Magnesium in PDB 6hgz: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose

The structure of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose, PDB code: 6hgz was solved by A.Ariza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.95 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.793, 97.638, 106.446, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21

The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose (pdb code 6hgz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose, PDB code: 6hgz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.6 occ:1.00 OD2 A:ASP305 2.2 29.2 1.0 OD1 A:ASP64 2.2 20.1 1.0 O A:HOH587 2.2 30.4 1.0 OD1 A:ASP63 2.2 23.8 1.0 OG1 A:THR62 2.3 22.9 1.0 O2D A:AR6403 2.4 27.3 1.0 CB A:THR62 3.2 22.2 1.0 MG A:MG402 3.3 31.1 1.0 CG A:ASP63 3.3 23.2 1.0 CG A:ASP305 3.4 27.1 1.0 CG A:ASP64 3.5 19.5 1.0 C2D A:AR6403 3.7 25.2 1.0 OD2 A:ASP63 3.9 23.4 1.0 N A:ASP63 3.9 21.5 1.0 OE2 A:GLU33 4.0 39.0 1.0 N A:ASP64 4.0 18.5 1.0 CG2 A:THR62 4.0 21.9 1.0 OE1 A:GLU33 4.2 35.5 1.0 O1D A:AR6403 4.2 27.7 1.0 O A:GLY101 4.2 23.3 1.0 CB A:ASP305 4.3 24.1 1.0 OD2 A:ASP64 4.3 19.2 1.0 OD1 A:ASP305 4.3 28.6 1.0 OD1 A:ASP26 4.3 20.2 1.0 OG1 A:THR306 4.4 24.3 1.0 CA A:THR62 4.4 20.9 1.0 O3D A:AR6403 4.4 23.8 1.0 CB A:ASP64 4.5 18.8 1.0 C1D A:AR6403 4.5 25.9 1.0 C A:THR62 4.5 20.6 1.0 CD A:GLU33 4.5 35.5 1.0 CB A:ASP63 4.5 22.1 1.0 CA A:ASP63 4.6 21.2 1.0 O A:HOH607 4.7 35.9 1.0 C A:ASP63 4.8 19.8 1.0 C3D A:AR6403 4.8 24.3 1.0 CA A:ASP64 4.8 18.9 1.0 O A:ARG100 4.9 23.3 1.0 C A:GLY101 4.9 22.9 1.0

Magnesium binding site 2 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:31.1 occ:1.00 O3D A:AR6403 2.2 23.8 1.0 OD2 A:ASP305 2.2 29.2 1.0 OD1 A:ASP305 2.2 28.6 1.0 OD1 A:ASP303 2.3 29.8 1.0 OE2 A:GLU33 2.3 39.0 1.0 O2D A:AR6403 2.4 27.3 1.0 OG1 A:THR306 2.4 24.3 1.0 CG A:ASP305 2.5 27.1 1.0 O1D A:AR6403 2.9 27.7 1.0 C2D A:AR6403 3.2 25.2 1.0 CG A:ASP303 3.2 25.7 1.0 MG A:MG401 3.3 26.6 1.0 C3D A:AR6403 3.3 24.3 1.0 CD A:GLU33 3.3 35.5 1.0 OD2 A:ASP303 3.5 23.5 1.0 CB A:THR306 3.7 21.1 1.0 C1D A:AR6403 3.7 25.9 1.0 OD1 A:ASP64 3.9 20.1 1.0 O A:HOH587 3.9 30.4 1.0 CB A:ASP305 3.9 24.1 1.0 N A:THR306 4.0 21.4 1.0 OE1 A:GLU33 4.0 35.5 1.0 C4D A:AR6403 4.2 25.1 1.0 CG A:GLU33 4.3 35.6 1.0 O4D A:AR6403 4.4 26.1 1.0 CA A:THR306 4.4 19.9 1.0 OD2 A:ASP64 4.4 19.2 1.0 CG A:ASP64 4.6 19.5 1.0 CB A:ASP303 4.6 25.0 1.0 C A:ASP305 4.7 21.9 1.0 CA A:ASP305 4.7 23.5 1.0 CG2 A:THR306 4.8 21.9 1.0 N A:ASP305 4.9 23.3 1.0 OD1 A:ASP63 4.9 23.8 1.0

