Magnesium in PDB 5zqy: Crystal Structure of A Poly(Adp-Ribose) Glycohydrolase

All present enzymatic activity of Crystal Structure of A Poly(Adp-Ribose) Glycohydrolase:
3.2.1.143;

The structure of Crystal Structure of A Poly(Adp-Ribose) Glycohydrolase, PDB code: 5zqy was solved by M.Wang, Z.Yuan, Y.Ma, J.Wang, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.35 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.880, 76.740, 48.530, 90.00, 103.00, 90.00
R / Rfree (%)	15.7 / 18

The binding sites of Magnesium atom in the Crystal Structure of A Poly(Adp-Ribose) Glycohydrolase (pdb code 5zqy). 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 A Poly(Adp-Ribose) Glycohydrolase, PDB code: 5zqy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Poly(Adp-Ribose) Glycohydrolase


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 A Poly(Adp-Ribose) Glycohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:12.7 occ:1.00 O A:HOH501 2.0 33.3 1.0 O3D A:AR6403 2.3 17.6 1.0 OD1 A:ASP314 2.4 21.2 1.0 OD1 A:ASP316 2.4 19.4 1.0 O A:HOH624 2.5 26.5 1.0 O1D A:AR6403 2.6 29.5 1.0 OG1 A:THR317 2.6 8.7 1.0 O2D A:AR6403 2.9 18.8 1.0 OD2 A:ASP316 3.1 35.4 1.0 OD2 A:ASP314 3.1 13.3 1.0 CG A:ASP314 3.1 16.9 1.0 CG A:ASP316 3.1 24.5 1.0 C3D A:AR6403 3.4 15.5 1.0 C2D A:AR6403 3.5 15.8 1.0 C1D A:AR6403 3.6 20.4 1.0 CB A:THR317 3.7 5.3 1.0 MG A:MG402 3.8 17.4 1.0 OE1 A:GLU41 3.9 39.1 1.0 N A:THR317 4.1 7.9 1.0 C4D A:AR6403 4.1 17.1 1.0 CD A:GLU41 4.2 27.9 1.0 OD1 A:ASP78 4.2 15.5 1.0 OE2 A:GLU41 4.3 28.6 1.0 O A:HOH553 4.4 35.4 1.0 O4D A:AR6403 4.5 25.1 1.0 CA A:THR317 4.5 6.5 1.0 CB A:ASP316 4.6 17.4 1.0 CB A:ASP314 4.6 8.4 1.0 O A:HOH648 4.6 24.2 1.0 OD2 A:ASP78 4.7 8.4 1.0 CG2 A:THR317 4.8 8.4 1.0 OD1 A:ASN151 4.8 8.5 1.0 CG A:ASP78 4.9 13.7 1.0 C A:ASP316 4.9 8.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Poly(Adp-Ribose) Glycohydrolase


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 A Poly(Adp-Ribose) Glycohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:17.4 occ:1.00 OD2 A:ASP316 2.0 35.4 1.0 O A:HOH501 2.1 33.3 1.0 OD1 A:ASP77 2.2 15.2 1.0 O A:HOH648 2.2 24.2 1.0 OD1 A:ASP78 2.4 15.5 1.0 OG1 A:THR76 2.5 11.9 1.0 CB A:THR76 3.2 12.6 1.0 O2D A:AR6403 3.3 18.8 1.0 CG A:ASP316 3.3 24.5 1.0 CG A:ASP77 3.4 13.7 1.0 O A:HOH624 3.4 26.5 1.0 CG A:ASP78 3.6 13.7 1.0 MG A:MG401 3.8 12.7 1.0 OD2 A:ASP77 4.0 10.6 1.0 N A:ASP77 4.0 8.7 1.0 OD1 A:ASP316 4.0 19.4 1.0 CG2 A:THR76 4.0 10.9 1.0 N A:ASP78 4.1 7.7 1.0 OD1 A:ASP34 4.2 10.9 1.0 CB A:ASP316 4.3 17.4 1.0 O A:GLY115 4.4 11.6 1.0 OD2 A:ASP78 4.4 8.4 1.0 CA A:THR76 4.5 7.4 1.0 CB A:ASP77 4.6 11.7 1.0 C A:THR76 4.6 8.2 1.0 CB A:ASP78 4.6 10.3 1.0 OG1 A:THR317 4.6 8.7 1.0 O A:ARG114 4.6 20.1 1.0 CA A:ASP77 4.7 7.8 1.0 C2D A:AR6403 4.7 15.8 1.0 C A:ASP77 4.9 8.0 1.0 OG A:SER38 4.9 10.4 0.3 O3D A:AR6403 4.9 17.6 1.0 O1D A:AR6403 4.9 29.5 1.0 CA A:ASP78 4.9 8.4 1.0

M.Wang, Z.Yuan, R.Xie, Y.Ma, X.Liu, X.Yu. Structure-Function Analyses Reveal the Mechanism of the ARH3-Dependent Hydrolysis of Adp-Ribosylation. J. Biol. Chem. V. 293 14470 2018.
ISSN: ESSN 1083-351X
PubMed: 30045870
DOI: 10.1074/JBC.RA118.004284