Magnesium in PDB 6hh3: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpd

The structure of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpd, PDB code: 6hh3 was solved by A.Ariza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.54 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.850, 98.248, 105.624, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21

The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpd (pdb code 6hh3). 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-Hpd, PDB code: 6hh3:
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-Hpd


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-Hpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:41.1 occ:1.00 OD2 A:ASP305 2.2 47.8 1.0 O A:HOH613 2.2 44.5 1.0 O2N A:A1R403 2.3 47.4 1.0 OD1 A:ASP63 2.3 36.5 1.0 OD1 A:ASP64 2.3 35.9 1.0 OG1 A:THR62 2.3 35.3 1.0 CB A:THR62 3.2 34.7 1.0 CG A:ASP305 3.3 42.5 1.0 C2N A:A1R403 3.3 46.1 1.0 CG A:ASP63 3.4 36.0 1.0 CG A:ASP64 3.4 33.9 1.0 C1N A:A1R403 3.7 45.7 1.0 MG A:MG402 3.7 49.5 1.0 OD1 A:ASP305 3.8 47.1 1.0 N A:ASP63 3.8 33.6 1.0 N A:ASP64 3.9 32.7 1.0 CG2 A:THR62 3.9 35.6 1.0 OD2 A:ASP63 4.0 36.0 1.0 OD1 A:ASP26 4.2 35.0 1.0 OD2 A:ASP64 4.3 34.8 1.0 OE1 A:GLU33 4.3 59.6 1.0 CB A:ASP64 4.3 33.5 1.0 CA A:THR62 4.4 34.0 1.0 CB A:ASP305 4.4 38.4 1.0 O A:GLY101 4.5 37.1 1.0 C A:THR62 4.5 33.5 1.0 CB A:ASP63 4.5 34.2 1.0 CA A:ASP63 4.6 33.6 1.0 OG1 A:THR306 4.6 38.7 1.0 C3N A:A1R403 4.7 46.8 1.0 CA A:ASP64 4.7 33.1 1.0 C A:ASP63 4.7 33.3 1.0 O A:ARG100 4.9 38.7 1.0

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


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-Hpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:49.5 occ:1.00 OD1 A:ASP303 2.2 40.8 1.0 O3N A:A1R403 2.2 50.7 1.0 O2N A:A1R403 2.2 47.4 1.0 OD1 A:ASP305 2.2 47.1 1.0 OG1 A:THR306 2.3 38.7 1.0 OE1 A:GLU33 2.3 59.6 1.0 C3N A:A1R403 2.9 46.8 1.0 C2N A:A1R403 2.9 46.1 1.0 CG A:ASP303 3.0 39.9 1.0 CG A:ASP305 3.1 42.5 1.0 OD2 A:ASP303 3.2 39.5 1.0 CD A:GLU33 3.3 63.9 1.0 OD2 A:ASP305 3.3 47.8 1.0 CB A:THR306 3.5 35.0 1.0 OE2 A:GLU33 3.6 65.9 1.0 C1N A:A1R403 3.6 45.7 1.0 MG A:MG401 3.7 41.1 1.0 N A:THR306 3.8 33.8 1.0 OD1 A:ASP64 4.0 35.9 1.0 C4N A:A1R403 4.1 45.7 1.0 CA A:THR306 4.2 32.7 1.0 OD2 A:ASP64 4.3 34.8 1.0 N4N A:A1R403 4.3 47.3 1.0 CB A:ASP303 4.4 38.5 1.0 CB A:ASP305 4.4 38.4 1.0 O A:HOH613 4.5 44.5 1.0 C A:ASP305 4.6 33.3 1.0 CG A:ASP64 4.6 33.9 1.0 CG2 A:THR306 4.6 35.0 1.0 N A:ASP305 4.7 34.1 1.0 CG A:GLU33 4.8 62.8 1.0 CA A:ASP305 4.8 35.9 1.0 CA A:ASP303 4.8 36.9 1.0 O A:ASP303 4.8 35.8 1.0 C A:ASP303 4.9 35.9 1.0

