Magnesium in PDB 7low: S-Adenosylmethionine Synthetase

All present enzymatic activity of S-Adenosylmethionine Synthetase:
2.5.1.6;

The structure of S-Adenosylmethionine Synthetase, PDB code: 7low was solved by L.L.Tan, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.10 / 2.39
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.954, 122.954, 288.087, 90, 90, 120
R / Rfree (%)	18.2 / 21.7

The binding sites of Magnesium atom in the S-Adenosylmethionine Synthetase (pdb code 7low). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S-Adenosylmethionine Synthetase, PDB code: 7low:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the S-Adenosylmethionine Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S-Adenosylmethionine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:49.8 occ:1.00 O3 A:POP401 2.0 60.2 1.0 O3 A:PO4402 2.0 51.1 1.0 O6 A:POP401 2.1 55.7 1.0 O A:HOH507 2.1 47.4 1.0 OD2 A:ASP16 2.2 56.7 1.0 O A:HOH531 2.5 44.9 1.0 P1 A:POP401 3.1 49.2 1.0 P2 A:POP401 3.1 56.1 1.0 CG A:ASP16 3.2 52.2 1.0 O A:POP401 3.2 44.7 1.0 NZ A:LYS245 3.3 39.7 1.0 P A:PO4402 3.4 64.8 1.0 OD1 A:ASP16 3.6 49.4 1.0 O5 A:POP401 3.8 60.1 1.0 O1 A:POP401 3.8 60.1 1.0 O4 A:PO4402 3.8 65.7 1.0 OD2 A:ASP238 3.9 114.6 1.0 O B:HOH503 4.1 73.2 1.0 CE1 A:HIS14 4.1 50.9 1.0 O1 A:PO4402 4.3 55.8 1.0 O2 A:POP401 4.3 47.7 1.0 O4 A:POP401 4.3 57.3 1.0 O2 A:PO4402 4.4 62.5 1.0 CB A:ASP16 4.5 41.9 1.0 O A:CYS239 4.5 52.3 1.0 CE A:LYS245 4.7 39.5 1.0 NH2 A:ARG244 4.8 44.0 1.0 NE2 A:HIS14 4.8 50.0 1.0 CB A:ARG244 4.9 41.6 1.0

Magnesium binding site 2 out of 4 in the S-Adenosylmethionine Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S-Adenosylmethionine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:65.1 occ:1.00 O6 B:POP401 2.0 58.3 1.0 OD2 A:ASP271 2.2 59.9 1.0 O2 A:PO4403 2.3 54.7 0.9 O2 B:POP401 2.6 64.3 1.0 CG A:ASP271 3.2 52.4 1.0 O B:HOH530 3.3 57.7 1.0 P2 B:POP401 3.4 57.2 1.0 OD1 A:ASP271 3.4 62.5 1.0 P A:PO4403 3.8 54.3 0.9 P1 B:POP401 3.8 64.1 1.0 O B:POP401 3.9 54.9 1.0 O4 B:POP401 4.2 63.5 1.0 NZ B:LYS245 4.3 55.2 1.0 O3 A:PO4403 4.4 46.1 0.9 O5 B:POP401 4.4 61.5 1.0 CA A:GLY260 4.4 49.6 1.0 O4 A:PO4403 4.5 46.5 0.9 OD2 A:ASP118 4.5 60.9 1.0 CB A:ASP271 4.6 48.2 1.0 NZ A:LYS265 4.6 56.3 1.0 NZ B:LYS165 4.6 51.7 1.0 O1 A:PO4403 4.7 65.3 0.9 O3 B:POP401 4.8 83.2 1.0 O1 B:POP401 4.8 64.7 1.0 OE2 B:GLU8 5.0 68.0 1.0 O B:HOH534 5.0 51.7 1.0

Magnesium binding site 3 out of 4 in the S-Adenosylmethionine Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S-Adenosylmethionine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:64.8 occ:1.00 O1 A:POP401 2.0 60.1 1.0 O4 A:PO4402 2.3 65.7 1.0 OD2 B:ASP271 2.4 52.6 1.0 O5 A:POP401 2.7 60.1 1.0 CG B:ASP271 3.2 51.1 1.0 OD1 B:ASP271 3.3 57.8 1.0 P1 A:POP401 3.4 49.2 1.0 O A:HOH525 3.5 48.7 1.0 P A:PO4402 3.8 64.8 1.0 P2 A:POP401 3.9 56.1 1.0 O A:POP401 3.9 44.7 1.0 O3 A:POP401 4.3 60.2 1.0 O2 A:POP401 4.3 47.7 1.0 OD2 B:ASP118 4.3 56.2 1.0 O1 A:PO4402 4.4 55.8 1.0 O3 A:PO4402 4.4 51.1 1.0 NZ B:LYS265 4.5 51.7 1.0 NZ A:LYS245 4.5 39.7 1.0 CA B:GLY260 4.5 51.9 1.0 CB B:ASP271 4.6 45.4 1.0 O2 A:PO4402 4.7 62.5 1.0 O6 A:POP401 4.8 55.7 1.0 NZ A:LYS165 4.8 43.6 1.0 OE2 A:GLU8 4.9 59.9 1.0 O4 A:POP401 5.0 57.3 1.0

Magnesium binding site 4 out of 4 in the S-Adenosylmethionine Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S-Adenosylmethionine Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:54.5 occ:1.00 O4 B:POP401 2.1 63.5 1.0 O3 A:PO4403 2.2 46.1 0.9 O B:HOH541 2.2 53.0 1.0 OD2 B:ASP16 2.3 60.9 1.0 O1 B:POP401 2.3 64.7 1.0 O B:HOH529 2.4 53.7 1.0 P2 B:POP401 3.2 57.2 1.0 P1 B:POP401 3.3 64.1 1.0 O B:POP401 3.3 54.9 1.0 CG B:ASP16 3.3 66.0 1.0 NZ B:LYS245 3.5 55.2 1.0 P A:PO4403 3.6 54.3 0.9 O A:HOH533 3.7 79.8 1.0 OD1 B:ASP16 3.7 62.2 1.0 O2 B:POP401 3.8 64.3 1.0 O6 B:POP401 4.0 58.3 1.0 O2 A:PO4403 4.1 54.7 0.9 CE1 B:HIS14 4.2 62.5 1.0 OD2 B:ASP238 4.3 116.0 1.0 O4 A:PO4403 4.3 46.5 0.9 O5 B:POP401 4.4 61.5 1.0 O B:CYS239 4.5 64.7 1.0 O1 A:PO4403 4.6 65.3 0.9 O3 B:POP401 4.6 83.2 1.0 O B:HOH552 4.6 68.6 1.0 CB B:ASP16 4.6 45.6 1.0 NH2 B:ARG244 4.6 65.4 1.0 CE B:LYS245 4.8 55.9 1.0 NE2 B:HIS14 4.8 59.3 1.0 CB B:ARG244 4.9 45.3 1.0

P.Laurino, C.J.Jackson. S-Adenosylmethionine Synthetase To Be Published.