of Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp, PDB code: 8swa was solved by K.J.Bruemmer, V.N.Pham, J.D.W.Toh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.86 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.698, 100.421, 122.74, 90, 90, 90
R / Rfree (%)	14.3 / 19.4

The structure of Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp (pdb code 8swa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp, PDB code: 8swa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:6.4 occ:1.00 O2G A:PPK601 1.9 15.0 1.0 O1B A:PPK601 2.0 10.9 1.0 O2A A:PPK601 2.0 11.7 1.0 O A:HOH736 2.0 10.9 1.0 OD2 A:ASP31 2.0 9.4 1.0 O A:HOH750 2.1 13.2 1.0 CG A:ASP31 3.0 11.1 1.0 PB A:PPK601 3.1 13.2 1.0 PG A:PPK601 3.1 22.6 1.0 PA A:PPK601 3.2 11.8 1.0 OD1 A:ASP31 3.4 9.6 1.0 O3A A:PPK601 3.5 14.9 1.0 N3B A:PPK601 3.5 15.8 1.0 NZ A:LYS265 3.6 9.9 1.0 K A:K604 3.8 27.6 1.0 O4A A:PPK601 4.0 12.7 1.0 O3G A:PPK601 4.0 16.4 1.0 O1G A:PPK601 4.1 17.4 1.0 NH1 A:ARG264 4.1 19.0 1.0 OD2 A:ASP258 4.3 18.5 1.0 CE1 A:HIS29 4.3 7.1 1.0 O2B A:PPK601 4.3 16.4 1.0 CB A:ASP31 4.3 8.7 1.0 O1A A:PPK601 4.4 12.9 1.0 O A:ALA259 4.5 13.6 1.0 CB A:ARG264 4.5 10.7 1.0 O A:HOH706 4.5 21.6 1.0 MG A:MG603 4.6 21.8 1.0 NE A:ARG264 4.6 14.4 1.0 CZ A:ARG264 4.6 15.4 1.0 CE A:LYS265 4.6 8.6 1.0 O A:ARG264 4.8 9.9 1.0 NE2 A:HIS29 4.8 8.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Human S-Adenosylmethionine Synthetase 1 in Complex with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:21.8 occ:1.00 N3B A:PPK601 1.9 15.8 1.0 O A:HOH778 1.9 17.3 1.0 O3G A:PPK601 2.1 16.4 1.0 O4A A:PPK601 2.2 12.7 1.0 PG A:PPK601 2.5 22.6 1.0 PB A:PPK601 3.2 13.2 1.0 PA A:PPK601 3.2 11.8 1.0 O3A A:PPK601 3.3 14.9 1.0 O1G A:PPK601 3.6 17.4 1.0 O2G A:PPK601 3.6 15.0 1.0 O2A A:PPK601 3.8 11.7 1.0 O A:HOH727 3.9 13.3 1.0 O A:HOH719 4.0 23.0 1.0 O A:HOH858 4.0 21.5 1.0 O1B A:PPK601 4.1 10.9 1.0 O2B A:PPK601 4.2 16.4 1.0 NZ A:LYS265 4.2 9.9 1.0 O1A A:PPK601 4.4 12.9 1.0 MG A:MG602 4.6 6.4 1.0 O A:HOH706 4.7 21.6 1.0 NZ A:LYS181 4.9 12.1 1.0

V.N.Pham, K.J.Bruemmer, J.D.W.Toh, E.J.Ge, L.Tenney, C.C.Ward, F.A.Dingler, C.L.Millington, C.A.Garcia-Prieto, M.C.Pulos-Holmes, N.T.Ingolia, L.B.Pontel, M.Esteller, K.J.Patel, D.K.Nomura, C.J.Chang. Formaldehyde Regulates S -Adenosylmethionine Biosynthesis and One-Carbon Metabolism. Science V. 382 P9201 2023.
ISSN: ESSN 1095-9203
PubMed: 37917677
DOI: 10.1126/SCIENCE.ABP9201