Magnesium in PDB 7l9h: Crystal Structure of Human ARH3-D77A Bound to Magnesium and Adp-Ribose

All present enzymatic activity of Crystal Structure of Human ARH3-D77A Bound to Magnesium and Adp-Ribose:
3.2.1.143;

The structure of Crystal Structure of Human ARH3-D77A Bound to Magnesium and Adp-Ribose, PDB code: 7l9h 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)	61.29 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.702, 71.611, 115.928, 94.24, 94.58, 107.62
R / Rfree (%)	18 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of Human ARH3-D77A Bound to Magnesium and Adp-Ribose (pdb code 7l9h). 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-D77A Bound to Magnesium and Adp-Ribose, PDB code: 7l9h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human ARH3-D77A 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-D77A Bound to Magnesium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:10.4 occ:1.00 OD1 C:ASP314 2.0 11.1 1.0 OD1 C:ASP316 2.0 14.7 1.0 OG1 C:THR317 2.0 10.7 1.0 O2D C:AR6401 2.0 9.7 1.0 O3D C:AR6401 2.1 14.2 1.0 O C:HOH642 2.2 13.9 1.0 HO2D C:AR6401 2.8 11.6 1.0 HO3D C:AR6401 2.8 17.0 1.0 C3D C:AR6401 2.9 11.6 1.0 C2D C:AR6401 3.0 10.6 1.0 CG C:ASP314 3.0 12.8 1.0 CG C:ASP316 3.0 14.6 1.0 H C:THR317 3.2 12.9 1.0 CB C:THR317 3.3 12.3 1.0 OD2 C:ASP314 3.3 11.1 1.0 H3D C:AR6401 3.3 13.9 1.0 HB C:THR317 3.4 14.8 1.0 OD2 C:ASP316 3.4 18.5 1.0 H2D C:AR6401 3.6 12.8 1.0 N C:THR317 3.6 10.7 1.0 O1D C:AR6401 3.8 27.2 1.0 CA C:THR317 4.0 10.3 1.0 C1D C:AR6401 4.0 15.4 1.0 OD1 C:ASP78 4.0 15.7 1.0 OD2 C:ASP78 4.2 13.0 1.0 O C:HOH531 4.2 31.0 1.0 OE2 C:GLU41 4.2 62.7 1.0 C4D C:AR6401 4.2 10.1 1.0 HG21 C:THR317 4.3 15.8 1.0 HA C:THR317 4.3 12.4 1.0 HD1 C:AR6401 4.3 32.6 1.0 H C:ASP316 4.3 16.3 1.0 CB C:ASP314 4.4 15.5 1.0 HA C:ASP314 4.4 16.4 1.0 CG2 C:THR317 4.4 13.2 1.0 H4D C:AR6401 4.4 12.2 1.0 CB C:ASP316 4.4 12.6 1.0 C C:ASP316 4.5 12.5 1.0 CG C:ASP78 4.6 14.1 1.0 O4D C:AR6401 4.7 17.5 1.0 N C:ASP316 4.7 13.6 1.0 CD C:GLU41 4.7 70.8 1.0 CA C:ASP314 4.7 13.7 1.0 OE1 C:GLU41 4.7 70.4 1.0 CA C:ASP316 4.7 13.6 1.0 HD21 C:ASN151 4.7 14.2 1.0 C C:ASP314 4.7 14.1 1.0 HG23 C:THR317 4.7 15.8 1.0 O C:ASP314 4.8 12.5 1.0 H1D C:AR6401 4.8 18.4 1.0 HB3 C:ASP314 4.9 18.6 1.0 HB2 C:ASP314 4.9 18.6 1.0 HB2 C:ASP316 4.9 15.1 1.0 HB3 C:ASP316 4.9 15.