Magnesium in PDB 7oy3: Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp

The structure of Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp, PDB code: 7oy3 was solved by H.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.78 / 1.78
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.806, 106.806, 108.457, 90, 90, 120
R / Rfree (%)	17 / 19.4

The structure of Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp (pdb code 7oy3). 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 Depupylase Dop in Complex with Phosphorylated Pup and Adp, PDB code: 7oy3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp


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 Phosphorylated Pup and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:30.3 occ:0.53 OA2 B:RGP71 1.9 35.3 0.6 O2B A:ADP612 2.1 33.6 0.6 O2A A:ADP612 2.1 30.8 0.6 OE1 A:GLU99 2.2 30.9 1.0 OE1 A:GLU8 2.2 41.1 1.0 OH A:TYR92 2.2 40.3 1.0 CD A:GLU99 3.1 29.6 1.0 CD A:GLU8 3.2 37.4 1.0 PA B:RGP71 3.2 32.7 0.3 PA A:ADP612 3.2 35.6 0.6 PB A:ADP612 3.2 40.6 0.6 O3A A:ADP612 3.3 38.2 0.6 CZ A:TYR92 3.5 35.9 1.0 OE2 A:GLU99 3.6 30.9 1.0 O B:HOH128 3.7 44.6 1.0 MG A:MG603 3.7 29.3 0.7 OA3 B:RGP71 3.8 34.7 0.7 O B:HOH103 3.8 42.1 1.0 CG A:GLU8 3.9 29.1 1.0 CB A:GLU8 3.9 22.4 1.0 O3B A:ADP612 3.9 37.4 0.6 K A:K601 3.9 26.6 0.9 CE1 A:TYR92 4.0 32.4 1.0 OA1 B:RGP71 4.0 35.9 0.6 OE2 A:GLU8 4.0 40.4 1.0 O5' A:ADP612 4.2 30.5 0.6 OG A:SER101 4.2 31.5 1.0 O A:HOH850 4.3 49.0 1.0 CG A:GLU99 4.4 22.4 1.0 O1A A:ADP612 4.4 35.7 0.6 O1B A:ADP612 4.5 40.9 0.6 OE2 B:RGP71 4.6 34.5 1.0 CE2 A:TYR92 4.6 36.4 1.0 OD2 A:ASP94 4.8 39.1 1.0 NH1 A:ARG90 4.8 37.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Depupylase Dop in Complex with Phosphorylated Pup and Adp


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 Phosphorylated Pup and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:29.3 occ:0.71 OD2 A:ASP94 2.0 39.1 1.0 OE2 A:GLU10 2.1 31.1 1.0 OE2 A:GLU99 2.1 30.9 1.0 OA2 B:RGP71 2.3 35.3 0.6 O B:HOH128 2.4 44.6 1.0 OE2 B:RGP71 2.5 34.5 1.0 CD A:GLU99 2.9 29.6 1.0 CD A:GLU10 3.0 28.8 1.0 PA B:RGP71 3.1 32.7 0.3 CG A:ASP94 3.1 42.7 1.0 OE1 A:GLU99 3.2 30.9 1.0 CG A:GLU10 3.4 19.4 1.0 CD B:RGP71 3.6 27.3 1.0 MG A:MG602 3.7 30.3 0.5 CB A:ASP94 3.7 35.2 1.0 OH A:TYR92 3.9 40.3 1.0 CG B:RGP71 4.0 22.3 1.0 OA3 B:RGP71 4.1 34.7 0.7 OE1 A:GLU10 4.1 21.2 1.0 OA1 B:RGP71 4.1 35.9 0.6 OD1 A:ASP94 4.2 43.3 1.0 CB B:RGP71 4.3 20.1 1.0 CG A:GLU99 4.3 22.4 1.0 OE1 A:GLU8 4.5 41.1 1.0 O B:HOH103 4.5 42.1 1.0 OE1 B:RGP71 4.6 29.1 1.0 CE1 A:HIS155 4.7 26.8 1.0 ND1 A:HIS95 4.7 53.9 1.0 CZ A:TYR92 4.7 35.9 1.0 CB A:GLU99 4.8 20.5 1.0 O2B A:ADP612 4.8 33.6 0.6 CB A:GLU10 4.9 17.5 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