Magnesium in PDB 7oxy: Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp

The structure of Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp, PDB code: 7oxy was solved by H.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.19 / 1.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.668, 106.668, 108.791, 90, 90, 120
R / Rfree (%)	17.3 / 19.5

The binding sites of Magnesium atom in the Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp (pdb code 7oxy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp, PDB code: 7oxy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp


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 Depupylase Dop in Complex with Pup and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:24.1 occ:0.67 OD2 A:ASP94 1.9 37.0 1.0 O A:HOH725 2.0 35.8 1.0 OE2 A:GLU10 2.1 30.8 1.0 O A:HOH731 2.1 37.1 1.0 OE1 B:GLN71 2.1 33.5 1.0 OE2 A:GLU99 2.2 31.6 1.0 CG A:ASP94 2.9 43.2 1.0 CD A:GLU99 3.0 34.1 1.0 CD A:GLU10 3.2 25.9 1.0 CD B:GLN71 3.2 30.2 1.0 OE1 A:GLU99 3.3 38.6 1.0 CB A:ASP94 3.6 34.1 1.0 CG A:GLU10 3.6 22.8 1.0 MG A:MG604 3.7 34.9 0.3 CG B:GLN71 3.8 23.9 1.0 OD1 A:ASP94 4.0 47.7 1.0 O A:HOH922 4.0 35.9 1.0 OH A:TYR92 4.1 38.5 1.0 OE1 A:GLU10 4.2 22.4 1.0 O A:HOH728 4.2 35.4 1.0 O A:HOH765 4.2 42.9 1.0 CB B:GLN71 4.3 22.5 1.0 NE2 B:GLN71 4.4 30.0 1.0 CG A:GLU99 4.4 27.1 1.0 O1G A:ACP610 4.5 38.3 0.7 OE2 A:GLU8 4.7 37.6 1.0 CE1 A:HIS155 4.9 23.2 1.0 C3B A:ACP610 4.9 29.1 0.7 CZ A:TYR92 5.0 30.5 1.0 CB A:GLU99 5.0 24.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp


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 Depupylase Dop in Complex with Pup and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:24.7 occ:0.56 O A:HOH728 2.1 35.4 1.0 NE2 A:HIS241 2.2 29.0 1.0 O2B A:ACP610 2.2 30.4 0.7 OE2 A:GLU8 2.3 37.6 1.0 OE1 A:GLU8 2.3 32.5 1.0 ND1 A:HIS155 2.4 24.7 1.0 CD A:GLU8 2.6 35.5 1.0 CE1 A:HIS241 3.1 28.0 1.0 CD2 A:HIS241 3.2 27.4 1.0 CE1 A:HIS155 3.3 23.2 1.0 PB A:ACP610 3.3 30.3 0.7 CG A:HIS155 3.4 22.7 1.0 CB A:HIS155 3.7 19.7 1.0 C3B A:ACP610 3.8 29.1 0.7 O3A A:ACP610 3.8 35.4 0.7 MG A:MG604 4.0 34.9 0.3 O A:HOH725 4.1 35.8 1.0 CG A:GLU8 4.1 28.6 1.0 O3G A:ACP610 4.2 36.6 0.7 ND1 A:HIS241 4.2 30.1 1.0 CG A:HIS241 4.3 22.8 1.0 NE2 A:HIS155 4.5 23.3 1.0 CD2 A:HIS155 4.5 21.6 1.0 O1B A:ACP610 4.6 34.5 0.7 PG A:ACP610 4.7 39.5 0.7 CB A:GLU8 4.7 27.8 1.0 OE1 B:GLN71 4.8 33.5 1.0 O A:HOH922 4.8 35.9 1.0 NH1 A:ARG239 4.8 37.3 1.0 OD1 A:ASN157 4.9 28.1 1.0 ND2 A:ASN157 4.9 31.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:38.5 occ:0.55 O A:HOH888 2.0 43.4 1.0 O1B A:ACP610 2.0 34.5 0.7 O A:HOH785 2.0 52.4 1.0 O2G A:ACP610 2.0 37.4 0.7 O A:HOH729 2.4 43.2 1.0 PB A:ACP610 3.2 30.3 0.7 PG A:ACP610 3.2 39.5 0.7 C3B A:ACP610 3.6 29.1 0.7 O A:HOH881 3.8 44.0 1.0 O A:HOH979 3.9 48.7 1.0 O3G A:ACP610 3.9 36.6 0.7 O2B A:ACP610 4.1 30.4 0.7 NH2 A:ARG239 4.1 33.4 1.0 O A:HOH895 4.3 50.9 1.0 O3A A:ACP610 4.4 35.4 0.7 O2A A:ACP610 4.4 37.6 0.7 NE2 A:HIS231 4.4 46.7 1.0 O1G A:ACP610 4.4 38.3 0.7 OE1 A:GLU229 4.5 40.4 1.0 CD A:GLU229 4.9 40.1 1.0 CE1 A:HIS231 4.9 45.1 1.0 O A:HOH771 5.0 38.5 1.0 PA A:ACP610 5.0 35.2 0.7

Magnesium binding site 4 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Depupylase Dop in Complex with Pup and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:34.9 occ:0.35 OH A:TYR92 2.1 38.5 1.0 OE1 A:GLU99 2.1 38.6 1.0 OE2 A:GLU8 2.3 37.6 1.0 O A:HOH731 2.5 37.1 1.0 C3B A:ACP610 2.5 29.1 0.7 O1A A:ACP610 2.5 34.6 0.7 O A:HOH725 3.1 35.8 1.0 CD A:GLU99 3.1 34.1 1.0 CD A:GLU8 3.3 35.5 1.0 O3A A:ACP610 3.4 35.4 0.7 CZ A:TYR92 3.4 30.5 1.0 PA A:ACP610 3.5 35.2 0.7 PB A:ACP610 3.6 30.3 0.7 OE2 A:GLU99 3.6 31.6 1.0 MG A:MG601 3.7 24.1 0.7 CG A:GLU8 3.8 28.6 1.0 CB A:GLU8 3.9 27.8 1.0 O A:HOH728 4.0 35.4 1.0 MG A:MG602 4.0 24.7 0.6 PG A:ACP610 4.0 39.5 0.7 OG A:SER101 4.1 33.6 1.0 O1G A:ACP610 4.1 38.3 0.7 CE1 A:TYR92 4.1 30.5 1.0 O2B A:ACP610 4.2 30.4 0.7 OE1 A:GLU8 4.3 32.5 1.0 CG A:GLU99 4.3 27.1 1.0 CE2 A:TYR92 4.4 33.1 1.0 O2A A:ACP610 4.5 37.6 0.7 OE1 B:GLN71 4.5 33.5 1.0 O5' A:ACP610 4.6 30.4 0.7 O3G A:ACP610 4.7 36.6 0.7 O A:HOH922 4.9 35.9 1.0 O A:HOH895 4.9 50.9 1.0 O1B A:ACP610 4.9 34.5 0.7 NH1 A:ARG90 5.0 37.5 1.0

H.Cui, A.U.Muller, M.Leibundgut, J.Tian, N.Ban, E.Weber-Ban. Structures of Prokaryotic Ubiquitin-Like Protein Pup in Complex with Depupylase Dop Reveal the Mechanism of Catalytic Phosphate Formation. Nat Commun V. 12 6635 2021.
ISSN: ESSN 2041-1723
PubMed: 34789727
DOI: 10.1038/S41467-021-26848-X