Magnesium in PDB 6nya: Crystal Structure of Ubiquitin E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin

All present enzymatic activity of Crystal Structure of Ubiquitin E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin:
2.3.2.23; 6.2.1.45;

The structure of Crystal Structure of Ubiquitin E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin, PDB code: 6nya was solved by S.K.Olsen, K.M.Williams, J.H.Atkison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.04 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	126.445, 68.544, 171.721, 90.00, 110.72, 90.00
R / Rfree (%)	18.7 / 21.7

The binding sites of Magnesium atom in the Crystal Structure of Ubiquitin E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin (pdb code 6nya). 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 E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin, PDB code: 6nya:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ubiquitin E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin


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 E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:24.9 occ:1.00 O2B A:ATP1101 2.0 22.5 1.0 OD2 A:ASP544 2.0 25.1 1.0 O3G A:ATP1101 2.0 25.7 1.0 O A:HOH1381 2.1 24.0 1.0 O2A A:ATP1101 2.2 23.5 1.0 O A:HOH1467 2.2 22.2 1.0 CG A:ASP544 3.1 24.5 1.0 PB A:ATP1101 3.2 24.6 1.0 PG A:ATP1101 3.2 24.7 1.0 O3B A:ATP1101 3.4 23.9 1.0 PA A:ATP1101 3.5 24.0 1.0 CB A:ASP544 3.5 21.4 1.0 O3A A:ATP1101 3.7 23.3 1.0 O A:HOH1407 3.9 22.7 1.0 O1G A:ATP1101 4.0 29.0 1.0 O A:HOH1285 4.1 30.2 1.0 O A:HOH1372 4.1 47.0 1.0 O A:HOH1299 4.1 27.9 1.0 C5' A:ATP1101 4.2 22.0 1.0 OD1 A:ASP544 4.2 26.7 1.0 O B:HOH114 4.2 28.3 1.0 O5' A:ATP1101 4.3 24.4 1.0 O2G A:ATP1101 4.4 22.6 1.0 O1B A:ATP1101 4.5 27.2 1.0 O A:HOH1583 4.6 40.8 1.0 O A:HOH1243 4.6 23.9 1.0 O1A A:ATP1101 4.6 27.1 1.0 C3' A:ATP1101 4.9 24.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ubiquitin E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin


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 E1 (UBA1) in Complex with UBC3 (CDC34) and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1201 b:31.0 occ:1.00 O2B D:ATP1202 2.0 33.6 1.0 O D:HOH1437 2.1 33.0 1.0 O D:HOH1504 2.1 33.2 1.0 O3G D:ATP1202 2.1 19.3 1.0 OD2 D:ASP544 2.2 25.7 1.0 O2A D:ATP1202 2.3 30.6 1.0 PB D:ATP1202 3.1 28.9 1.0 CG D:ASP544 3.2 28.4 1.0 PG D:ATP1202 3.3 24.1 1.0 O3B D:ATP1202 3.3 25.7 1.0 CB D:ASP544 3.5 26.6 1.0 PA D:ATP1202 3.6 25.0 1.0 O D:HOH1366 3.7 26.0 1.0 O3A D:ATP1202 3.8 25.8 1.0 O D:HOH1526 3.9 39.1 1.0 O1G D:ATP1202 4.0 24.5 1.0 O D:HOH1456 4.2 59.9 1.0 O E:HOH112 4.3 25.9 1.0 O D:HOH1341 4.3 24.5 1.0 C5' D:ATP1202 4.3 27.2 1.0 OD1 D:ASP544 4.3 28.5 1.0 O D:HOH1465 4.4 24.9 1.0 O1B D:ATP1202 4.4 31.2 1.0 O2G D:ATP1202 4.5 29.6 1.0 O5' D:ATP1202 4.5 30.0 1.0 O D:HOH1550 4.5 43.8 1.0 O1A D:ATP1202 4.8 26.0 1.0 O D:HOH1514 4.9 44.4 1.0

K.M.Williams, S.Qie, J.H.Atkison, S.Salazar-Arango, J.Alan Diehl, S.K.Olsen. Structural Insights Into E1 Recognition and the Ubiquitin-Conjugating Activity of the E2 Enzyme CDC34. Nat Commun V. 10 3296 2019.
ISSN: ESSN 2041-1723
PubMed: 31341161
DOI: 10.1038/S41467-019-11061-8