Magnesium in PDB 6hoz: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Inosine Diphosphate Ribose (Idpr)

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

Resolution Low / High (Å)	72.10 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.844, 96.933, 107.519, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.9

The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Inosine Diphosphate Ribose (Idpr) (pdb code 6hoz). 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 Inosine Diphosphate Ribose (Idpr), PDB code: 6hoz:
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 Inosine Diphosphate Ribose (Idpr)


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 Inosine Diphosphate Ribose (Idpr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:28.9 occ:1.00 O2D A:R7I404 2.2 32.4 0.5 O A:HOH627 2.2 30.8 1.0 OD2 A:ASP305 2.2 33.9 1.0 O2D A:R5I403 2.3 30.6 0.5 OD1 A:ASP64 2.3 24.4 1.0 OD1 A:ASP63 2.3 28.3 1.0 OG1 A:THR62 2.3 24.7 1.0 CB A:THR62 3.2 25.4 1.0 CG A:ASP305 3.2 31.2 1.0 C2D A:R7I404 3.3 31.9 0.5 C2D A:R5I403 3.3 31.1 0.5 O1D A:R5I403 3.3 34.0 0.5 CG A:ASP63 3.4 26.0 1.0 CG A:ASP64 3.5 23.0 1.0 C1D A:R5I403 3.7 32.1 0.5 MG A:MG402 3.8 34.4 1.0 OD1 A:ASP305 3.8 33.3 1.0 N A:ASP63 4.0 24.1 1.0 OD2 A:ASP63 4.0 25.6 1.0 OE2 A:GLU33 4.0 39.3 1.0 C1D A:R7I404 4.0 33.7 0.5 N A:ASP64 4.1 22.6 1.0 CG2 A:THR62 4.1 25.3 1.0 OD1 A:ASP26 4.2 23.0 1.0 OE1 A:GLU33 4.2 45.3 1.0 O A:HOH563 4.3 43.6 1.0 OD2 A:ASP64 4.3 24.2 1.0 O A:GLY101 4.3 29.1 1.0 CB A:ASP305 4.3 26.2 1.0 CD A:GLU33 4.4 43.5 1.0 CB A:ASP64 4.5 22.3 1.0 CA A:THR62 4.5 24.2 1.0 O1D A:R7I404 4.5 35.7 0.5 C A:THR62 4.5 23.9 1.0 CB A:ASP63 4.6 25.5 1.0 O A:HOH672 4.6 39.2 1.0 C3D A:R7I404 4.6 31.6 0.5 OG1 A:THR306 4.7 25.2 1.0 CA A:ASP63 4.7 24.4 1.0 C3D A:R5I403 4.7 30.7 0.5 O A:ARG100 4.8 28.0 1.0 C A:ASP63 4.9 23.0 1.0 CA A:ASP64 4.9 22.2 1.0 C A:GLY101 4.9 29.4 1.0

Magnesium binding site 2 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Inosine Diphosphate Ribose (Idpr)


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 Inosine Diphosphate Ribose (Idpr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:34.4 occ:1.00 OD1 A:ASP303 2.1 28.5 1.0 OD1 A:ASP305 2.1 33.3 1.0 OE2 A:GLU33 2.2 39.3 1.0 O3D A:R5I403 2.2 32.5 0.5 O2D A:R5I403 2.2 30.6 0.5 O3D A:R7I404 2.2 33.6 0.5 O2D A:R7I404 2.2 32.4 0.5 OG1 A:THR306 2.2 25.2 1.0 C2D A:R5I403 2.7 31.1 0.5 C3D A:R5I403 2.8 30.7 0.5 C3D A:R7I404 2.9 31.6 0.5 C2D A:R7I404 3.0 31.9 0.5 CG A:ASP303 3.0 28.1 1.0 CG A:ASP305 3.0 31.2 1.0 CD A:GLU33 3.2 43.5 1.0 O1D A:R7I404 3.2 35.7 0.5 OD2 A:ASP303 3.3 27.4 1.0 CB A:THR306 3.3 23.0 1.0 C1D A:R5I403 3.4 32.1 0.5 OD2 A:ASP305 3.4 33.9 1.0 N A:THR306 3.6 22.3 1.0 C1D A:R7I404 3.7 33.7 0.5 MG A:MG401 3.8 28.9 1.0 CG A:GLU33 3.8 42.0 1.0 C4D A:R5I403 4.0 30.4 0.5 CA A:THR306 4.1 21.3 1.0 OD1 A:ASP64 4.1 24.4 1.0 OE1 A:GLU33 4.1 45.3 1.0 O4D A:R5I403 4.2 32.8 0.5 C4D A:R7I404 4.2 32.0 0.5 OD2 A:ASP64 4.2 24.2 1.0 O1D A:R5I403 4.3 34.0 0.5 CB A:ASP305 4.3 26.2 1.0 CB A:ASP303 4.4 26.6 1.0 O A:HOH627 4.5 30.8 1.0 C A:ASP305 4.5 22.4 1.0 O A:HOH510 4.5 50.1 1.0 CG2 A:THR306 4.5 22.8 1.0 N A:ASP305 4.5 22.8 1.0 CG A:ASP64 4.6 23.0 1.0 C A:ASP303 4.6 26.0 1.0 O A:ASP303 4.6 24.8 1.0 CA A:ASP303 4.6 26.1 1.0 CA A:ASP305 4.6 24.3 1.0 O4D A:R7I404 4.7 32.9 0.5

