Magnesium in PDB 6d3a: Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium

All present enzymatic activity of Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium:
3.2.1.143;

The structure of Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium, PDB code: 6d3a was solved by Y.Pourfarjam, J.Ventura, I.Kurinov, I.K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.48 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.901, 72.229, 115.906, 83.01, 85.73, 72.43
R / Rfree (%)	16.7 / 19.8

The binding sites of Magnesium atom in the Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium (pdb code 6d3a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium, PDB code: 6d3a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:37.4 occ:1.00 O C:HOH602 1.9 39.9 1.0 O C:HOH504 2.2 32.4 1.0 OD1 C:ASP78 2.5 22.1 1.0 OG1 C:THR76 2.6 18.0 1.0 OD2 C:ASP316 2.6 54.9 1.0 OD1 C:ASP77 2.6 25.2 1.0 HO2D C:AR6401 2.7 41.1 1.0 O2D C:AR6401 3.0 34.3 1.0 HB C:THR76 3.1 23.2 1.0 HG1 C:THR76 3.2 21.6 1.0 CB C:THR76 3.4 19.3 1.0 CG C:ASP316 3.4 43.7 1.0 H C:ASP78 3.5 20.1 1.0 HG21 C:THR76 3.6 29.9 1.0 H C:ASP77 3.7 22.9 1.0 CG C:ASP78 3.7 21.7 1.0 CG C:ASP77 3.8 24.1 1.0 HB3 C:ASP316 3.8 31.5 1.0 OD1 C:ASP316 4.0 45.7 1.0 CG2 C:THR76 4.0 24.9 1.0 HO3D C:AR6401 4.0 36.1 1.0 O C:HOH618 4.2 45.7 1.0 CB C:ASP316 4.2 26.2 1.0 HG1 C:THR317 4.2 28.3 1.0 N C:ASP77 4.2 19.1 1.0 N C:ASP78 4.3 16.7 1.0 OD2 C:ASP77 4.3 22.4 1.0 OD1 C:ASP34 4.3 20.0 1.0 C2D C:AR6401 4.4 26.6 1.0 OD2 C:ASP78 4.4 23.2 1.0 OG1 C:THR317 4.5 23.6 1.0 O C:GLY115 4.5 24.0 1.0 HG23 C:THR76 4.6 29.9 1.0 HA3 C:GLY115 4.6 27.0 1.0 HB2 C:ASP78 4.6 20.2 1.0 O1D C:AR6401 4.6 39.3 1.0 HB2 C:ASP316 4.6 31.5 1.0 CB C:ASP78 4.7 16.8 1.0 O C:HOH580 4.7 31.1 1.0 O3D C:AR6401 4.7 30.1 1.0 CA C:THR76 4.7 16.6 1.0 HG22 C:THR76 4.7 29.9 1.0 O C:ARG114 4.8 29.5 1.0 C C:THR76 4.8 16.7 1.0 CB C:ASP77 4.9 19.7 1.0 H2D C:AR6401 4.9 32.0 1.0 CA C:ASP77 5.0 18.2 1.0

Magnesium binding site 2 out of 4 in the Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:30.9 occ:1.00 OD2 D:ASP316 2.3 54.8 1.0 O D:HOH502 2.4 32.2 1.0 OG1 D:THR76 2.5 18.8 1.0 OD1 D:ASP78 2.5 23.5 1.0 OD1 D:ASP77 2.6 21.7 1.0 O D:HOH697 2.8 50.9 1.0 HB D:THR76 2.9 22.9 1.0 HO2D D:AR6401 3.0 38.5 1.0 HG1 D:THR76 3.2 22.6 1.0 O2D D:AR6401 3.2 32.1 1.0 CB D:THR76 3.2 19.1 1.0 O D:HOH514 3.4 33.7 1.0 H D:ASP78 3.4 21.6 1.0 HG21 D:THR76 3.4 24.9 1.0 CG D:ASP316 3.5 43.4 1.0 H D:ASP77 3.5 19.4 1.0 CG D:ASP77 3.6 24.3 1.0 CG D:ASP78 3.7 24.3 1.0 CG2 D:THR76 3.9 20.7 1.0 HB3 D:ASP316 4.0 36.6 1.0 N D:ASP77 4.1 16.2 1.0 OD2 D:ASP77 4.1 22.3 1.0 HO3D D:AR6401 4.1 59.2 1.0 N D:ASP78 4.2 18.0 1.0 O D:HOH686 4.3 40.6 1.0 CB D:ASP316 4.3 30.5 1.0 OD1 D:ASP316 4.3 51.8 1.0 OD1 D:ASP34 4.3 18.4 1.0 HG23 D:THR76 4.5 24.9 1.0 OD2 D:ASP78 4.5 26.8 1.0 HA3 D:GLY115 4.5 29.0 1.0 HB2 D:ASP78 4.5 20.1 1.0 O D:GLY115 4.5 24.7 1.0 CA D:THR76 4.6 17.1 1.0 HG22 D:THR76 4.6 24.9 1.0 OG1 D:THR317 4.6 29.0 1.0 CB D:ASP78 4.6 16.7 1.0 C2D D:AR6401 4.6 35.3 1.0 HB2 D:ASP316 4.7 36.6 1.0 C D:THR76 4.7 16.7 1.0 O D:ARG114 4.8 23.3 1.0 HG1 D:THR317 4.8 34.8 1.0 CB D:ASP77 4.8 23.7 1.0 O3D D:AR6401 4.8 49.3 1.0 O1D D:AR6401 4.8 34.3 1.0 CA D:ASP77 4.8 18.8 1.0 C D:ASP77 5.0 19.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:31.0 occ:1.00 O A:HOH645 2.2 32.8 1.0 OD2 A:ASP316 2.3 53.1 1.0 OD1 A:ASP78 2.3 24.5 1.0 O A:HOH550 2.3 40.2 1.0 OD1 A:ASP77 2.4 23.6 1.0 OG1 A:THR76 2.4 20.5 1.0 HG1 A:THR76 3.0 24.6 1.0 HB A:THR76 3.1 23.8 1.0 CB A:THR76 3.3 19.8 1.0 CG A:ASP316 3.3 39.5 1.0 H A:ASP78 3.3 24.4 1.0 HO3D A:AR6401 3.5 40.1 1.0 CG A:ASP78 3.6 25.6 1.0 HG21 A:THR76 3.6 30.6 1.0 O3D A:AR6401 3.6 33.4 1.0 CG A:ASP77 3.6 24.2 1.0 H A:ASP77 3.6 23.8 1.0 HB3 A:ASP316 4.0 33.0 1.0 CG2 A:THR76 4.0 25.5 1.0 OD1 A:ASP316 4.0 40.3 1.0 O A:HOH539 4.0 68.0 1.0 N A:ASP77 4.1 19.9 1.0 N A:ASP78 4.1 20.3 1.0 O A:HOH646 4.2 36.6 1.0 OD1 A:ASP34 4.2 20.5 1.0 HG1 A:THR317 4.2 33.1 1.0 OD2 A:ASP77 4.2 22.0 1.0 CB A:ASP316 4.2 27.5 1.0 OD2 A:ASP78 4.4 23.0 1.0 HB2 A:ASP78 4.4 22.9 1.0 HG23 A:THR76 4.5 30.6 1.0 OG1 A:THR317 4.5 27.6 1.0 CB A:ASP78 4.5 19.1 1.0 O A:GLY115 4.5 23.3 1.0 O A:ARG114 4.5 30.2 1.0 CA A:THR76 4.6 19.8 1.0 HB2 A:ASP316 4.6 33.0 1.0 C A:THR76 4.7 19.8 1.0 O A:HOH681 4.7 37.5 1.0 HG22 A:THR76 4.7 30.6 1.0 CB A:ASP77 4.8 20.5 1.0 CA A:ASP77 4.8 20.3 1.0 O A:HOH503 4.9 35.0 1.0 CA A:ASP78 4.9 19.2 1.0 C A:ASP77 4.9 20.1 1.0 HA3 A:GLY115 4.9 28.4 1.0 HB2 A:SER38 5.0 44.1 1.0 H4D A:AR6401 5.0 56.0 1.0

