Magnesium in PDB 5inl: Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine

The structure of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine, PDB code: 5inl was solved by M.J.Schellenberg, C.K.Vilas, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.08 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.903, 69.051, 167.805, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 16.8

The binding sites of Magnesium atom in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine (pdb code 5inl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine, PDB code: 5inl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.2 occ:1.00 O A:HOH519 2.1 15.2 1.0 OE2 A:GLU162 2.1 14.9 1.0 O A:HOH523 2.1 13.2 1.0 OP2 D:DA1 2.1 14.4 1.0 O A:HOH550 2.1 14.6 1.0 O D:HOH117 2.2 17.6 1.0 CD A:GLU162 3.0 16.0 1.0 P D:DA1 3.3 15.8 1.0 OE1 A:GLU162 3.3 16.8 1.0 OP1 D:DA1 3.8 16.4 1.0 O5' D:DA1 3.8 15.3 1.0 ND2 A:ASN130 4.0 13.4 1.0 OD2 A:ASP358 4.1 15.4 1.0 NE2 A:HIS359 4.2 12.6 1.0 OD1 A:ASN130 4.3 13.2 1.0 C8 D:DA1 4.3 15.4 1.0 OD1 A:ASP358 4.3 14.2 1.0 OD1 A:ASP132 4.4 21.9 1.0 CG A:GLU162 4.4 14.5 1.0 CG A:ASN130 4.5 13.5 1.0 C5' D:DA1 4.5 14.5 1.0 O D:HOH130 4.5 28.9 0.5 OP3 D:DA1 4.6 16.7 1.0 CG A:ASP358 4.6 14.4 1.0 O4' D:DA1 4.6 14.7 1.0 O D:HOH111 4.7 40.3 1.0 CD2 A:HIS359 4.7 12.5 1.0 N7 D:DA1 4.8 17.5 1.0 CG A:ASP132 4.9 20.2 1.0 CE1 A:HIS236 4.9 14.4 1.0 NE2 A:HIS236 4.9 14.4 1.0

Magnesium binding site 2 out of 3 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:18.7 occ:1.00 O B:HOH533 2.1 18.6 1.0 O B:HOH556 2.1 21.1 1.0 O B:HOH527 2.1 21.3 1.0 OP2 C:DA1 2.1 17.8 1.0 OE2 B:GLU162 2.1 19.2 1.0 O C:HOH120 2.2 21.3 1.0 CD B:GLU162 3.0 19.6 1.0 P C:DA1 3.3 18.6 1.0 OE1 B:GLU162 3.3 20.0 1.0 OP1 C:DA1 3.8 20.1 1.0 O5' C:DA1 3.9 19.6 1.0 ND2 B:ASN130 3.9 15.8 1.0 OD2 B:ASP358 4.1 20.3 1.0 NE2 B:HIS359 4.2 18.7 1.0 OD1 B:ASN130 4.2 15.9 1.0 C8 C:DA1 4.2 22.1 1.0 OD1 B:ASP358 4.3 19.3 1.0 OD1 B:ASP132 4.4 26.9 1.0 O C:HOH134 4.4 47.2 1.0 CG B:GLU162 4.4 17.1 1.0 CG B:ASN130 4.4 16.6 1.0 O C:HOH105 4.5 41.9 1.0 OP3 C:DA1 4.5 20.2 1.0 C5' C:DA1 4.6 18.7 1.0 O4' C:DA1 4.6 20.0 1.0 CG B:ASP358 4.6 19.8 1.0 CD2 B:HIS359 4.6 17.8 1.0 N7 C:DA1 4.8 22.3 1.0 CG B:ASP132 4.8 26.2 1.0 CE1 B:HIS236 4.9 19.6 1.0 NE2 B:HIS236 4.9 18.1 1.0

Magnesium binding site 3 out of 3 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:51.8 occ:1.00 O B:HOH704 1.9 36.2 0.6 O B:HOH754 2.1 45.7 1.0 O B:HOH704 2.1 34.8 0.4 O B:HOH585 2.2 39.3 1.0 OE1 B:GLN340 2.3 42.5 1.0 CD B:GLN340 3.5 41.5 1.0 O B:HOH571 4.0 37.2 1.0 O B:GLN340 4.1 27.2 1.0 NE2 B:GLN340 4.2 43.6 1.0 O B:HOH693 4.4 67.6 1.0 CA B:GLN340 4.6 27.7 1.0 CG B:GLN340 4.7 36.0 1.0 CB B:GLN340 4.7 31.9 1.0 C B:GLN340 4.9 26.5 1.0

M.J.Schellenberg, L.Perera, C.N.Strom, C.A.Waters, B.Monian, C.D.Appel, C.K.Vilas, J.G.Williams, D.A.Ramsden, R.S.Williams. Reversal of Dna Damage Induced Topoisomerase 2 Dna-Protein Crosslinks By TDP2. Nucleic Acids Res. V. 44 3829 2016.
ISSN: ESSN 1362-4962
PubMed: 27060144
DOI: 10.1093/NAR/GKW228