Magnesium binding site 3 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Inosine Diphosphate Ribose (Idpr)


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 Inosine Diphosphate Ribose (Idpr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:24.0 occ:1.00 O B:HOH616 2.2 28.7 1.0 O2D B:R7I404 2.2 26.4 0.5 O2D B:R5I403 2.2 26.3 0.5 OD2 B:ASP305 2.3 28.6 1.0 OD1 B:ASP63 2.3 22.8 1.0 OD1 B:ASP64 2.3 21.1 1.0 OG1 B:THR62 2.3 21.9 1.0 O1D B:R5I403 3.0 29.4 0.5 C2D B:R7I404 3.2 25.8 0.5 CB B:THR62 3.2 22.2 1.0 C2D B:R5I403 3.3 26.0 0.5 CG B:ASP305 3.3 25.6 1.0 CG B:ASP63 3.4 21.6 1.0 C1D B:R5I403 3.5 27.1 0.5 CG B:ASP64 3.5 20.4 1.0 C1D B:R7I404 3.8 27.7 0.5 MG B:MG402 3.9 29.1 1.0 OD1 B:ASP305 3.9 28.0 1.0 N B:ASP63 4.0 20.4 1.0 OD2 B:ASP63 4.0 19.0 1.0 OE2 B:GLU33 4.0 32.1 1.0 N B:ASP64 4.0 19.4 1.0 CG2 B:THR62 4.1 22.3 1.0 OE1 B:GLU33 4.1 36.3 1.0 O1D B:R7I404 4.2 30.6 0.5 OD1 B:ASP26 4.2 20.8 1.0 OD2 B:ASP64 4.3 20.7 1.0 O B:GLY101 4.3 21.4 1.0 CD B:GLU33 4.4 35.8 1.0 O B:HOH517 4.4 43.7 1.0 CB B:ASP305 4.4 23.3 1.0 CA B:THR62 4.5 20.9 1.0 CB B:ASP64 4.5 20.1 1.0 C3D B:R7I404 4.5 26.4 0.5 C B:THR62 4.6 20.6 1.0 CB B:ASP63 4.6 20.5 1.0 CA B:ASP63 4.6 20.6 1.0 C3D B:R5I403 4.7 26.3 0.5 OG1 B:THR306 4.7 20.4 1.0 C B:ASP63 4.8 20.1 1.0 O4D B:R5I403 4.8 28.3 0.5 O B:ARG100 4.8 21.0 1.0 CA B:ASP64 4.9 19.6 1.0 O3D B:R7I404 4.9 27.3 0.5 C B:GLY101 4.9 21.3 1.0

Magnesium binding site 4 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Inosine Diphosphate Ribose (Idpr)


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 Inosine Diphosphate Ribose (Idpr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:29.1 occ:1.00 OD1 B:ASP303 2.1 23.0 1.0 OD1 B:ASP305 2.1 28.0 1.0 O3D B:R5I403 2.1 27.0 0.5 O2D B:R5I403 2.2 26.3 0.5 O3D B:R7I404 2.2 27.3 0.5 OE2 B:GLU33 2.2 32.1 1.0 O2D B:R7I404 2.2 26.4 0.5 OG1 B:THR306 2.2 20.4 1.0 C3D B:R5I403 2.7 26.3 0.5 C2D B:R5I403 2.7 26.0 0.5 CG B:ASP303 3.0 21.9 1.0 CG B:ASP305 3.0 25.6 1.0 C3D B:R7I404 3.0 26.4 0.5 C2D B:R7I404 3.1 25.8 0.5 CD B:GLU33 3.2 35.8 1.0 OD2 B:ASP303 3.3 21.1 1.0 O1D B:R7I404 3.3 30.6 0.5 CB B:THR306 3.3 20.2 1.0 OD2 B:ASP305 3.3 28.6 1.0 C1D B:R5I403 3.4 27.1 0.5 N B:THR306 3.6 20.7 1.0 C1D B:R7I404 3.8 27.7 0.5 MG B:MG401 3.9 24.0 1.0 CG B:GLU33 3.9 34.0 1.0 C4D B:R5I403 4.0 25.1 0.5 CA B:THR306 4.0 18.9 1.0 OD1 B:ASP64 4.1 21.1 1.0 OE1 B:GLU33 4.1 36.3 1.0 O1D B:R5I403 4.2 29.4 0.5 O4D B:R5I403 4.3 28.3 0.5 OD2 B:ASP64 4.3 20.7 1.0 C4D B:R7I404 4.3 26.3 0.5 O B:HOH524 4.3 56.9 1.0 CB B:ASP305 4.3 23.3 1.0 CB B:ASP303 4.3 21.9 1.0 C B:ASP305 4.5 20.0 1.0 CG2 B:THR306 4.5 19.6 1.0 N B:ASP305 4.6 20.6 1.0 CG B:ASP64 4.6 20.4 1.0 O B:ASP303 4.6 20.4 1.0 O B:HOH616 4.6 28.7 1.0 CA B:ASP305 4.6 21.7 1.0 CA B:ASP303 4.6 21.5 1.0 C B:ASP303 4.6 21.4 1.0 O4D B:R7I404 4.7 28.2 0.5

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