Magnesium in PDB 1y8r: Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-Mg-Atp Complex, PDB code: 1y8r 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)	19.99 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.197, 215.151, 100.870, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.6

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-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-SUMO1-Mg-Atp Complex (pdb code 1y8r). 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-SUMO1-Mg-Atp Complex, PDB code: 1y8r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-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-SUMO1-Mg-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg641 b:16.1 occ:1.00 OD2 B:ASP117 2.1 37.3 1.0 O3B B:ATP802 2.2 33.3 1.0 O B:HOH803 2.2 11.5 1.0 O2A B:ATP802 2.3 26.6 1.0 O2B B:ATP802 2.4 33.8 1.0 O B:HOH804 2.5 25.4 1.0 PB B:ATP802 2.5 34.0 1.0 O3A B:ATP802 2.8 30.7 1.0 PA B:ATP802 3.1 28.1 1.0 CG B:ASP117 3.1 36.5 1.0 PG B:ATP802 3.3 33.5 1.0 O3G B:ATP802 3.3 34.6 1.0 CB B:ASP117 3.7 33.6 1.0 C5' B:ATP802 3.7 27.4 1.0 O1G B:ATP802 3.8 35.7 1.0 O5' B:ATP802 3.9 27.9 1.0 O1B B:ATP802 4.0 34.0 1.0 OD1 B:ASP117 4.2 37.4 1.0 O1A B:ATP802 4.3 26.1 1.0 O B:HOH852 4.5 29.5 1.0 O2G B:ATP802 4.6 30.3 1.0 C3' B:ATP802 4.6 28.6 1.0 C4' B:ATP802 4.7 28.9 1.0

Magnesium binding site 2 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-SUMO1-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-SUMO1-Mg-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg641 b:31.1 occ:1.00 O2B E:ATP801 2.0 25.4 1.0 O E:HOH852 2.2 20.2 1.0 O2G E:ATP801 2.6 29.8 1.0 OD1 E:ASP117 2.7 37.0 1.0 O E:HOH853 2.8 33.1 1.0 O3B E:ATP801 2.9 29.6 1.0 PB E:ATP801 2.9 25.1 1.0 PG E:ATP801 3.2 32.2 1.0 O1G E:ATP801 3.7 29.3 1.0 O2A E:ATP801 3.8 22.7 1.0 O1B E:ATP801 3.9 26.8 1.0 CG E:ASP117 3.9 36.0 1.0 O E:HOH817 4.0 22.9 1.0 O3A E:ATP801 4.1 28.0 1.0 NZ E:LYS346 4.4 54.7 1.0 O3G E:ATP801 4.6 28.9 1.0 PA E:ATP801 4.6 27.4 1.0 OD2 E:ASP117 4.6 33.9 1.0 O E:HOH827 4.8 32.3 1.0 CB E:ASP117 4.8 34.5 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