Calcium in PDB 5inq: Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex

The structure of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex, PDB code: 5inq 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)	39.08 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.702, 67.504, 167.529, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.5

The binding sites of Calcium atom in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex (pdb code 5inq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex, PDB code: 5inq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:38.4 occ:1.00 OE2 A:GLU162 2.2 41.3 1.0 O A:HOH525 2.3 75.9 1.0 OP2 D:DC1 2.3 41.8 1.0 O A:HOH585 2.3 37.8 1.0 O A:HOH542 2.3 29.2 1.0 OE1 A:GLU162 2.5 37.7 1.0 O D:HOH106 2.6 68.1 1.0 CD A:GLU162 2.7 29.1 1.0 OD1 A:ASP132 3.4 40.1 1.0 O A:HOH504 3.6 45.3 1.0 P D:DC1 3.6 46.2 1.0 OP1 D:DC1 4.1 50.7 1.0 CG A:ASP132 4.2 37.1 1.0 CG A:GLU162 4.2 47.1 1.0 C5 D:DC1 4.3 65.9 1.0 C6 D:DC1 4.3 41.6 1.0 OD1 A:ASP358 4.5 29.2 1.0 OD1 A:ASN130 4.5 28.6 1.0 OD2 A:ASP358 4.5 29.1 1.0 O A:HOH655 4.6 62.7 1.0 OP3 D:DC1 4.6 46.6 1.0 ND2 A:ASN130 4.6 28.4 1.0 O5' D:DC1 4.6 46.4 1.0 CA A:ASP132 4.7 25.4 1.0 CB A:ASP132 4.8 26.8 1.0 O D:HOH110 4.8 56.5 1.0 OD2 A:ASP132 4.8 40.9 1.0 CD1 A:LEU134 4.9 35.9 1.0 CG A:ASP358 4.9 30.2 1.0 CG A:ASN130 5.0 30.4 1.0

Calcium binding site 2 out of 2 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-CA2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:57.7 occ:1.00 OE2 B:GLU162 2.2 49.6 1.0 O B:HOH569 2.2 51.2 1.0 OP2 C:DC1 2.3 58.7 1.0 O B:HOH529 2.4 35.0 1.0 O B:HOH506 2.4 71.2 1.0 OE1 B:GLU162 2.5 39.3 1.0 O C:HOH104 2.6 54.1 1.0 CD B:GLU162 2.7 37.6 1.0 OD1 B:ASP132 3.5 51.7 1.0 P C:DC1 3.6 58.1 1.0 C5 C:DC1 3.9 87.1 1.0 OP1 C:DC1 4.0 68.0 1.0 C6 C:DC1 4.0 71.6 1.0 CG B:ASP132 4.1 56.9 1.0 CG B:GLU162 4.2 52.9 1.0 O B:HOH533 4.3 56.3 1.0 ND2 B:ASN130 4.4 30.2 1.0 OD1 B:ASN130 4.4 34.0 1.0 OP3 C:DC1 4.5 56.9 1.0 OD1 B:ASP358 4.6 40.1 1.0 OD2 B:ASP358 4.6 37.3 1.0 O5' C:DC1 4.6 54.4 1.0 OD2 B:ASP132 4.7 47.6 1.0 CA B:ASP132 4.7 35.9 1.0 O C:HOH105 4.7 55.4 0.6 CB B:ASP132 4.8 39.7 1.0 CG B:ASN130 4.9 32.2 1.0 CD1 B:LEU134 4.9 46.4 1.0 CG B:ASP358 5.0 37.6 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