Magnesium binding site 3 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:27.9 occ:1.00 OD2 B:ASP305 2.2 34.0 1.0 O B:HOH572 2.2 32.9 1.0 OD1 B:ASP64 2.3 22.8 1.0 OD1 B:ASP63 2.3 25.6 1.0 OG1 B:THR62 2.3 25.6 1.0 O2D B:AR6403 2.3 32.9 1.0 CB B:THR62 3.3 24.9 1.0 MG B:MG402 3.3 36.2 1.0 CG B:ASP63 3.3 25.1 1.0 CG B:ASP305 3.4 30.1 1.0 CG B:ASP64 3.5 21.5 1.0 C2D B:AR6403 3.7 30.4 1.0 OD2 B:ASP63 3.9 27.1 1.0 N B:ASP63 3.9 22.4 1.0 OE2 B:GLU33 4.0 43.5 1.0 CG2 B:THR62 4.0 25.6 1.0 N B:ASP64 4.0 20.5 1.0 O B:GLY101 4.1 27.2 1.0 O1D B:AR6403 4.3 33.7 1.0 OD2 B:ASP64 4.3 22.4 1.0 CB B:ASP305 4.3 27.3 1.0 OD1 B:ASP305 4.3 33.5 1.0 OD1 B:ASP26 4.3 21.3 1.0 OG1 B:THR306 4.4 27.7 1.0 C1D B:AR6403 4.4 32.1 1.0 CB B:ASP64 4.5 20.0 1.0 CA B:THR62 4.5 23.1 1.0 CB B:ASP63 4.5 24.1 1.0 O3D B:AR6403 4.5 30.4 1.0 C B:THR62 4.6 22.2 1.0 CA B:ASP63 4.6 22.9 1.0 OE1 B:GLU33 4.6 46.0 1.0 CD B:GLU33 4.6 42.3 1.0 C3D B:AR6403 4.7 30.2 1.0 C B:ASP63 4.8 21.5 1.0 C B:GLY101 4.9 27.1 1.0 CA B:ASP64 4.9 19.9 1.0 O B:ARG100 4.9 26.2 1.0

Magnesium binding site 4 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:36.2 occ:1.00 O3D B:AR6403 2.2 30.4 1.0 OD2 B:ASP305 2.2 34.0 1.0 OD1 B:ASP305 2.2 33.5 1.0 OE2 B:GLU33 2.3 43.5 1.0 OD1 B:ASP303 2.3 34.1 1.0 OG1 B:THR306 2.4 27.7 1.0 O2D B:AR6403 2.4 32.9 1.0 CG B:ASP305 2.5 30.1 1.0 O1D B:AR6403 2.9 33.7 1.0 C3D B:AR6403 3.2 30.2 1.0 CG B:ASP303 3.2 32.4 1.0 C2D B:AR6403 3.2 30.4 1.0 MG B:MG401 3.3 27.9 1.0 CD B:GLU33 3.4 42.3 1.0 OD2 B:ASP303 3.5 31.6 1.0 CB B:THR306 3.6 25.1 1.0 O B:HOH572 3.7 32.9 1.0 C1D B:AR6403 3.7 32.1 1.0 OD1 B:ASP64 3.8 22.8 1.0 N B:THR306 3.9 24.5 1.0 CB B:ASP305 4.0 27.3 1.0 C4D B:AR6403 4.1 30.9 1.0 CG B:GLU33 4.3 40.1 1.0 OE1 B:GLU33 4.3 46.0 1.0 CA B:THR306 4.3 23.6 1.0 OD2 B:ASP64 4.3 22.4 1.0 O4D B:AR6403 4.4 32.5 1.0 CG B:ASP64 4.5 21.5 1.0 C B:ASP305 4.6 24.7 1.0 CB B:ASP303 4.6 32.6 1.0 CA B:ASP305 4.7 26.5 1.0 CG2 B:THR306 4.8 24.8 1.0 N B:ASP305 4.8 26.3 1.0 OD1 B:ASP63 5.0 25.6 1.0

J.G.M.Rack, A.Ariza, B.S.Drown, C.Henfrey, E.Bartlett, T.Shirai, P.J.Hergenrother, I.Ahel. (Adp-Ribosyl)Hydrolases: Structural Basis For Differential Substrate Recognition and Inhibition. Cell Chem Biol V. 25 1533 2018.
ISSN: ESSN 2451-9448
PubMed: 30472116
DOI: 10.1016/J.CHEMBIOL.2018.11.001