Magnesium in PDB 4gz1: Mus Musculus TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution

The structure of Mus Musculus TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution, PDB code: 4gz1 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)	30.07 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.200, 69.139, 167.789, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17.5

The binding sites of Magnesium atom in the Mus Musculus TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution (pdb code 4gz1). 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 (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution, PDB code: 4gz1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mus Musculus TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution


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 (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.9 occ:1.00 O A:HOH616 2.0 23.2 1.0 O A:HOH739 2.1 23.8 1.0 OE2 A:GLU162 2.1 21.2 1.0 OP2 D:DC1 2.1 21.8 1.0 O A:HOH735 2.1 19.5 1.0 O D:HOH104 2.1 24.7 1.0 CD A:GLU162 3.0 21.7 1.0 OE1 A:GLU162 3.3 23.8 1.0 P D:DC1 3.3 23.0 1.0 OP1 D:DC1 3.8 24.3 1.0 O5' D:DC1 3.9 22.4 1.0 ND2 A:ASN130 4.0 19.2 1.0 C6 D:DC1 4.1 29.7 1.0 OD2 A:ASP358 4.1 20.9 1.0 OD1 A:ASP132 4.3 30.7 1.0 OD1 A:ASN130 4.3 18.0 1.0 OD1 A:ASP358 4.3 19.6 1.0 NE2 A:HIS359 4.3 19.0 1.0 C5 D:DC1 4.3 32.6 1.0 CG A:GLU162 4.4 20.4 1.0 CG A:ASN130 4.5 19.0 1.0 C5' D:DC1 4.5 23.0 1.0 OP3 D:DC1 4.6 24.9 1.0 CG A:ASP358 4.7 19.6 1.0 O4' D:DC1 4.8 25.4 1.0 CG A:ASP132 4.8 28.2 1.0 CD2 A:HIS359 4.8 18.8 1.0 O A:HOH664 4.9 63.9 1.0 CE1 A:HIS236 4.9 20.8 1.0 NE2 A:HIS236 5.0 21.2 1.0

Magnesium binding site 2 out of 2 in the Mus Musculus TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution


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 (5'-Phosphorylated Dna)-MG2+ Complex at 1.5 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:24.8 occ:1.00 O B:HOH598 2.1 27.6 1.0 O B:HOH597 2.1 28.9 1.0 OE2 B:GLU162 2.1 24.2 1.0 O B:HOH596 2.1 23.3 1.0 OP2 C:DC1 2.1 24.5 1.0 O C:HOH118 2.1 28.1 1.0 CD B:GLU162 3.0 26.2 1.0 OE1 B:GLU162 3.3 29.7 1.0 P C:DC1 3.3 25.6 1.0 OP1 C:DC1 3.8 26.3 1.0 ND2 B:ASN130 3.9 21.4 1.0 O5' C:DC1 3.9 26.1 1.0 C6 C:DC1 4.1 34.6 1.0 OD2 B:ASP358 4.1 24.7 1.0 OD1 B:ASN130 4.2 21.6 1.0 O B:HOH562 4.3 46.4 1.0 NE2 B:HIS359 4.3 24.1 1.0 OD1 B:ASP132 4.3 35.1 1.0 C5 C:DC1 4.3 37.7 1.0 OD1 B:ASP358 4.3 25.3 1.0 CG B:GLU162 4.4 23.4 1.0 O C:HOH117 4.4 72.6 1.0 CG B:ASN130 4.5 20.2 1.0 C5' C:DC1 4.5 26.2 1.0 OP3 C:DC1 4.5 26.1 1.0 CG B:ASP358 4.7 24.8 1.0 CD2 B:HIS359 4.7 22.8 1.0 CG B:ASP132 4.7 33.7 1.0 O4' C:DC1 4.9 27.8 1.0 CE1 B:HIS236 4.9 21.1 1.0 NE2 B:HIS236 5.0 23.3 1.0

M.J.Schellenberg, C.D.Appel, S.Adhikari, P.D.Robertson, D.A.Ramsden, R.S.Williams. Mechanism of Repair of 5'-Topoisomerase II-Dna Adducts By Mammalian Tyrosyl-Dna Phosphodiesterase 2. Nat.Struct.Mol.Biol. V. 19 1363 2012.
ISSN: ISSN 1545-9993
PubMed: 23104055
DOI: 10.1038/NSMB.2418