Magnesium in PDB 7zh9: UBA1 in Complex with Atp

All present enzymatic activity of UBA1 in Complex with Atp:
6.2.1.45;

The structure of UBA1 in Complex with Atp, PDB code: 7zh9 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)	47.24 / 1.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.72, 118.064, 196.654, 90, 90, 90
R / Rfree (%)	16.5 / 20.6

The structure of UBA1 in Complex with Atp also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the UBA1 in Complex with Atp (pdb code 7zh9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the UBA1 in Complex with Atp, PDB code: 7zh9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the UBA1 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of UBA1 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:29.5 occ:1.00 O A:HOH1481 2.1 36.4 1.0 O1G A:ATP1101 2.1 19.9 1.0 O A:HOH1521 2.1 30.0 1.0 O2B A:ATP1101 2.1 26.8 1.0 OD2 A:ASP544 2.2 25.3 1.0 O2A A:ATP1101 2.3 25.5 1.0 PB A:ATP1101 3.1 27.1 1.0 CG A:ASP544 3.2 26.6 1.0 PG A:ATP1101 3.3 23.4 1.0 HB2 A:ASP544 3.3 26.0 1.0 O3B A:ATP1101 3.5 23.0 1.0 H5'1 A:ATP1101 3.5 24.6 1.0 HB3 A:ASP544 3.5 26.0 1.0 CB A:ASP544 3.6 21.7 1.0 PA A:ATP1101 3.6 26.6 1.0 O A:HOH1483 3.7 44.9 1.0 O3A A:ATP1101 3.7 24.8 1.0 O A:HOH1355 3.8 28.3 1.0 O2G A:ATP1101 4.0 26.9 1.0 O A:HOH1333 4.1 32.3 1.0 H3' A:ATP1101 4.3 20.9 1.0 O A:HOH1359 4.3 35.0 1.0 OD1 A:ASP544 4.3 28.0 1.0 O3G A:ATP1101 4.4 29.0 1.0 C5' A:ATP1101 4.4 20.5 1.0 HD12 A:ILE863 4.5 103.3 1.0 O1B A:ATP1101 4.5 27.4 1.0 O5' A:ATP1101 4.6 22.8 1.0 O A:HOH1472 4.6 32.4 1.0 HH21 A:ARG481 4.7 29.4 1.0 O A:HOH1927 4.7 41.8 1.0 O1A A:ATP1101 4.8 24.7 1.0 O A:HOH1780 4.8 45.9 1.0 O A:HOH1793 4.8 45.6 1.0 HH22 A:ARG481 4.9 29.4 1.0 H5'2 A:ATP1101 5.0 24.6 1.0

Magnesium binding site 2 out of 3 in the UBA1 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of UBA1 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:36.2 occ:1.00 O A:HOH1467 2.1 28.8 1.0 O A:HOH1402 2.1 36.4 1.0 O A:HOH1513 2.1 35.2 1.0 O A:HOH1930 2.1 31.9 1.0 HG3 A:GLU231 3.6 42.8 1.0 OD2 A:ASP207 4.1 29.9 1.0 O A:VAL232 4.1 21.5 1.0 HG2 A:GLU231 4.3 42.8 1.0 CG A:GLU231 4.4 35.7 1.0 OE2 A:GLU231 4.4 52.6 1.0 O A:HOH1885 4.5 39.3 1.0 OD1 A:ASP207 4.5 20.4 1.0 HG22 A:VAL232 4.7 28.2 0.6 CG A:ASP207 4.7 30.4 1.0 CD A:GLU231 4.9 55.6 1.0

Magnesium binding site 3 out of 3 in the UBA1 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of UBA1 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:41.0 occ:1.00 O A:HOH1461 2.0 25.0 1.0 O A:HOH1359 2.1 35.0 1.0 O A:HOH1229 2.2 45.2 1.0 O A:HOH1266 2.2 29.8 1.0 O1B A:ATP1101 2.3 27.4 1.0 OD2 A:ASP472 2.3 43.0 1.0 CG A:ASP472 3.4 52.7 1.0 HZ2 A:LYS494 3.4 37.7 1.0 HD21 A:ASN478 3.5 29.4 1.0 PB A:ATP1101 3.5 27.1 1.0 O A:HOH1926 3.6 50.3 1.0 O A:HOH1535 3.7 95.4 1.0 OD1 A:ASP472 3.8 31.6 1.0 O2B A:ATP1101 3.8 26.8 1.0 O2G A:ATP1101 3.9 26.9 1.0 HZ1 A:LYS494 3.9 37.7 1.0 OE2 A:GLU475 4.0 79.5 1.0 HE3 A:LYS494 4.0 33.9 1.0 NZ A:LYS494 4.0 31.4 1.0 CD A:GLU475 4.1 84.9 1.0 OE1 A:GLU475 4.1 93.3 1.0 O3B A:ATP1101 4.2 23.0 1.0 ND2 A:ASN478 4.3 24.5 1.0 OD1 A:ASN478 4.4 23.0 1.0 O A:HOH1333 4.5 32.3 1.0 HB2 A:GLU475 4.5 35.7 1.0 O A:SER473 4.5 27.6 1.0 CE A:LYS494 4.6 28.3 1.0 O A:HOH1483 4.6 44.9 1.0 HG3 A:GLU475 4.7 55.6 1.0 CB A:ASP472 4.7 32.0 1.0 PG A:ATP1101 4.7 23.4 1.0 HB3 A:ASP472 4.8 38.4 1.0 H3' A:ATP1101 4.8 20.9 1.0 O3A A:ATP1101 4.8 24.8 1.0 CG A:ASN478 4.8 21.8 1.0 HZ3 A:LYS494 4.8 37.7 1.0 HO3' A:ATP1101 4.8 29.9 1.0 CG A:GLU475 4.9 46.3 1.0 HB2 A:ASP472 4.9 38.4 1.0 HE2 A:LYS494 5.0 33.9 1.0 HD22 A:ASN478 5.0 29.4 1.0

N.Truongvan, S.Li, M.Misra, M.Kuhn, H.Schindelin. Structures of UBA6 Explain Its Dual Specificity For Ubiquitin and FAT10. Nat Commun V. 13 4789 2022.
ISSN: ESSN 2041-1723
PubMed: 35970836
DOI: 10.1038/S41467-022-32040-6