Magnesium in PDB 6hh5: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm

The structure of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm, PDB code: 6hh5 was solved by A.Ariza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.46 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.869, 98.178, 105.554, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.4

The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm (pdb code 6hh5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm, PDB code: 6hh5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm


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-Hpm within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:62.2 occ:1.00 O A:HOH518 2.2 49.7 1.0 OG1 A:THR62 2.2 53.0 1.0 O A:HOH540 2.2 50.7 1.0 OD1 A:ASP64 2.2 55.3 1.0 OD2 A:ASP305 2.2 66.1 0.6 OD2 A:ASP305 2.2 61.6 0.4 OD1 A:ASP63 2.3 58.1 1.0 CG A:ASP305 3.0 65.0 0.6 CG A:ASP305 3.2 60.0 0.4 CB A:THR62 3.2 52.5 1.0 CB A:ASP305 3.4 57.6 0.4 CG A:ASP64 3.5 52.8 1.0 CG A:ASP63 3.5 57.4 1.0 CB A:ASP305 3.8 60.2 0.6 OD1 A:ASP305 3.8 70.6 0.6 CG2 A:THR62 3.9 53.5 1.0 OD1 A:ASP26 3.9 51.0 1.0 C1N A:A3R402 3.9 70.6 1.0 N A:ASP63 4.1 52.9 1.0 N A:ASP64 4.1 51.3 1.0 OD2 A:ASP63 4.1 57.6 1.0 CB A:ASP64 4.3 50.0 1.0 C2N A:A3R402 4.3 72.3 1.0 OD2 A:ASP64 4.3 53.6 1.0 OD1 A:ASP305 4.4 60.2 0.4 CA A:THR62 4.4 50.9 1.0 OG1 A:THR306 4.5 56.9 1.0 C A:THR62 4.6 51.0 1.0 O A:GLY101 4.6 59.2 1.0 CB A:ASP63 4.7 56.3 1.0 N4N A:A3R402 4.8 68.8 1.0 CA A:ASP63 4.8 53.7 1.0 CA A:ASP64 4.8 49.4 1.0 OE1 A:GLU33 4.8 75.9 1.0 CA A:ASP305 4.9 57.6 0.4 C A:ASP63 4.9 51.6 1.0 CG A:ASP26 4.9 48.4 1.0 C3N A:A3R402 5.0 69.4 1.0

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


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-Hpm within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:44.5 occ:1.00 O B:HOH535 2.2 45.7 1.0 OG1 B:THR62 2.2 41.5 1.0 O B:HOH604 2.2 39.3 1.0 OD1 B:ASP64 2.2 40.8 1.0 OD2 B:ASP305 2.2 46.0 0.4 OD2 B:ASP305 2.3 50.5 0.6 OD1 B:ASP63 2.3 43.6 1.0 CG B:ASP305 2.8 44.5 0.4 CB B:THR62 3.2 41.1 1.0 CG B:ASP305 3.2 50.1 0.6 CG B:ASP64 3.4 41.0 1.0 OD1 B:ASP305 3.5 43.8 0.4 CG B:ASP63 3.5 43.5 1.0 CB B:ASP305 3.6 44.0 0.4 C1N B:A3R402 3.7 49.3 1.0 CG2 B:THR62 3.9 42.4 1.0 CB B:ASP305 4.0 46.8 0.6 N4N B:A3R402 4.0 47.4 1.0 OD1 B:ASP305 4.0 55.5 0.6 N B:ASP63 4.1 41.7 1.0 OD1 B:ASP26 4.1 39.6 1.0 N B:ASP64 4.1 39.3 1.0 OE1 B:GLU33 4.1 53.0 0.5 OD2 B:ASP63 4.2 43.3 1.0 CB B:ASP64 4.3 40.0 1.0 OD2 B:ASP64 4.3 40.8 1.0 OG1 B:THR306 4.4 42.2 1.0 CA B:THR62 4.4 40.8 1.0 C B:THR62 4.6 40.8 1.0 O B:HOH612 4.6 56.0 1.0 O B:GLY101 4.6 44.2 1.0 CB B:ASP63 4.7 42.9 1.0 CA B:ASP63 4.8 41.7 1.0 CA B:ASP64 4.8 40.3 1.0 C B:ASP63 4.9 40.8 1.0 O B:HOH503 5.0 45.7 1.0 CA B:ASP305 5.0 43.2 0.4

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