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human ARH3-D77A 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-D77A Bound to Magnesium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:12.1 occ:1.00 O2D D:AR6401 2.0 12.1 1.0 O3D D:AR6401 2.1 14.1 1.0 OD1 D:ASP316 2.1 12.5 1.0 OD1 D:ASP314 2.1 13.0 1.0 OG1 D:THR317 2.1 9.4 1.0 O D:HOH633 2.2 14.2 1.0 HO2D D:AR6401 2.7 14.5 1.0 HO3D D:AR6401 2.8 16.9 1.0 C2D D:AR6401 2.9 10.8 1.0 C3D D:AR6401 2.9 11.2 1.0 CG D:ASP314 3.0 11.9 1.0 CG D:ASP316 3.0 14.8 1.0 H D:THR317 3.3 12.9 1.0 OD2 D:ASP314 3.3 12.8 1.0 CB D:THR317 3.3 10.3 1.0 HB D:THR317 3.3 12.4 1.0 H3D D:AR6401 3.4 13.4 1.0 OD2 D:ASP316 3.4 20.8 1.0 H2D D:AR6401 3.6 13.0 1.0 O1D D:AR6401 3.6 31.2 1.0 N D:THR317 3.8 10.8 1.0 C1D D:AR6401 3.8 17.3 1.0 O D:HOH508 4.1 34.0 1.0 CA D:THR317 4.1 10.8 1.0 OD1 D:ASP78 4.2 13.6 1.0 OD2 D:ASP78 4.2 13.1 1.0 C4D D:AR6401 4.2 14.0 1.0 HG21 D:THR317 4.2 13.9 1.0 H D:ASP316 4.3 11.8 1.0 CG2 D:THR317 4.4 11.6 1.0 CB D:ASP314 4.4 13.7 1.0 H4D D:AR6401 4.4 16.8 1.0 O D:HOH629 4.4 23.8 1.0 CB D:ASP316 4.4 11.6 1.0 HD1 D:AR6401 4.4 37.4 1.0 HA D:ASP314 4.4 13.0 1.0 HA D:THR317 4.5 13.0 1.0 O4D D:AR6401 4.6 18.1 1.0 C D:ASP316 4.6 8.9 1.0 CG D:ASP78 4.6 13.7 1.0 H1D D:AR6401 4.7 20.8 1.0 N D:ASP316 4.7 9.8 1.0 O D:ASP314 4.7 12.3 1.0 C D:ASP314 4.7 12.8 1.0 HD21 D:ASN151 4.7 11.1 1.0 CA D:ASP314 4.7 10.8 1.0 HG22 D:ILE271 4.7 39.5 1.0 CA D:ASP316 4.8 11.5 1.0 HG23 D:THR317 4.8 13.9 1.0 HB3 D:ASP314 4.9 16.4 1.0 HB2 D:ASP314 4.9 16.4 1.0 HB2 D:ASP316 4.9 13.9 1.0 HB3 D:ASP316 5.0 13.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human ARH3-D77A 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-D77A Bound to Magnesium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:14.8 occ:1.00 OD1 A:ASP316 2.0 16.2 1.0 O2D A:AR6401 2.0 13.1 1.0 OD1 A:ASP314 2.1 16.1 1.0 O3D A:AR6401 2.1 16.4 1.0 OG1 A:THR317 2.1 14.3 1.0 O A:HOH612 2.1 14.6 1.0 HO2D A:AR6401 2.7 15.7 1.0 HO3D A:AR6401 2.8 19.7 1.0 CG A:ASP316 3.0 20.7 1.0 CG A:ASP314 3.0 15.0 1.0 C3D A:AR6401 3.0 15.2 1.0 C2D A:AR6401 3.0 13.3 1.0 H A:THR317 3.2 17.2 1.0 OD2 A:ASP314 3.2 17.0 1.0 CB A:THR317 3.3 15.5 1.0 OD2 A:ASP316 3.3 30.5 1.0 HB A:THR317 3.4 18.6 1.0 H3D A:AR6401 3.5 18.3 1.0 N A:THR317 3.7 14.3 1.0 H2D A:AR6401 3.7 15.9 1.0 O1D A:AR6401 3.8 35.3 1.0 C1D A:AR6401 4.0 21.8 1.0 OE1 A:GLU41 4.1 