Magnesium in PDB 6zhu: Yeast UBA1 in Complex with UBC3 and Atp

All present enzymatic activity of Yeast UBA1 in Complex with UBC3 and Atp:
2.3.2.23; 6.2.1.45;

The structure of Yeast UBA1 in Complex with UBC3 and Atp, PDB code: 6zhu was solved by M.Misra, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.81 / 3.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.636, 152.408, 252.567, 90, 90.45, 90
R / Rfree (%)	21.7 / 26.3

The binding sites of Magnesium atom in the Yeast UBA1 in Complex with UBC3 and Atp (pdb code 6zhu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Yeast UBA1 in Complex with UBC3 and Atp, PDB code: 6zhu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:72.3 occ:1.00 O A:HOH1203 2.0 72.8 1.0 OD2 A:ASP544 2.3 53.0 1.0 O A:HOH1201 2.4 75.1 1.0 O2G A:ATP1101 2.5 55.5 1.0 O2A A:ATP1101 2.8 54.9 1.0 HB2 A:ASP544 2.9 61.4 1.0 O1B A:ATP1101 2.9 55.5 1.0 CG A:ASP544 3.2 52.3 1.0 CB A:ASP544 3.5 51.2 1.0 HD12 A:ILE863 3.7 58.9 1.0 HB3 A:ASP544 3.7 61.4 1.0 PG A:ATP1101 3.8 49.4 1.0 PB A:ATP1101 3.9 49.7 1.0 O3B A:ATP1101 4.0 47.2 1.0 H5'2 A:ATP1101 4.1 64.1 1.0 PA A:ATP1101 4.2 46.0 1.0 O1G A:ATP1101 4.2 49.3 1.0 OD1 A:ASP544 4.3 53.1 1.0 O3A A:ATP1101 4.4 44.2 1.0 HB A:ILE863 4.5 58.4 1.0 O A:ASP544 4.5 52.5 1.0 CD1 A:ILE863 4.6 49.1 1.0 CA A:ASP544 4.8 51.2 1.0 HG13 A:ILE863 4.9 59.0 1.0 HD11 A:ILE863 5.0 58.9 1.0 O3G A:ATP1101 5.0 46.0 1.0

Magnesium binding site 2 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1102 b:67.6 occ:1.00 O E:HOH1202 1.7 69.4 1.0 O E:HOH1201 1.8 68.3 1.0 OD2 E:ASP544 2.2 59.7 1.0 O2G E:ATP1101 2.3 61.3 1.0 O1B E:ATP1101 2.3 61.0 1.0 O1A E:ATP1101 2.5 50.9 1.0 HB2 E:ASP544 2.8 65.9 1.0 CG E:ASP544 3.1 58.0 1.0 CB E:ASP544 3.3 54.9 1.0 HB3 E:ASP544 3.4 65.9 1.0 PG E:ATP1101 3.5 54.7 1.0 PB E:ATP1101 3.5 52.6 1.0 O3B E:ATP1101 3.7 51.9 1.0 PA E:ATP1101 3.8 47.3 1.0 HD12 E:ILE863 3.9 65.4 1.0 H5'1 E:ATP1101 3.9 66.7 1.0 O3A E:ATP1101 4.0 47.2 1.0 O1G E:ATP1101 4.2 56.4 1.0 OD1 E:ASP544 4.3 57.9 1.0 HB E:ILE863 4.4 66.1 1.0 O E:ASP544 4.6 54.5 1.0 HH21 E:ARG481 4.6 70.7 1.0 O3G E:ATP1101 4.7 50.5 1.0 CA E:ASP544 4.7 52.5 1.0 O2B E:ATP1101 4.8 56.6 1.0 O5' E:ATP1101 4.8 54.2 1.0 O2A E:ATP1101 4.8 43.5 1.0 CD1 E:ILE863 4.8 54.5 1.0 C5' E:ATP1101 4.8 55.6 1.0 H3' E:ATP1101 5.0 61.1 1.0

Magnesium binding site 3 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1102 b:69.0 occ:1.00 O C:HOH1201 1.8 69.4 1.0 O C:HOH1202 2.1 72.2 1.0 O2G C:ATP1101 2.2 59.5 1.0 O2B C:ATP1101 2.8 58.0 1.0 O2A C:ATP1101 2.9 51.7 1.0 OD2 C:ASP544 3.0 61.0 1.0 HB2 C:ASP544 3.1 71.5 1.0 PG C:ATP1101 3.3 48.9 1.0 HD12 C:ILE863 3.6 63.7 1.0 O1G C:ATP1101 3.7 44.5 1.0 O3B C:ATP1101 3.7 47.7 1.0 CG C:ASP544 3.7 60.9 1.0 PB C:ATP1101 3.8 50.6 1.0 CB C:ASP544 3.8 59.6 1.0 HB C:ILE863 4.0 61.6 1.0 HB3 C:ASP544 4.0 71.5 1.0 PA C:ATP1101 4.2 45.6 1.0 O3A C:ATP1101 4.4 46.3 1.0 CD1 C:ILE863 4.5 53.0 1.0 H5'1 C:ATP1101 4.5 62.8 1.0 H C:ILE863 4.6 58.0 1.0 O3G C:ATP1101 4.6 47.3 1.0 HG13 C:ILE863 4.7 61.2 1.0 HH21 C:ARG481 4.7 71.6 1.0 CB C:ILE863 4.8 51.3 1.0 HD11 C:ILE863 4.9 63.7 1.0 OD1 C:ASP544 4.9 61.1 1.0 O C:ASP544 4.9 60.2 1.0 CG1 C:ILE863 4.9 51.0 1.0

Magnesium binding site 4 out of 4 in the Yeast UBA1 in Complex with UBC3 and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1102 b:62.5 occ:1.00 O G:HOH1201 1.8 73.6 1.0 OD2 G:ASP544 2.0 77.8 1.0 O2A G:ATP1101 2.4 66.3 1.0 O1G G:ATP1101 2.5 71.5 1.0 O2B G:ATP1101 2.6 67.5 1.0 HB2 G:ASP544 2.6 84.5 1.0 O G:HOH1202 2.8 80.7 1.0 CG G:ASP544 2.9 70.2 1.0 CB G:ASP544 3.1 70.4 1.0 HB3 G:ASP544 3.3 84.5 1.0 PB G:ATP1101 3.6 64.2 1.0 PG G:ATP1101 3.7 67.7 1.0 PA G:ATP1101 3.7 65.2 1.0 H5'2 G:ATP1101 3.8 81.6 1.0 O3B G:ATP1101 3.8 65.1 1.0 OD1 G:ASP544 4.0 70.9 1.0 O3A G:ATP1101 4.1 64.1 1.0 O3G G:ATP1101 4.2 67.5 1.0 O G:ASP544 4.5 70.5 1.0 CA G:ASP544 4.5 71.3 1.0 HD12 G:ILE863 4.6 79.8 1.0 C5' G:ATP1101 4.7 68.0 1.0 HB G:ILE863 4.7 78.7 1.0 O5' G:ATP1101 4.7 67.8 1.0 O1A G:ATP1101 4.8 69.7 1.0 HH21 G:ARG481 4.9 88.6 1.0 H3' G:ATP1101 4.9 78.3 1.0 HA G:ASP544 4.9 85.5 1.0 C G:ASP544 5.0 71.2 1.0

M.Misra, A.Schaefer, M.Kuhn, L.Pluska, I.Tessmer, T.Sommer, H.Schindelin. Atp Induced Conformational Changes Facilitate E1-E2 Disulfide Bridging in the Ubiquitin System To Be Published.