Manganese in PDB 5inp: Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex

The structure of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex, PDB code: 5inp 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)	29.84 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.592, 68.521, 166.899, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 17

The binding sites of Manganese atom in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex (pdb code 5inp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex, PDB code: 5inp:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:22.0 occ:1.00 OP2 D:DC1 2.2 30.5 1.0 OE2 A:GLU162 2.2 23.0 1.0 O A:HOH534 2.2 24.2 1.0 O A:HOH516 2.2 25.5 1.0 O D:HOH106 2.3 34.6 1.0 O A:HOH546 2.3 18.2 1.0 CD A:GLU162 3.1 23.5 1.0 OE1 A:GLU162 3.3 25.6 1.0 P D:DC1 3.3 31.8 1.0 OP1 D:DC1 3.8 31.9 1.0 ND2 A:ASN130 4.0 20.5 1.0 O5' D:DC1 4.0 29.4 1.0 C6 D:DC1 4.0 34.6 1.0 OD2 A:ASP358 4.1 20.4 1.0 C5 D:DC1 4.2 36.1 1.0 OD1 A:ASN130 4.2 20.7 1.0 O A:HOH525 4.3 25.5 0.5 OD1 A:ASP132 4.3 26.2 1.0 OD1 A:ASP358 4.3 20.8 1.0 NE2 A:HIS359 4.4 21.4 1.0 CG A:GLU162 4.4 21.2 1.0 CG A:ASN130 4.5 19.9 1.0 OP3 D:DC1 4.6 26.8 1.0 CG A:ASP358 4.6 20.7 1.0 C5' D:DC1 4.7 28.0 1.0 CG A:ASP132 4.7 25.0 1.0 CD2 A:HIS359 4.8 20.6 1.0 O4' D:DC1 4.9 28.2 1.0 CE1 A:HIS236 4.9 22.2 1.0 O D:HOH107 4.9 23.8 0.5 NE2 A:HIS236 5.0 22.4 1.0

Manganese binding site 2 out of 2 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:25.9 occ:1.00 OP2 C:DC1 2.1 31.1 1.0 OE2 B:GLU162 2.1 29.0 1.0 O B:HOH513 2.2 30.9 1.0 O B:HOH528 2.2 25.7 1.0 O B:HOH532 2.2 25.1 1.0 O C:HOH106 2.2 36.5 1.0 CD B:GLU162 3.1 30.0 1.0 P C:DC1 3.3 32.9 1.0 OE1 B:GLU162 3.3 31.6 1.0 OP1 C:DC1 3.7 35.4 1.0 ND2 B:ASN130 3.9 21.7 1.0 O5' C:DC1 3.9 33.4 1.0 C6 C:DC1 4.0 38.9 1.0 C5 C:DC1 4.1 40.2 1.0 OD2 B:ASP358 4.2 26.9 1.0 O B:HOH507 4.2 37.3 1.0 OD1 B:ASP132 4.2 33.0 1.0 OD1 B:ASN130 4.2 23.8 1.0 OD1 B:ASP358 4.3 25.0 1.0 NE2 B:HIS359 4.3 23.4 1.0 CG B:GLU162 4.4 29.2 1.0 CG B:ASN130 4.5 22.1 1.0 CG B:ASP132 4.6 31.7 1.0 OP3 C:DC1 4.6 34.8 1.0 CG B:ASP358 4.6 25.8 1.0 C5' C:DC1 4.7 33.1 1.0 CD2 B:HIS359 4.7 24.1 1.0 CE1 B:HIS236 4.9 26.0 1.0 O B:HOH663 4.9 55.2 0.5 O4' C:DC1 4.9 33.9 1.0 NE2 B:HIS236 5.0 25.4 1.0 O C:HOH108 5.0 57.2 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