Magnesium in PDB 6b09: Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked)

All present enzymatic activity of Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked):
3.6.1.62; 3.6.1.64;

The structure of Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked), PDB code: 6b09 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)	37.62 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.395, 47.063, 75.792, 90.00, 108.74, 90.00
R / Rfree (%)	25.6 / 27.9

The structure of Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked) (pdb code 6b09). 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 HSNUDT16 in Complex with Diadpr (Soaked), PDB code: 6b09:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked)


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 HSNUDT16 in Complex with Diadpr (Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.1 occ:1.00 OE2 A:GLU80 2.5 36.0 1.0 O5 A:C7G401 3.0 42.7 1.0 O4 A:C7G401 3.1 42.0 1.0 O A:GLY59 3.1 42.6 1.0 NH1 A:ARG50 3.2 36.8 1.0 O7 A:C7G401 3.2 44.1 1.0 CD A:GLU80 3.4 38.2 1.0 P A:C7G401 3.5 40.9 1.0 OE1 A:GLU80 3.6 39.7 1.0 O A:HOH501 3.6 49.1 1.0 OE2 A:GLU136 3.9 40.9 1.0 NE2 A:GLN48 4.1 50.1 1.0 O6 A:C7G401 4.1 46.5 1.0 MG A:MG403 4.1 12.4 1.0 C A:GLY59 4.3 38.1 1.0 CZ A:ARG50 4.3 38.5 1.0 P1 A:C7G401 4.3 46.2 1.0 NE2 A:HIS24 4.4 61.6 1.0 CD A:GLU136 4.5 45.7 1.0 CG A:GLU80 4.7 39.7 1.0 OE1 A:GLU136 4.8 42.9 1.0 CD2 A:HIS24 4.8 63.4 1.0 NH2 A:ARG50 4.8 38.0 1.0 CA A:GLY60 4.9 39.0 1.0 N A:GLY59 4.9 40.0 1.0 O3 A:C7G401 4.9 37.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked)


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 HSNUDT16 in Complex with Diadpr (Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:12.4 occ:1.00 OE2 A:GLU136 2.1 40.9 1.0 OE1 A:GLU76 2.5 28.9 1.0 O7 A:C7G401 2.6 44.1 1.0 OE2 A:GLU80 2.7 36.0 1.0 CD A:GLU136 3.2 45.7 1.0 CD A:GLU80 3.6 38.2 1.0 OD2 A:ASP132 3.6 44.4 1.0 OE1 A:GLU136 3.7 42.9 1.0 CD A:GLU76 3.7 32.8 1.0 CG A:GLU80 3.7 39.7 1.0 P1 A:C7G401 3.9 46.2 1.0 NA A:NA405 3.9 24.0 1.0 OE2 A:GLU79 4.0 34.8 1.0 O A:GLY59 4.0 42.6 1.0 O9 A:C7G401 4.1 47.7 1.0 MG A:MG402 4.1 16.1 1.0 OE2 A:GLU76 4.3 30.6 1.0 CG A:GLU136 4.5 50.5 1.0 O A:GLU76 4.6 47.0 1.0 CD A:GLU79 4.6 37.4 1.0 O8 A:C7G401 4.7 43.4 1.0 CB A:GLU76 4.8 34.3 1.0 CB A:GLU136 4.8 52.4 1.0 OE1 A:GLU80 4.8 39.7 1.0 CG A:GLU76 4.8 32.7 1.0 C A:GLY59 4.8 38.1 1.0 CB A:GLU79 4.8 49.0 1.0 CG A:ASP132 4.9 41.0 1.0 CA A:GLY60 5.0 39.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked)


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 HSNUDT16 in Complex with Diadpr (Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:29.5 occ:1.00 OE2 B:GLU76 2.3 44.8 1.0 O9 B:C7G401 2.9 40.5 1.0 CD B:GLU76 3.3 45.3 1.0 OE1 B:GLU76 3.6 49.1 1.0 NH1 B:ARG75 3.9 49.8 1.0 O7 B:C7G401 4.0 56.4 1.0 O11 B:C7G401 4.0 74.6 1.0 P1 B:C7G401 4.0 55.5 1.0 MG B:MG403 4.1 15.4 1.0 CG B:GLU76 4.6 46.2 1.0 N B:PHE61 4.6 44.9 1.0 O8 B:C7G401 4.8 63.3 1.0 O B:PHE61 4.8 40.7 1.0 CB B:PHE61 4.8 52.0 1.0 OE2 B:GLU79 4.9 51.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of HSNUDT16 in Complex with Diadpr (Soaked)


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 HSNUDT16 in Complex with Diadpr (Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:15.4 occ:1.00 OE2 B:GLU80 1.8 47.6 1.0 O7 B:C7G401 2.3 56.4 1.0 OE1 B:GLU76 2.6 49.1 1.0 OD2 B:ASP132 2.8 44.5 1.0 CD B:GLU80 3.0 43.5 1.0 CG B:GLU80 3.6 43.3 1.0 CD B:GLU76 3.7 45.3 1.0 OE2 B:GLU136 3.7 81.3 1.0 P1 B:C7G401 3.7 55.5 1.0 CG B:ASP132 3.8 41.9 1.0 CD B:GLU136 3.8 91.7 1.0 CG B:GLU136 3.9 88.3 1.0 OE2 B:GLU79 4.0 51.8 1.0 OE2 B:GLU76 4.0 44.8 1.0 OE1 B:GLU80 4.0 35.4 1.0 MG B:MG402 4.1 29.5 1.0 O9 B:C7G401 4.2 40.5 1.0 OD1 B:ASP132 4.3 38.2 1.0 O11 B:C7G401 4.3 74.6 1.0 OE1 B:GLU136 4.4 94.0 1.0 CB B:GLU136 4.5 79.7 1.0 O8 B:C7G401 4.6 63.3 1.0 O6 B:C7G401 4.7 47.7 1.0 CD B:GLU79 4.8 55.0 1.0 CB B:ASP132 4.8 45.4 1.0 CB B:GLU79 4.9 57.9 1.0 CB B:GLU80 4.9 41.7 1.0 CG B:GLU76 5.0 46.2 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