67.9 1.0 OD1 A:ASP78 4.1 18.3 1.0 O A:HOH573 4.1 29.6 1.0 CA A:THR317 4.1 15.6 1.0 OD2 A:ASP78 4.2 13.4 1.0 HG21 A:THR317 4.2 18.7 1.0 C4D A:AR6401 4.3 16.0 1.0 H A:ASP316 4.3 20.6 1.0 CG2 A:THR317 4.3 15.6 1.0 CB A:ASP316 4.4 18.8 1.0 CB A:ASP314 4.4 14.4 1.0 H4D A:AR6401 4.4 19.2 1.0 HA A:ASP314 4.5 18.6 1.0 HA A:THR317 4.5 18.7 1.0 C A:ASP316 4.5 15.6 1.0 HD1 A:AR6401 4.5 42.3 1.0 CG A:ASP78 4.6 18.2 1.0 HD21 A:ASN151 4.7 19.5 1.0 N A:ASP316 4.7 17.2 1.0 O4D A:AR6401 4.7 21.2 1.0 HG23 A:THR317 4.7 18.7 1.0 O A:ASP314 4.7 18.2 1.0 CA A:ASP316 4.8 16.5 1.0 C A:ASP314 4.8 18.9 1.0 CA A:ASP314 4.8 15.5 1.0 H1D A:AR6401 4.9 26.1 1.0 HB3 A:ASP314 4.9 17.3 1.0 HB2 A:ASP316 4.9 22.6 1.0 HB3 A:ASP316 4.9 22.6 1.0 HB2 A:ASP314 4.9 17.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human ARH3-D77A 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-D77A Bound to Magnesium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:17.6 occ:1.00 OD1 B:ASP314 2.0 18.1 1.0 OD1 B:ASP316 2.0 21.4 1.0 OG1 B:THR317 2.1 13.3 1.0 O2D B:AR6401 2.1 15.6 1.0 O3D B:AR6401 2.1 19.8 1.0 O B:HOH601 2.2 25.6 1.0 HO2D B:AR6401 2.8 18.8 1.0 HO3D B:AR6401 2.8 23.7 1.0 CG B:ASP314 2.9 17.9 1.0 C3D B:AR6401 3.0 15.9 1.0 CG B:ASP316 3.0 20.6 1.0 C2D B:AR6401 3.1 16.9 1.0 H B:THR317 3.2 17.4 1.0 OD2 B:ASP314 3.2 22.6 1.0 CB B:THR317 3.2 17.3 1.0 HB B:THR317 3.2 20.7 1.0 H3D B:AR6401 3.3 19.1 1.0 OD2 B:ASP316 3.4 30.1 1.0 HD1 B:AR6401 3.4 39.2 1.0 N B:THR317 3.6 14.5 1.0 H2D B:AR6401 3.8 20.3 1.0 O1D B:AR6401 4.0 32.7 1.0 CA B:THR317 4.0 15.3 1.0 OD2 B:ASP78 4.1 12.4 1.0 C1D B:AR6401 4.1 17.0 1.0 HG21 B:THR317 4.2 19.2 1.0 OD1 B:ASP78 4.2 16.3 1.0 CB B:ASP314 4.2 16.3 1.0 H B:ASP316 4.3 21.1 1.0 C4D B:AR6401 4.3 22.1 1.0 HA B:ASP314 4.3 24.9 1.0 CG2 B:THR317 4.3 16.0 1.0 H4D B:AR6401 4.3 26.6 1.0 HA B:THR317 4.4 18.4 1.0 CB B:ASP316 4.4 16.8 1.0 C B:ASP316 4.5 14.4 1.0 O B:HOH603 4.5 24.8 1.0 O B:ASP314 4.5 18.9 1.0 HD21 B:ASN151 4.6 19.5 1.0 C B:ASP314 4.6 21.3 1.0 CA B:ASP314 4.6 20.8 1.0 CG B:ASP78 4.6 18.0 1.0 N B:ASP316 4.6 17.5 1.0 HG22 B:ILE271 4.7 43.8 1.0 CA B:ASP316 4.7 17.3 1.0 HB3 B:ASP314 4.7 19.6 1.0 HG23 B:THR317 4.7 19.2 1.0 HB2 B:ASP314 4.8 19.6 1.0 O4D B:AR6401 4.8 24.4 1.0 HB3 B:ASP316 4.9 20.2 1.0 HB2 B:ASP316 4.9 20.2 1.0 H1D B:AR6401 4.9 20.4 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