Magnesium in PDB 5ink: Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-Abasic/Thf-MG2+ Complex

The structure of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-Abasic/Thf-MG2+ Complex, PDB code: 5ink 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)	45.68 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.615, 67.662, 166.745, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.1

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

Magnesium binding site 1 out of 2 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-Abasic/Thf-MG2+ Complex


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)-Abasic/Thf-MG2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:18.3 occ:1.00 O A:HOH538 2.0 18.2 1.0 OP1 D:3DR1 2.1 23.1 1.0 OE2 A:GLU162 2.1 23.4 1.0 O A:HOH534 2.1 16.6 1.0 O A:HOH519 2.2 16.2 1.0 O D:HOH109 2.2 17.7 1.0 CD A:GLU162 3.0 24.3 1.0 P D:3DR1 3.3 25.0 1.0 OE1 A:GLU162 3.3 24.3 1.0 OP2 D:3DR1 3.7 25.6 1.0 O5' D:3DR1 3.8 25.0 1.0 ND2 A:ASN130 3.9 17.2 1.0 OD2 A:ASP358 3.9 18.6 1.0 O D:HOH111 4.0 37.2 1.0 NE2 A:HIS359 4.0 17.4 1.0 OD1 A:ASN130 4.1 18.4 1.0 OD1 A:ASP358 4.3 17.9 1.0 CG A:ASN130 4.4 26.3 1.0 OD1 A:ASP132 4.4 21.2 1.0 CG A:GLU162 4.4 23.0 1.0 O4' D:3DR1 4.4 27.6 1.0 C5' D:3DR1 4.5 25.3 1.0 CG A:ASP358 4.5 20.9 1.0 CD2 A:HIS359 4.6 16.2 1.0 OP3 D:3DR1 4.6 24.0 1.0 CE1 A:HIS236 4.8 18.4 1.0 NE2 A:HIS236 4.8 18.0 1.0 C1' D:3DR1 4.9 28.0 1.0 CG A:ASP132 4.9 20.8 1.0 O A:HOH706 5.0 50.9 1.0

Magnesium binding site 2 out of 2 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-Abasic/Thf-MG2+ Complex


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)-Abasic/Thf-MG2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:29.1 occ:1.00 OE2 B:GLU162 2.0 29.4 1.0 O B:HOH531 2.1 26.2 1.0 O B:HOH523 2.1 28.6 1.0 O B:HOH528 2.1 21.1 1.0 OP2 C:3DR1 2.1 22.0 1.0 O C:HOH107 2.1 24.3 1.0 CD B:GLU162 3.0 30.9 1.0 OE1 B:GLU162 3.3 34.0 1.0 P C:3DR1 3.3 27.0 1.0 OP1 C:3DR1 3.6 27.6 1.0 ND2 B:ASN130 3.8 21.0 1.0 O5' C:3DR1 3.8 29.0 1.0 O C:HOH113 4.0 34.3 1.0 NE2 B:HIS359 4.0 25.7 1.0 OD2 B:ASP358 4.1 35.5 1.0 OD1 B:ASN130 4.2 21.5 1.0 CG B:GLU162 4.3 27.1 1.0 O B:HOH674 4.3 46.2 1.0 CG B:ASN130 4.3 20.9 1.0 O4' C:3DR1 4.4 31.8 1.0 OD1 B:ASP132 4.4 29.0 1.0 OD1 B:ASP358 4.4 26.6 1.0 CD2 B:HIS359 4.5 26.8 1.0 OP3 C:3DR1 4.6 30.1 1.0 CG B:ASP358 4.7 30.3 1.0 C5' C:3DR1 4.7 27.6 1.0 CE1 B:HIS236 4.8 21.9 1.0 NE2 B:HIS236 4.8 24.6 1.0 C1' C:3DR1 4.8 29.9 1.0 CG B:ASP132 4.9 30.0 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