Magnesium in PDB 5j3p: Crystal Structure of the Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2

The structure of Crystal Structure of the Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2, PDB code: 5j3p was solved by P.Hornyak, L.H.Pearl, K.W.Caldecott, A.W.Oliver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.79 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.545, 92.545, 119.075, 90.00, 90.00, 120.00
R / Rfree (%)	25.6 / 29.1

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2 (pdb code 5j3p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2, PDB code: 5j3p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2


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 Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:65.3 occ:1.00 O A:HOH501 2.1 50.5 1.0 OD1 A:ASP122 2.3 85.2 1.0 OE1 A:GLU152 2.5 66.1 1.0 OE2 A:GLU152 2.8 65.9 1.0 CD A:GLU152 3.0 66.0 1.0 CG A:ASP122 3.4 85.1 1.0 OD2 A:ASP350 4.1 62.4 1.0 OD2 A:ASP122 4.2 84.0 1.0 CB A:ASP122 4.3 82.8 1.0 CA A:ASP122 4.5 84.5 1.0 CG A:GLU152 4.5 66.2 1.0 CB A:LEU124 4.7 67.2 1.0 CD1 A:LEU124 4.8 79.7 1.0 OD1 A:ASP350 4.8 75.7 1.0 CG A:ASP350 4.8 62.9 1.0 CG A:LEU124 4.9 76.2 1.0 O3 B:GOL401 5.0 90.2 1.0 ND2 A:ASN120 5.0 67.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2


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 Catalytic Domain of Human Tyrosyl Dna Phosphodiesterase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:76.6 occ:1.00 OD1 B:ASP122 2.5 88.4 1.0 O B:HOH501 2.6 52.4 1.0 OD2 B:ASP350 2.8 92.9 1.0 OE2 B:GLU152 3.1 97.4 1.0 CG B:ASP122 3.2 90.1 1.0 OE1 B:GLU152 3.3 96.8 1.0 CG B:ASP350 3.6 91.6 1.0 CD B:GLU152 3.6 98.5 1.0 OD1 B:ASP350 3.7 95.0 1.0 OD1 B:ASN120 3.8 89.8 1.0 OD2 B:ASP122 4.0 91.3 1.0 CB B:ASP122 4.0 91.4 1.0 CA B:ASP122 4.5 88.2 1.0 NE2 B:HIS351 4.5 81.9 1.0 CD2 B:HIS351 4.5 76.5 1.0 CG B:ASN120 4.8 91.3 1.0 CB B:ASP350 4.9 86.7 1.0

P.Hornyak, T.Askwith, S.Walker, E.Komulainen, M.Paradowski, L.E.Pennicott, E.J.Bartlett, N.C.Brissett, A.Raoof, M.Watson, A.M.Jordan, D.J.Ogilvie, S.E.Ward, J.R.Atack, L.H.Pearl, K.W.Caldecott, A.W.Oliver. Mode of Action of Dna-Competitive Small Molecule Inhibitors of Tyrosyl Dna Phosphodiesterase 2. Biochem.J. V. 473 1869 2016.
ISSN: ESSN 1470-8728
PubMed: 27099339
DOI: 10.1042/BCJ20160180