Magnesium in PDB 5w6x: Crystal Structure of the HSNUDT16 in Complex with Mg+2 and Adp-Ribose

All present enzymatic activity of Crystal Structure of the HSNUDT16 in Complex with Mg+2 and Adp-Ribose:
3.6.1.62; 3.6.1.64;

The structure of Crystal Structure of the HSNUDT16 in Complex with Mg+2 and Adp-Ribose, PDB code: 5w6x was solved by P.Thirawatananond, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.755, 46.319, 74.238, 90.00, 107.65, 90.00
R / Rfree (%)	18.1 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of the HSNUDT16 in Complex with Mg+2 and Adp-Ribose (pdb code 5w6x). 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 the HSNUDT16 in Complex with Mg+2 and Adp-Ribose, PDB code: 5w6x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the HSNUDT16 in Complex with Mg+2 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 the HSNUDT16 in Complex with Mg+2 and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.4 occ:1.00 OE2 A:GLU136 2.3 28.9 1.0 O A:HOH562 2.3 16.9 1.0 OE1 A:GLU76 2.3 28.4 1.0 O1B A:APR401 2.3 31.8 1.0 OE2 A:GLU80 2.4 24.5 1.0 O A:HOH549 2.6 27.3 1.0 CD A:GLU80 3.4 22.2 1.0 CD A:GLU136 3.4 28.4 1.0 PB A:APR401 3.5 32.7 1.0 CD A:GLU76 3.5 25.6 1.0 MG A:MG403 3.6 29.8 1.0 CG A:GLU80 3.7 22.8 1.0 OE1 A:GLU136 3.9 29.9 1.0 O A:GLY59 3.9 22.0 1.0 O2B A:APR401 3.9 28.7 1.0 O5D A:APR401 4.0 41.4 1.0 OE2 A:GLU76 4.1 26.8 1.0 O A:HOH526 4.1 31.7 1.0 O A:HOH613 4.2 25.0 1.0 OD2 A:ASP132 4.4 22.8 1.0 OE2 A:GLU79 4.5 26.0 1.0 OE1 A:GLU80 4.5 17.9 1.0 CA A:GLY60 4.7 20.9 1.0 CG A:GLU76 4.7 25.6 1.0 CG A:GLU136 4.7 24.1 1.0 O3A A:APR401 4.7 29.6 1.0 C A:GLY59 4.8 21.2 1.0 CB A:GLU76 4.9 24.2 1.0 CB A:GLU136 4.9 21.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the HSNUDT16 in Complex with Mg+2 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 the HSNUDT16 in Complex with Mg+2 and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:29.8 occ:1.00 O1A A:APR401 2.3 26.6 1.0 OE2 A:GLU80 2.3 24.5 1.0 O A:GLY59 2.3 22.0 1.0 O1B A:APR401 2.4 31.8 1.0 O A:HOH605 2.5 39.2 1.0 O A:HOH613 2.5 25.0 1.0 CD A:GLU80 3.2 22.2 1.0 PA A:APR401 3.3 28.0 1.0 OE1 A:GLU80 3.3 17.9 1.0 C A:GLY59 3.5 21.2 1.0 MG A:MG402 3.6 15.4 1.0 O3A A:APR401 3.6 29.6 1.0 PB A:APR401 3.6 32.7 1.0 O2A A:APR401 3.8 28.2 1.0 O A:HOH583 3.9 31.7 1.0 CA A:GLY60 4.0 20.9 1.0 OE2 A:GLU136 4.0 28.9 1.0 NH1 A:ARG50 4.1 21.6 1.0 N A:GLY60 4.2 21.9 1.0 N A:GLY59 4.3 18.2 1.0 O5D A:APR401 4.4 41.4 1.0 NE2 A:HIS24 4.5 20.9 1.0 CG A:GLU80 4.6 22.8 1.0 CA A:GLY59 4.6 20.1 1.0 O5' A:APR401 4.7 30.8 1.0 CD2 A:HIS24 4.7 18.8 1.0 OE1 A:GLU76 4.7 28.4 1.0 NE2 A:GLN48 4.7 27.9 1.0 O2B A:APR401 4.8 28.7 1.0 O A:PHE57 4.9 16.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the HSNUDT16 in Complex with Mg+2 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 the HSNUDT16 in Complex with Mg+2 and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:59.4 occ:1.00 O2B B:APR401 2.3 63.6 1.0 OE2 B:GLU80 2.3 37.9 1.0 O B:HOH553 2.7 39.3 1.0 OE1 B:GLU136 2.7 31.3 0.5 OE1 B:GLU76 3.1 37.3 1.0 CD B:GLU80 3.3 40.3 1.0 OD2 B:ASP132 3.4 42.1 1.0 PB B:APR401 3.5 65.1 1.0 CG B:GLU80 3.6 39.0 1.0 MG B:MG403 3.8 45.9 1.0 O B:GLY59 3.8 28.5 1.0 O B:HOH587 3.9 46.7 1.0 CD B:GLU136 4.0 30.7 0.5 O1B B:APR401 4.0 59.9 1.0 CD B:GLU76 4.3 36.1 1.0 CG B:ASP132 4.5 38.3 1.0 OE1 B:GLU80 4.5 29.8 1.0 O5D B:APR401 4.6 71.3 1.0 O3A B:APR401 4.7 60.7 1.0 OE2 B:GLU136 4.8 34.6 0.5 CG B:GLU136 4.8 29.6 0.5 C5D B:APR401 4.8 76.2 1.0 CA B:GLY60 4.9 32.1 1.0 C B:GLY59 4.9 28.3 1.0 OE2 B:GLU76 4.9 35.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the HSNUDT16 in Complex with Mg+2 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 the HSNUDT16 in Complex with Mg+2 and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:45.9 occ:1.00 OE2 B:GLU80 2.4 37.9 1.0 O1A B:APR401 2.6 50.4 1.0 O B:HOH587 2.9 46.7 1.0 O B:GLY59 2.9 28.5 1.0 CD B:GLU80 3.1 40.3 1.0 OE1 B:GLU80 3.2 29.8 1.0 O2B B:APR401 3.2 63.6 1.0 PA B:APR401 3.6 59.6 1.0 MG B:MG402 3.8 59.4 1.0 O B:HOH582 3.8 32.8 1.0 C B:GLY59 3.9 28.3 1.0 O2A B:APR401 3.9 49.0 1.0 O3A B:APR401 4.1 60.7 1.0 N B:GLY59 4.3 23.7 1.0 PB B:APR401 4.3 65.1 1.0 NE2 B:HIS24 4.4 23.4 1.0 O B:PHE57 4.5 21.4 1.0 CG B:GLU80 4.5 39.0 1.0 CD2 B:HIS24 4.6 26.2 1.0 CA B:GLY60 4.7 32.1 1.0 N B:GLY60 4.7 30.5 1.0 CA B:GLY59 4.7 27.9 1.0 NE2 B:GLN48 4.8 38.3 1.0 O5' B:APR401 5.0 62.6 1.0

P.Thirawatananond, R.L.Mcpherson, J.Malhi, S.Nathan, M.J.Lambrecht, M.Brichacek, P.J.Hergenrother, A.K.L.Leung, S.B.Gabelli. Structural Analyses of NUDT16-Adp-Ribose Complexes Direct Rational Design of Mutants with Improved Processing of Poly(Adp-Ribosyl)Ated Proteins. Sci Rep V. 9 5940 2019.
ISSN: ESSN 2045-2322
PubMed: 30976021
DOI: 10.1038/S41598-019-39491-W