Magnesium in PDB 5inm: Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations

The structure of Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations, PDB code: 5inm 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)	48.82 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.851, 113.445, 114.959, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23

The binding sites of Magnesium atom in the Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations (pdb code 5inm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations, PDB code: 5inm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:52.1 occ:1.00 O A:HOH501 2.0 42.3 1.0 O A:HOH539 2.1 38.6 1.0 O A:HOH536 2.1 35.2 1.0 OE1 A:GLU162 2.1 42.3 1.0 O A:HOH514 2.1 29.2 1.0 OD1 A:ASP132 2.1 33.4 1.0 OE2 A:GLU162 2.3 37.5 1.0 CD A:GLU162 2.5 37.8 1.0 CG A:ASP132 3.1 35.5 1.0 O A:HOH502 3.6 31.7 1.0 CB A:ASP132 3.7 30.0 1.0 CA A:ASP132 3.7 33.9 1.0 OD1 A:ASN130 3.9 32.6 1.0 CG A:GLU162 3.9 40.6 1.0 OD2 A:ASP132 4.0 38.7 1.0 O A:HOH581 4.0 39.9 1.0 OD1 A:ASP358 4.1 34.2 1.0 OD2 A:ASP358 4.4 36.7 1.0 C A:ASP132 4.6 30.6 1.0 CB A:GLU162 4.6 33.3 1.0 CB A:LEU134 4.6 33.9 1.0 CG A:ASP358 4.6 33.4 1.0 CG A:ASN130 4.6 30.6 1.0 ND2 A:ASN130 4.7 29.3 1.0 N A:ASP132 4.7 31.3 1.0 CD1 A:LEU134 4.8 35.1 1.0

Magnesium binding site 2 out of 4 in the Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:93.8 occ:1.00 OE2 B:GLU162 2.0 44.2 1.0 O B:HOH528 2.0 44.3 1.0 O B:HOH525 2.1 29.9 1.0 O B:HOH529 2.1 52.9 1.0 O B:HOH506 2.1 39.3 1.0 OE1 B:GLU162 2.2 43.7 1.0 CD B:GLU162 2.4 41.9 1.0 OD1 B:ASP132 2.9 42.2 1.0 OD1 B:ASN130 3.9 24.7 1.0 CG B:GLU162 3.9 41.9 1.0 CG B:ASP132 3.9 41.0 1.0 CA B:ASP132 4.1 29.6 1.0 ND2 B:ASN130 4.2 31.8 1.0 OD1 B:ASP358 4.3 38.8 1.0 CB B:ASP132 4.4 33.3 1.0 CG B:ASN130 4.4 27.9 1.0 OD2 B:ASP358 4.4 43.0 1.0 CB B:GLU162 4.6 32.7 1.0 CB B:LEU134 4.6 30.9 1.0 O B:HOH577 4.7 32.8 1.0 CD1 B:LEU134 4.7 31.0 1.0 CG B:ASP358 4.8 35.3 1.0 NE2 B:HIS359 4.8 42.4 1.0 OD2 B:ASP132 4.9 46.6 1.0 N B:ASP132 4.9 31.5 1.0 C B:ASP132 4.9 35.9 1.0

Magnesium binding site 3 out of 4 in the Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:52.8 occ:1.00 O D:HOH502 2.1 39.0 1.0 O D:HOH554 2.1 53.8 1.0 O D:HOH513 2.1 47.3 1.0 O D:HOH504 2.1 28.6 1.0 OD1 D:ASP132 2.1 50.8 1.0 OE1 D:GLU162 2.2 38.0 1.0 CD D:GLU162 2.9 36.2 1.0 OE2 D:GLU162 2.9 38.6 1.0 CG D:ASP132 3.2 48.0 1.0 CA D:ASP132 3.9 39.7 1.0 CB D:ASP132 4.0 39.9 1.0 OD1 D:ASP358 4.0 36.7 1.0 O D:HOH531 4.0 45.7 1.0 OD2 D:ASP132 4.2 50.3 1.0 OD2 D:ASP358 4.3 39.6 1.0 CB D:LEU134 4.3 53.1 1.0 OD1 D:ASN130 4.3 34.0 1.0 CG D:GLU162 4.3 40.3 1.0 CD1 D:LEU134 4.4 50.1 1.0 CG D:ASP358 4.5 36.5 1.0 C D:ASP132 4.6 46.8 1.0 CG D:LEU134 4.7 51.3 1.0 CB D:GLU162 4.9 34.3 1.0 N D:ASP132 4.9 38.6 1.0 ND2 D:ASN130 4.9 33.4 1.0 N D:LEU134 5.0 51.2 1.0

Magnesium binding site 4 out of 4 in the Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mouse TDP2 Protein, Apo State with Variable Dna-Binding Grasp Conformations within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:52.7 occ:1.00 O E:HOH501 2.1 49.7 1.0 O E:HOH513 2.1 30.3 1.0 OD1 E:ASP132 2.1 41.9 1.0 OE1 E:GLU162 2.2 43.7 1.0 OE2 E:GLU162 2.7 43.2 1.0 CD E:GLU162 2.8 43.0 1.0 CG E:ASP132 3.3 40.4 1.0 CA E:ASP132 3.9 33.1 1.0 CB E:LEU134 4.0 44.0 1.0 CB E:ASP132 4.0 38.1 1.0 OD2 E:ASP358 4.0 42.2 1.0 OD2 E:ASP132 4.2 40.7 1.0 CD1 E:LEU134 4.3 37.0 1.0 OD1 E:ASP358 4.3 41.7 1.0 CG E:GLU162 4.3 45.0 1.0 OD1 E:ASN130 4.5 31.3 1.0 C E:ASP132 4.5 34.6 1.0 CG E:ASP358 4.6 41.4 1.0 CG E:LEU134 4.6 38.4 1.0 N E:LEU134 4.7 43.2 1.0 O E:ASP132 4.9 36.7 1.0 CA E:LEU134 4.9 44.1 1.0 N E:ASP135 5.0 52.5 1.0 CB E:GLU162 5.0 40.3 1.0 N E:ASP132 5.0 32.2 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