Magnesium binding site 4 out of 4 in the Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human ARH3 D314E Bound to Adp-Ribose and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:32.8 occ:1.00 O B:HOH554 2.1 40.7 1.0 O B:HOH503 2.2 32.9 1.0 OD1 B:ASP78 2.5 25.9 1.0 OG1 B:THR76 2.5 22.2 1.0 OD2 B:ASP316 2.6 58.8 1.0 OD1 B:ASP77 2.7 26.5 1.0 HO2D B:AR6401 3.0 40.2 1.0 HB B:THR76 3.1 27.6 1.0 HG1 B:THR76 3.1 26.6 1.0 O2D B:AR6401 3.2 33.5 1.0 O B:HOH640 3.3 58.8 1.0 CB B:THR76 3.3 23.0 1.0 H B:ASP78 3.4 24.4 1.0 CG B:ASP316 3.5 47.0 1.0 HG21 B:THR76 3.5 27.6 1.0 O B:HOH531 3.6 37.9 1.0 CG B:ASP78 3.6 25.9 1.0 CG B:ASP77 3.7 27.5 1.0 HB3 B:ASP316 3.8 38.0 1.0 H B:ASP77 3.8 25.3 1.0 CG2 B:THR76 4.0 23.0 1.0 HO3D B:AR6401 4.1 83.0 1.0 CB B:ASP316 4.2 31.7 1.0 O B:HOH616 4.2 43.7 1.0 OD2 B:ASP77 4.2 28.0 1.0 N B:ASP78 4.2 20.3 1.0 N B:ASP77 4.3 21.1 1.0 OD1 B:ASP316 4.3 50.3 1.0 OD1 B:ASP34 4.3 21.2 1.0 OD2 B:ASP78 4.4 35.2 1.0 OG1 B:THR317 4.4 33.1 1.0 HB2 B:ASP78 4.5 25.3 1.0 HG23 B:THR76 4.5 27.6 1.0 HB2 B:ASP316 4.6 38.0 1.0 CB B:ASP78 4.6 21.1 1.0 HA3 B:GLY115 4.6 34.1 1.0 C2D B:AR6401 4.6 44.7 1.0 HG1 B:THR317 4.6 39.7 1.0 CA B:THR76 4.7 17.4 1.0 O B:GLY115 4.7 26.1 1.0 HG22 B:THR76 4.7 27.6 1.0 O3D B:AR6401 4.8 69.2 1.0 C B:THR76 4.8 16.1 1.0 O1D B:AR6401 4.8 40.9 1.0 CB B:ASP77 4.9 21.9 1.0 O B:ARG114 4.9 31.2 1.0 CA B:ASP77 5.0 21.5 1.0

Y.Pourfarjam, J.Ventura, I.Kurinov, A.Cho, J.Moss, I.K.Kim. Structure of Human Adp-Ribosyl-Acceptor Hydrolase 3 Bound to Adp-Ribose Reveals A Conformational Switch That Enables Specific Substrate Recognition. J.Biol.Chem. V. 293 12350 2018.
ISSN: ESSN 1083-351X
PubMed: 29907568
DOI: 10.1074/JBC.RA118.003586