Magnesium in PDB 4gz2: Mus Musculus TDP2 Excluded Ssdna Complex

The structure of Mus Musculus TDP2 Excluded Ssdna Complex, PDB code: 4gz2 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)	24.47 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.483, 42.972, 107.951, 90.00, 95.89, 90.00
R / Rfree (%)	20.5 / 24.5

The binding sites of Magnesium atom in the Mus Musculus TDP2 Excluded Ssdna Complex (pdb code 4gz2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mus Musculus TDP2 Excluded Ssdna Complex, PDB code: 4gz2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mus Musculus TDP2 Excluded Ssdna Complex


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 Excluded Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.7 occ:1.00 O A:HOH556 2.0 17.1 1.0 O A:HOH557 2.1 23.3 1.0 O A:HOH603 2.1 20.1 1.0 OE1 A:GLU162 2.1 20.1 1.0 O2 D:DT3 2.2 33.6 1.0 OD1 A:ASP132 2.2 19.4 1.0 OE2 A:GLU162 2.5 21.4 1.0 CD A:GLU162 2.6 21.0 1.0 CG A:ASP132 3.1 21.8 1.0 C2 D:DT3 3.2 33.9 1.0 N3 D:DT3 3.6 33.7 1.0 O A:HOH578 3.7 33.9 1.0 OD2 A:ASP132 3.9 25.1 1.0 CA A:ASP132 4.0 17.4 1.0 CB A:ASP132 4.0 20.4 1.0 OD1 A:ASP358 4.1 23.1 1.0 CG A:GLU162 4.2 20.3 1.0 OD1 A:ASN130 4.3 13.8 1.0 OD2 A:ASP358 4.4 25.4 1.0 N1 D:DT3 4.4 32.8 1.0 CB A:LEU134 4.6 20.5 1.0 CG A:ASP358 4.6 26.1 1.0 O A:HOH584 4.6 37.7 1.0 O4' D:DC4 4.7 28.3 1.0 CD1 A:LEU134 4.7 26.0 1.0 ND2 A:ASN130 4.8 15.3 1.0 C6 D:DC4 4.8 28.3 1.0 C1' D:DT3 4.8 32.3 1.0 C A:ASP132 4.9 16.6 1.0 CB A:GLU162 4.9 19.7 1.0 CG A:ASN130 4.9 14.3 1.0 N A:ASP132 4.9 16.1 1.0 C4 D:DT3 4.9 34.5 1.0 C1' D:DC4 5.0 27.6 1.0

Magnesium binding site 2 out of 4 in the Mus Musculus TDP2 Excluded Ssdna Complex


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 Excluded Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:27.3 occ:1.00 O D:HOH220 2.0 27.4 1.0 O A:HOH612 2.1 38.2 1.0 O A:HOH613 2.1 24.6 1.0 O D:HOH210 2.1 24.5 1.0 O C:HOH231 2.1 26.5 1.0 O D:HOH219 2.1 21.2 0.6 O6 D:DG6 4.1 35.5 1.0 O A:HOH570 4.1 36.2 1.0 O2 D:DC4 4.3 28.5 1.0 OP2 D:DC4 4.3 34.8 1.0 O4 C:DT10 4.4 32.3 1.0 OP2 D:DC5 4.4 27.5 1.0 N7 D:DG6 4.5 31.0 1.0 O D:HOH216 4.5 47.2 1.0 O A:HOH614 4.5 34.6 1.0 O D:HOH208 4.5 30.6 1.0 C7 C:DT10 4.7 32.0 1.0 O D:HOH209 4.7 37.7 1.0 C7 C:DT9 4.9 30.2 1.0 C5 D:DC5 5.0 28.9 1.0 C6 D:DG6 5.0 33.6 1.0

Magnesium binding site 3 out of 4 in the Mus Musculus TDP2 Excluded Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mus Musculus TDP2 Excluded Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:14.1 occ:1.00 O2 C:DT3 2.0 23.8 1.0 O B:HOH587 2.0 13.0 1.0 OE1 B:GLU162 2.0 18.0 1.0 O B:HOH628 2.1 14.6 1.0 OD1 B:ASP132 2.1 18.1 1.0 O B:HOH577 2.1 15.0 1.0 CD B:GLU162 2.9 20.0 1.0 C2 C:DT3 3.0 23.5 1.0 CG B:ASP132 3.0 19.4 1.0 OE2 B:GLU162 3.1 18.0 1.0 N3 C:DT3 3.4 24.1 1.0 OD2 B:ASP132 3.8 22.2 1.0 CB B:ASP132 3.9 15.1 1.0 CA B:ASP132 4.0 12.3 1.0 O B:HOH533 4.1 30.6 1.0 OD1 B:ASP358 4.1 16.6 1.0 OD2 B:ASP358 4.2 20.9 1.0 O B:HOH667 4.2 38.8 1.0 N1 C:DT3 4.3 23.9 1.0 CG B:GLU162 4.3 21.4 1.0 OD1 B:ASN130 4.4 10.2 1.0 CG B:ASP358 4.5 19.0 1.0 O4' C:DC4 4.6 19.6 1.0 CB B:LEU134 4.7 16.3 1.0 C6 C:DC4 4.7 20.2 1.0 CD1 B:LEU134 4.7 20.6 1.0 C1' C:DT3 4.7 23.5 1.0 C4 C:DT3 4.7 27.1 1.0 C B:ASP132 4.8 12.2 1.0 C1' C:DC4 4.9 20.3 1.0 N B:ASP132 5.0 10.7 1.0

Magnesium binding site 4 out of 4 in the Mus Musculus TDP2 Excluded Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mus Musculus TDP2 Excluded Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:23.0 occ:1.00 O C:HOH218 2.0 24.0 1.0 O C:HOH230 2.1 28.6 1.0 O C:HOH211 2.1 24.7 1.0 O C:HOH207 2.1 34.3 1.0 O D:HOH218 2.1 21.2 1.0 O C:HOH208 2.1 27.6 1.0 O B:HOH592 4.1 32.7 1.0 O2 C:DC4 4.2 22.1 1.0 O6 C:DG6 4.2 23.2 1.0 O4 D:DT10 4.3 28.3 1.0 OP2 C:DC5 4.4 18.9 1.0 OP2 C:DC4 4.4 25.0 1.0 N7 C:DG6 4.4 21.8 1.0 O C:HOH204 4.5 24.4 1.0 O C:HOH228 4.5 25.1 1.0 C5 C:DC5 4.8 20.4 1.0 C7 D:DT10 4.9 33.7 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