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


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-Hpd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:48.3 occ:1.00 OG1 B:THR62 2.2 40.9 1.0 O2N B:A1R403 2.2 59.0 1.0 OD2 B:ASP305 2.2 56.4 1.0 OD1 B:ASP64 2.3 40.5 1.0 OD1 B:ASP63 2.3 44.2 1.0 CB B:THR62 3.1 41.1 1.0 CG B:ASP305 3.2 51.2 1.0 CG B:ASP63 3.5 43.4 1.0 CG B:ASP64 3.5 39.0 1.0 C2N B:A1R403 3.5 58.0 1.0 MG B:MG402 3.7 60.5 1.0 OD1 B:ASP305 3.8 56.8 1.0 CG2 B:THR62 3.8 41.5 1.0 N B:ASP63 3.9 40.2 1.0 N B:ASP64 4.0 38.3 1.0 OD2 B:ASP63 4.1 43.0 1.0 OD1 B:ASP26 4.1 40.3 1.0 C1N B:A1R403 4.1 56.3 1.0 OD2 B:ASP64 4.3 39.2 1.0 CB B:ASP305 4.3 44.6 1.0 OE1 B:GLU33 4.3 65.0 1.0 CA B:THR62 4.4 39.6 1.0 CB B:ASP64 4.4 37.5 1.0 O B:GLY101 4.4 50.0 1.0 C B:THR62 4.5 40.1 1.0 CB B:ASP63 4.6 42.4 1.0 CA B:ASP63 4.6 40.4 1.0 OG1 B:THR306 4.7 45.9 1.0 O B:HOH599 4.7 54.3 1.0 C3N B:A1R403 4.8 58.0 1.0 CA B:ASP64 4.8 36.7 1.0 C B:ASP63 4.8 39.4 1.0 O B:ARG100 4.9 46.3 1.0

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


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-Hpd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:60.5 occ:1.00 O3N B:A1R403 2.2 64.4 1.0 OD1 B:ASP305 2.2 56.8 1.0 OD1 B:ASP303 2.2 53.6 1.0 O2N B:A1R403 2.2 59.0 1.0 OG1 B:THR306 2.3 45.9 1.0 OE1 B:GLU33 2.3 65.0 1.0 C3N B:A1R403 2.7 58.0 1.0 C2N B:A1R403 2.9 58.0 1.0 CG B:ASP305 3.1 51.2 1.0 CG B:ASP303 3.1 50.5 1.0 CD B:GLU33 3.3 68.2 1.0 OD2 B:ASP303 3.3 50.0 1.0 OD2 B:ASP305 3.4 56.4 1.0 CB B:THR306 3.5 42.8 1.0 OE2 B:GLU33 3.5 70.2 1.0 MG B:MG401 3.7 48.3 1.0 C1N B:A1R403 3.7 56.3 1.0 N B:THR306 3.8 39.6 1.0 OD1 B:ASP64 3.9 40.5 1.0 C4N B:A1R403 4.1 56.3 1.0 CA B:THR306 4.2 40.6 1.0 OD2 B:ASP64 4.3 39.2 1.0 N4N B:A1R403 4.3 59.1 1.0 CB B:ASP305 4.4 44.6 1.0 CB B:ASP303 4.5 51.0 1.0 CG B:ASP64 4.5 39.0 1.0 C B:ASP305 4.5 40.1 1.0 CG2 B:THR306 4.7 44.1 1.0 N B:ASP305 4.7 40.6 1.0 CG B:GLU33 4.7 66.4 1.0 CA B:ASP305 4.7 41.4 1.0 CA B:ASP303 4.8 49.5 1.0 O B:ASP303 4.9 48.2 1.0 C B:ASP303 4.9 47.9 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