Magnesium in PDB 6o82: S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic

All present enzymatic activity of S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic:
6.2.1.45;

The structure of S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic, PDB code: 6o82 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)	42.39 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	182.061, 114.616, 125.967, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23

The binding sites of Magnesium atom in the S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic (pdb code 6o82). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic, PDB code: 6o82:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:32.5 occ:1.00 O A:HOH1262 2.1 32.0 1.0 O2 A:POP1103 2.1 35.1 1.0 OD2 A:ASP537 2.1 43.7 1.0 O2S B:JZU101 2.1 31.2 1.0 O A:HOH1293 2.1 33.3 1.0 O6 A:POP1103 2.3 40.1 1.0 CG A:ASP537 3.0 37.6 1.0 CB A:ASP537 3.3 32.4 1.0 P2 A:POP1103 3.4 39.4 1.0 P1 A:POP1103 3.5 39.8 1.0 S B:JZU101 3.5 33.5 1.0 O5 A:POP1103 3.8 38.7 1.0 O A:POP1103 3.9 41.3 1.0 N5' B:JZU101 4.0 35.2 1.0 O A:HOH1313 4.0 38.4 1.0 N18 B:JZU101 4.1 24.6 1.0 O A:HOH1225 4.1 29.9 1.0 OD1 A:ASP537 4.2 39.5 1.0 O3 A:POP1103 4.2 39.8 1.0 C5' B:JZU101 4.3 33.8 1.0 O1 A:POP1103 4.4 38.2 1.0 O3S B:JZU101 4.5 34.5 1.0 O A:HOH1314 4.5 42.9 1.0 O A:HOH1239 4.5 35.8 1.0 O B:HOH217 4.6 34.1 1.0 O4 A:POP1103 4.7 37.0 1.0 C3' B:JZU101 4.8 34.1 1.0 CA A:ASP537 4.8 29.1 1.0 NH2 A:ARG474 4.9 35.8 1.0 O A:HOH1371 5.0 39.8 1.0

Magnesium binding site 2 out of 4 in the S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:29.6 occ:1.00 OD2 A:ASP465 2.1 50.3 1.0 O4 A:POP1103 2.1 37.0 1.0 O A:HOH1225 2.1 29.9 1.0 O A:HOH1217 2.1 32.6 1.0 O A:HOH1230 2.1 33.1 1.0 O A:HOH1246 2.3 42.8 1.0 P2 A:POP1103 3.0 39.4 1.0 O A:POP1103 3.2 41.3 1.0 CG A:ASP465 3.2 46.1 1.0 O6 A:POP1103 3.4 40.1 1.0 OD1 A:ASP465 3.7 49.3 1.0 NZ A:LYS487 3.8 37.8 1.0 ND2 A:ASN471 4.0 36.2 1.0 O B:HOH210 4.0 40.9 1.0 OD1 A:ASN471 4.2 35.7 1.0 OE1 A:GLU468 4.3 57.2 1.0 O5 A:POP1103 4.4 38.7 1.0 CD A:GLU468 4.4 56.4 1.0 CE A:LYS487 4.4 38.4 1.0 CB A:ASP465 4.4 40.7 1.0 P1 A:POP1103 4.5 39.8 1.0 O A:SER466 4.5 42.1 1.0 O3 A:POP1103 4.5 39.8 1.0 OE2 A:GLU468 4.5 57.1 1.0 CG A:ASN471 4.6 37.1 1.0 O A:HOH1262 5.0 32.0 1.0 CG A:GLU468 5.0 53.6 1.0

Magnesium binding site 3 out of 4 in the S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:41.3 occ:1.00 OD2 C:ASP537 2.1 71.8 1.0 O1 C:POP1103 2.2 54.8 1.0 O C:HOH1210 2.2 69.8 1.0 O C:HOH1203 2.2 59.4 1.0 O2S D:JZU101 2.3 45.6 1.0 O4 C:POP1103 2.3 67.8 1.0 CG C:ASP537 3.0 59.9 1.0 CB C:ASP537 3.2 53.5 1.0 P2 C:POP1103 3.5 67.7 1.0 P1 C:POP1103 3.6 64.8 1.0 S D:JZU101 3.6 42.8 1.0 O5 C:POP1103 3.7 64.8 1.0 N5' D:JZU101 3.9 42.1 1.0 O C:POP1103 4.0 67.6 1.0 C5' D:JZU101 4.2 41.8 1.0 OD1 C:ASP537 4.2 61.5 1.0 N18 D:JZU101 4.4 26.3 1.0 O3 C:POP1103 4.4 66.8 1.0 O2 C:POP1103 4.5 65.8 1.0 NH2 C:ARG474 4.7 65.9 1.0 O3S D:JZU101 4.7 46.7 1.0 C3' D:JZU101 4.7 44.9 1.0 O6 C:POP1103 4.8 67.5 1.0 CA C:ASP537 4.8 51.9 1.0

Magnesium binding site 4 out of 4 in the S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Pombe Ubiquitin E1 Complex with A Ubiquitin-Amp Mimic within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1102 b:34.9 occ:1.00 OD2 C:ASP465 2.1 83.1 1.0 O6 C:POP1103 2.4 67.5 1.0 CG C:ASP465 3.1 77.1 1.0 O C:POP1103 3.3 67.6 1.0 P2 C:POP1103 3.3 67.7 1.0 OE2 C:GLU468 3.5 76.1 1.0 OD1 C:ASP465 3.5 80.7 1.0 CD C:GLU468 3.7 75.5 1.0 O4 C:POP1103 3.7 67.8 1.0 ND2 C:ASN471 3.9 70.0 1.0 OE1 C:GLU468 4.0 75.8 1.0 O C:SER466 4.3 83.2 1.0 CG C:GLU468 4.4 74.0 1.0 NZ C:LYS487 4.4 71.1 1.0 OD1 C:ASN471 4.4 70.1 1.0 CB C:ASP465 4.5 70.1 1.0 CG C:ASN471 4.6 69.9 1.0 P1 C:POP1103 4.6 64.8 1.0 O5 C:POP1103 4.7 64.8 1.0 O3 C:POP1103 4.8 66.8 1.0 CE C:LYS487 4.9 71.6 1.0

Z.S.Hann, C.Ji, S.K.Olsen, X.Lu, M.C.Lux, D.S.Tan, C.D.Lima. Structural Basis For Adenylation and Thioester Bond Formation in the Ubiquitin E1. Proc.Natl.Acad.Sci.Usa V. 116 15475 2019.
ISSN: ESSN 1091-6490
PubMed: 31235585
DOI: 10.1073/PNAS.1905488116