Magnesium in PDB 7l9i: Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose

All present enzymatic activity of Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose:
3.2.1.143;

The structure of Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose, PDB code: 7l9i was solved by Y.Pourfarjam, I.Kurinov, J.Moss, I.K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.64 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.808, 71.428, 115.803, 94.03, 94.63, 107.86
R / Rfree (%)	18.9 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose (pdb code 7l9i). 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 Human ARH3-D314A Bound to Magnesium and Adp- Ribose, PDB code: 7l9i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose


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 Human ARH3-D314A Bound to Magnesium and Adp- Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:24.1 occ:1.00 O C:HOH501 2.0 21.8 1.0 O C:HOH591 2.0 24.1 1.0 OD2 C:ASP316 2.1 23.4 1.0 OD1 C:ASP78 2.2 19.3 1.0 OD1 C:ASP77 2.4 18.6 1.0 OG1 C:THR76 2.4 16.0 1.0 HO2D C:AR6401 2.8 36.2 1.0 O2D C:AR6401 2.9 30.1 1.0 HG1 C:THR76 3.0 19.2 1.0 HB C:THR76 3.1 14.2 1.0 CG C:ASP316 3.3 25.0 1.0 H C:ASP78 3.3 13.1 1.0 CB C:THR76 3.3 11.8 1.0 CG C:ASP78 3.5 16.5 1.0 CG C:ASP77 3.5 17.4 1.0 H C:ASP77 3.6 15.6 1.0 HG22 C:THR76 3.7 20.8 1.0 OD1 C:ASP316 3.8 34.0 1.0 CG2 C:THR76 4.0 17.4 1.0 HO3D C:AR6401 4.0 42.8 1.0 OD2 C:ASP77 4.0 17.1 1.0 N C:ASP77 4.1 13.0 1.0 N C:ASP78 4.1 10.9 1.0 OD2 C:ASP78 4.1 14.8 1.0 HG1 C:THR317 4.2 27.4 1.0 OD1 C:ASP34 4.2 16.3 1.0 O1D C:AR6401 4.3 35.7 1.0 HG21 C:THR76 4.3 20.8 1.0 C2D C:AR6401 4.3 23.3 1.0 HB2 C:ASP316 4.4 32.3 1.0 OG1 C:THR317 4.4 22.8 1.0 O3D C:AR6401 4.4 35.7 1.0 CB C:ASP316 4.5 26.9 1.0 HB2 C:ASP78 4.5 16.8 1.0 CB C:ASP78 4.5 14.0 1.0 O C:GLY115 4.5 17.1 1.0 CA C:THR76 4.6 14.0 1.0 C C:THR76 4.7 14.0 1.0 CB C:ASP77 4.7 17.2 1.0 CA C:ASP77 4.8 12.9 1.0 O C:ARG114 4.8 22.7 1.0 HA3 C:GLY115 4.8 24.7 1.0 HG23 C:THR76 4.8 20.8 1.0 O C:HOH503 4.9 32.1 1.0 H2D C:AR6401 4.9 27.9 1.0 HB3 C:ASP316 4.9 32.3 1.0 CA C:ASP78 4.9 15.9 1.0 C1D C:AR6401 4.9 31.5 1.0 C C:ASP77 4.9 11.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose


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 Human ARH3-D314A Bound to Magnesium and Adp- Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:18.4 occ:1.00 O D:HOH501 1.9 21.5 1.0 O D:HOH578 2.1 22.0 1.0 OD2 D:ASP316 2.1 24.0 1.0 OD1 D:ASP78 2.2 14.9 1.0 OD1 D:ASP77 2.3 20.4 1.0 OG1 D:THR76 2.4 17.1 1.0 HG1 D:THR76 3.0 20.6 1.0 HO2D D:AR6401 3.0 39.4 1.0 HB D:THR76 3.1 18.3 1.0 O2D D:AR6401 3.1 32.9 1.0 H D:ASP78 3.2 14.8 1.0 CG D:ASP316 3.3 25.9 1.0 CB D:THR76 3.3 15.3 1.0 CG D:ASP78 3.4 17.7 1.0 H D:ASP77 3.4 16.1 1.0 CG D:ASP77 3.4 18.7 1.0 HG23 D:THR76 3.7 18.8 1.0 OD1 D:ASP316 3.8 31.0 1.0 HO3D D:AR6401 3.9 39.2 1.0 N D:ASP77 3.9 13.4 1.0 OD2 D:ASP77 4.0 17.7 1.0 N D:ASP78 4.0 12.4 1.0 CG2 D:THR76 4.0 15.7 1.0 OD1 D:ASP34 4.1 11.5 1.0 HG1 D:THR317 4.1 24.5 1.0 OD2 D:ASP78 4.1 16.3 1.0 HE2 D:MET155 4.3 35.8 1.0 HB2 D:ASP78 4.3 16.0 1.0 OG1 D:THR317 4.4 20.4 1.0 HB2 D:ASP316 4.4 24.9 1.0 CB D:ASP78 4.4 13.4 1.0 O D:HOH671 4.4 28.4 1.0 HG22 D:THR76 4.4 18.8 1.0 CB D:ASP316 4.5 20.8 1.0 C2D D:AR6401 4.5 24.1 1.0 O D:GLY115 4.5 18.2 1.0 CA D:THR76 4.5 14.7 1.0 C D:THR76 4.5 11.6 1.0 CB D:ASP77 4.6 17.4 1.0 CA D:ASP77 4.7 13.2 1.0 CA D:ASP78 4.8 14.5 1.0 C D:ASP77 4.8 14.9 1.0 HG21 D:THR76 4.8 18.8 1.0 O3D D:AR6401 4.9 32.6 1.0 H2D D:AR6401 4.9 28.9 1.0 HA3 D:GLY115 4.9 20.9 1.0 HB3 D:ASP316 4.9 24.9 1.0 HB3 D:ASP77 4.9 20.9 1.0 O1D D:AR6401 5.0 30.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose


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 Human ARH3-D314A Bound to Magnesium and Adp- Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.6 occ:1.00 O A:HOH632 2.0 26.4 1.0 O A:HOH503 2.1 26.1 1.0 OD2 A:ASP316 2.2 30.3 1.0 OD1 A:ASP78 2.2 17.3 1.0 OD1 A:ASP77 2.3 17.6 1.0 OG1 A:THR76 2.3 16.0 1.0 HG1 A:THR76 2.9 19.2 1.0 O2D A:AR6401 3.1 26.6 1.0 HB A:THR76 3.1 16.2 1.0 HO2D A:AR6401 3.2 31.9 1.0 H A:ASP78 3.2 15.3 1.0 CB A:THR76 3.3 13.5 1.0 CG A:ASP316 3.4 30.1 1.0 CG A:ASP77 3.4 17.1 1.0 CG A:ASP78 3.5 17.4 1.0 H A:ASP77 3.5 15.0 1.0 HG22 A:THR76 3.7 21.8 1.0 HO3D A:AR6401 3.8 46.0 1.0 O A:HOH671 3.9 34.4 1.0 OD1 A:ASP316 3.9 33.6 1.0 N A:ASP77 4.0 12.5 1.0 CG2 A:THR76 4.0 18.2 1.0 OD2 A:ASP77 4.0 15.5 1.0 N A:ASP78 4.0 12.8 1.0 OD1 A:ASP34 4.2 15.7 1.0 OD2 A:ASP78 4.2 16.0 1.0 O A:HOH501 4.3 28.5 1.0 HG21 A:THR76 4.3 21.8 1.0 O3D A:AR6401 4.3 38.3 1.0 HB2 A:ASP316 4.4 33.0 1.0 HB2 A:ASP78 4.4 13.9 1.0 CB A:ASP78 4.4 11.6 1.0 O A:GLY115 4.5 13.6 1.0 C2D A:AR6401 4.5 22.4 1.0 CB A:ASP316 4.5 27.5 1.0 CA A:THR76 4.5 13.2 1.0 C A:THR76 4.6 13.8 1.0 OG1 A:THR317 4.6 26.7 1.0 O A:ARG114 4.6 20.4 1.0 CB A:ASP77 4.6 15.6 1.0 O1D A:AR6401 4.7 38.3 1.0 CA A:ASP77 4.7 13.4 1.0 HG1 A:THR317 4.7 32.0 1.0 CA A:ASP78 4.8 12.1 1.0 HG23 A:THR76 4.8 21.8 1.0 C A:ASP77 4.8 13.2 1.0 HA3 A:GLY115 4.9 23.5 1.0 HB3 A:ASP316 4.9 33.0 1.0 HB3 A:ASP77 5.0 18.7 1.0 C3D A:AR6401 5.0 28.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human ARH3-D314A Bound to Magnesium and Adp- Ribose


