Magnesium in PDB 1y8q: Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex, PDB code: 1y8q was solved by L.M.Lois, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.245, 116.667, 106.078, 90.00, 112.67, 90.00
R / Rfree (%)	20.8 / 24.8

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex (pdb code 1y8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex, PDB code: 1y8q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg641 b:35.0 occ:1.00 O B:HOH1065 1.9 30.8 1.0 O B:HOH935 2.0 25.2 1.0 O B:HOH978 2.0 36.5 1.0 O3G B:ATP802 2.0 28.4 1.0 OD2 B:ASP117 2.1 44.0 1.0 O2B B:ATP802 2.2 31.9 1.0 CG B:ASP117 3.3 40.8 1.0 PB B:ATP802 3.3 28.5 1.0 PG B:ATP802 3.3 27.7 1.0 O3B B:ATP802 3.5 27.0 1.0 CB B:ASP117 4.0 38.2 1.0 O2A B:ATP802 4.0 30.5 1.0 NZ B:LYS346 4.1 38.7 1.0 O1G B:ATP802 4.1 29.8 1.0 O B:HOH981 4.2 42.8 1.0 OD1 B:ASP117 4.3 42.0 1.0 O B:HOH880 4.3 41.9 1.0 O1B B:ATP802 4.3 31.5 1.0 O3A B:ATP802 4.4 27.2 1.0 O2G B:ATP802 4.4 29.0 1.0 O B:HOH873 4.5 35.0 1.0 O B:HOH829 4.7 25.8 1.0 PA B:ATP802 4.7 29.3 1.0 C5' B:ATP802 4.8 29.3 1.0 C3' B:ATP802 5.0 30.7 1.0

Magnesium binding site 2 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg641 b:33.6 occ:1.00 O D:HOH903 1.9 24.4 1.0 O2G D:ATP801 2.0 23.4 1.0 O D:HOH991 2.0 29.0 1.0 OD1 D:ASP117 2.1 51.9 1.0 O2B D:ATP801 2.1 22.1 1.0 O D:HOH851 2.6 32.5 1.0 PG D:ATP801 3.3 25.3 1.0 PB D:ATP801 3.3 24.2 1.0 CG D:ASP117 3.3 50.1 1.0 O3B D:ATP801 3.6 26.2 1.0 NZ D:LYS346 3.8 38.5 1.0 O3G D:ATP801 4.1 28.8 1.0 O2A D:ATP801 4.1 27.7 1.0 OD2 D:ASP117 4.2 51.7 1.0 CB D:ASP117 4.2 47.2 1.0 O D:HOH897 4.3 57.0 1.0 O1B D:ATP801 4.3 26.0 1.0 O1G D:ATP801 4.4 28.3 1.0 O D:HOH873 4.4 46.9 1.0 O3A D:ATP801 4.4 30.8 1.0 O D:HOH886 4.4 34.1 1.0 O D:HOH866 4.6 29.1 1.0 C5' D:ATP801 4.7 20.2 1.0 PA D:ATP801 4.8 26.2 1.0 CE D:LYS346 4.8 37.6 1.0

L.M.Lois, C.D.Lima. Structures of the Sumo E1 Provide Mechanistic Insights Into Sumo Activation and E2 Recruitment to E1 Embo J. V. 24 439 2005.
ISSN: ISSN 0261-4189
PubMed: 15660128
DOI: 10.1038/SJ.EMBOJ.7600552