Magnesium in PDB 4ii2: Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg

All present enzymatic activity of Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg:
6.3.2.19;

The structure of Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg, PDB code: 4ii2 was solved by S.K.Olsen, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.600, 111.200, 181.300, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.4

The binding sites of Magnesium atom in the Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg (pdb code 4ii2). 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 Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg, PDB code: 4ii2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg


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 Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:52.7 occ:1.00 OD2 A:ASP537 2.3 44.6 1.0 O3G A:ATP1103 2.4 40.7 1.0 O A:HOH1210 2.4 45.2 1.0 O A:HOH1208 2.4 42.4 1.0 O2B A:ATP1103 2.4 40.2 1.0 O2A A:ATP1103 2.6 38.3 1.0 CG A:ASP537 3.2 41.7 1.0 CB A:ASP537 3.5 40.0 1.0 PB A:ATP1103 3.5 37.8 1.0 PG A:ATP1103 3.5 39.2 1.0 O3B A:ATP1103 3.7 40.4 1.0 PA A:ATP1103 3.8 34.5 1.0 O3A A:ATP1103 4.0 39.4 1.0 O A:HOH1205 4.2 42.0 1.0 O1G A:ATP1103 4.3 39.1 1.0 OD1 A:ASP537 4.3 44.1 1.0 O A:HOH1211 4.4 43.4 1.0 C5' A:ATP1103 4.4 37.3 1.0 O A:HOH1318 4.4 62.3 1.0 O A:HOH1207 4.5 38.0 1.0 O A:HOH1206 4.5 43.0 1.0 O5' A:ATP1103 4.6 38.4 1.0 O2G A:ATP1103 4.7 44.2 1.0 O B:HOH201 4.7 35.3 1.0 O1B A:ATP1103 4.9 45.7 1.0 CA A:ASP537 5.0 38.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg


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 Ubiquitin Activating Enzyme 1 (UBA1) in Complex with the Ub E2 UBC4, Ubiquitin, and Atp/Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:47.0 occ:1.00 O A:HOH1211 2.3 43.4 1.0 O A:HOH1201 2.3 37.0 1.0 O A:HOH1209 2.4 42.6 1.0 OD2 A:ASP465 2.5 54.9 1.0 O1B A:ATP1103 2.5 45.7 1.0 O A:HOH1204 2.6 45.3 1.0 CG A:ASP465 3.3 51.8 1.0 PB A:ATP1103 3.4 37.8 1.0 OD1 A:ASP465 3.4 51.2 1.0 O2B A:ATP1103 3.5 40.2 1.0 OE2 A:GLU468 3.8 52.8 1.0 O1G A:ATP1103 3.9 39.1 1.0 O3B A:ATP1103 4.1 40.4 1.0 CD A:GLU468 4.2 50.7 1.0 NZ A:LYS487 4.2 39.4 1.0 OD1 A:ASN471 4.3 35.7 1.0 ND2 A:ASN471 4.4 33.0 1.0 OE1 A:GLU468 4.5 55.8 1.0 O A:SER466 4.5 38.9 1.0 CB A:ASP465 4.6 47.8 1.0 CE A:LYS487 4.6 37.6 1.0 O3A A:ATP1103 4.7 39.4 1.0 PG A:ATP1103 4.7 39.2 1.0 O A:HOH1206 4.8 43.0 1.0 CG A:ASN471 4.8 35.6 1.0 CG A:GLU468 4.9 47.0 1.0

S.K.Olsen, C.D.Lima. Structure of A Ubiquitin E1-E2 Complex: Insights to E1-E2 Thioester Transfer. Mol.Cell V. 49 884 2013.
ISSN: ISSN 1097-2765
PubMed: 23416107
DOI: 10.1016/J.MOLCEL.2013.01.013