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 Human ARH3-D314A Bound to Magnesium and Adp- Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:26.3 occ:1.00 HG1 B:THR76 1.8 20.2 1.0 O B:HOH501 1.9 22.7 1.0 O B:HOH617 2.1 28.0 1.0 OD2 B:ASP316 2.1 28.1 1.0 OD1 B:ASP78 2.2 19.2 1.0 OD1 B:ASP77 2.3 25.1 1.0 OG1 B:THR76 2.5 16.8 1.0 HO2D B:AR6401 2.9 35.3 1.0 O2D B:AR6401 3.0 29.4 1.0 HB B:THR76 3.1 19.6 1.0 CG B:ASP316 3.1 28.1 1.0 CB B:THR76 3.3 16.3 1.0 H B:ASP78 3.4 20.8 1.0 CG B:ASP78 3.5 20.0 1.0 CG B:ASP77 3.5 21.4 1.0 OD1 B:ASP316 3.5 36.2 1.0 HG22 B:THR76 3.6 23.1 1.0 H B:ASP77 3.7 18.9 1.0 HO3D B:AR6401 3.9 41.7 1.0 HG1 B:THR317 4.0 32.2 1.0 OD2 B:ASP77 4.0 19.7 1.0 CG2 B:THR76 4.0 19.3 1.0 N B:ASP77 4.1 15.7 1.0 N B:ASP78 4.1 17.4 1.0 OD2 B:ASP78 4.2 20.3 1.0 OD1 B:ASP34 4.3 17.1 1.0 OG1 B:THR317 4.3 26.8 1.0 C2D B:AR6401 4.4 27.3 1.0 O3D B:AR6401 4.4 34.8 1.0 HG21 B:THR76 4.4 23.1 1.0 O B:HOH647 4.5 32.5 1.0 CB B:ASP316 4.5 26.0 1.0 O B:GLY115 4.5 19.5 1.0 HB2 B:ASP78 4.5 19.6 1.0 HB2 B:ASP316 4.5 31.2 1.0 CB B:ASP78 4.5 16.3 1.0 CA B:THR76 4.6 15.9 1.0 CB B:ASP77 4.7 18.3 1.0 C B:THR76 4.7 14.9 1.0 O1D B:AR6401 4.7 32.4 1.0 CA B:ASP77 4.8 15.2 1.0 HG23 B:THR76 4.8 23.1 1.0 HA3 B:GLY115 4.8 23.9 1.0 HB3 B:ASP316 4.8 31.2 1.0 H2D B:AR6401 4.8 32.8 1.0 CA B:ASP78 4.9 16.7 1.0 C B:ASP77 5.0 19.1 1.0

Y.Pourfarjam, Z.Ma, I.Kurinov, J.Moss, I.K.Kim. Structural and Biochemical Analysis of Human Adp-Ribosyl-Acceptor Hydrolase 3 (ARH3) Reveals the Basis of Metal Selectivity and Different Roles For the Two Mg Ions J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X