Magnesium in PDB 4puq: Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+

The structure of Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+, PDB code: 4puq was solved by M.J.Schellenberg, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.03 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.828, 69.258, 167.107, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 17.1

The binding sites of Magnesium atom in the Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+ (pdb code 4puq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+, PDB code: 4puq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.1 occ:1.00 OP2 D:C1 2.0 15.0 1.0 OE2 A:GLU162 2.0 15.0 1.0 O A:HOH704 2.1 15.8 1.0 O A:HOH612 2.1 14.2 1.0 O D:HOH202 2.1 17.9 1.0 O A:HOH701 2.1 13.5 1.0 CD A:GLU162 3.0 15.0 1.0 P D:C1 3.2 16.5 1.0 OE1 A:GLU162 3.3 15.4 1.0 OP1 D:C1 3.8 16.6 1.0 O5' D:C1 3.8 16.2 1.0 ND2 A:ASN130 3.9 13.8 1.0 OD2 A:ASP358 4.1 15.6 1.0 C6 D:C1 4.1 20.9 1.0 NE2 A:HIS359 4.2 12.5 1.0 OD1 A:ASN130 4.2 13.8 1.0 OD1 A:ASP358 4.3 14.3 1.0 OD1 A:ASP132 4.4 20.3 1.0 CG A:GLU162 4.4 14.4 1.0 C5 D:C1 4.4 20.7 1.0 CG A:ASN130 4.4 12.8 1.0 C5' D:C1 4.5 16.9 1.0 OP3 D:C1 4.5 16.4 1.0 CG A:ASP358 4.6 14.2 1.0 O A:HOH651 4.7 34.2 1.0 O4' D:C1 4.7 16.6 1.0 CD2 A:HIS359 4.7 12.4 1.0 CE1 A:HIS236 4.8 15.7 1.0 CG A:ASP132 4.8 19.0 1.0 NE2 A:HIS236 4.9 14.9 1.0 O A:HOH708 4.9 52.1 1.0

Magnesium binding site 2 out of 2 in the Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mus Musculus TDP2 Reaction Product Complex with 5'-Phosphorylated Rna/Dna, Glycerol, and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:19.0 occ:1.00 O B:HOH592 2.1 17.6 1.0 O B:HOH594 2.1 20.4 1.0 O B:HOH593 2.1 20.9 1.0 OP2 C:C1 2.1 17.8 1.0 OE2 B:GLU162 2.1 18.8 1.0 O1 B:GOL402 2.1 22.7 1.0 C1 B:GOL402 3.0 31.0 1.0 CD B:GLU162 3.0 19.6 1.0 P C:C1 3.3 20.0 1.0 OE1 B:GLU162 3.3 23.3 1.0 OP1 C:C1 3.7 19.4 1.0 O5' C:C1 3.9 20.2 1.0 ND2 B:ASN130 3.9 16.8 1.0 C6 C:C1 4.1 23.6 1.0 O B:HOH561 4.1 34.1 1.0 OD2 B:ASP358 4.1 21.3 1.0 OD1 B:ASN130 4.2 16.5 1.0 OD1 B:ASP358 4.2 20.0 1.0 OD1 B:ASP132 4.3 26.4 1.0 C5 C:C1 4.3 25.0 1.0 NE2 B:HIS359 4.3 17.8 1.0 C2 B:GOL402 4.4 36.1 1.0 CG B:GLU162 4.4 18.7 1.0 CG B:ASN130 4.4 15.8 1.0 OP3 C:C1 4.5 20.7 1.0 C5' C:C1 4.5 20.7 1.0 CG B:ASP358 4.6 21.3 1.0 CD2 B:HIS359 4.7 16.7 1.0 CG B:ASP132 4.7 24.9 1.0 CE1 B:HIS236 4.8 16.4 1.0 O4' C:C1 4.8 20.1 1.0 NE2 B:HIS236 4.9 17.0 1.0 O2 B:GOL402 5.0 39.1 1.0

R.Gao, M.J.Schellenberg, S.Y.Huang, M.Abdelmalak, C.Marchand, K.C.Nitiss, J.L.Nitiss, R.S.Williams, Y.Pommier. Proteolytic Degradation of Topoisomerase II (TOP2) Enables the Processing of TOP2DNA and TOP2RNA Covalent Complexes By Tyrosyl-Dna-Phosphodiesterase 2 (TDP2). J.Biol.Chem. V. 289 17960 2014.
ISSN: ISSN 0021-9258
PubMed: 24808172
DOI: 10.1074/JBC.M114.565374