Magnesium in PDB 5ht2: Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with 1-N6-Etheno-Adenine

The structure of Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with 1-N6-Etheno-Adenine, PDB code: 5ht2 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)	29.93 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.884, 68.604, 167.247, 90.00, 90.00, 90.00
R / Rfree (%)	11.6 / 15

The binding sites of Magnesium atom in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with 1-N6-Etheno-Adenine (pdb code 5ht2). 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 1-N6-Etheno-Adenine, PDB code: 5ht2:
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 1-N6-Etheno-Adenine


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 1-N6-Etheno-Adenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.8 occ:1.00 O A:HOH522 2.1 16.2 1.0 OP1 D:EDA1 2.1 14.8 1.0 OE2 A:GLU162 2.1 14.4 1.0 O A:HOH553 2.1 15.4 1.0 O A:HOH551 2.1 13.2 1.0 O D:HOH116 2.1 16.9 1.0 CD A:GLU162 3.0 14.8 1.0 OE1 A:GLU162 3.3 16.0 1.0 P D:EDA1 3.3 15.7 1.0 HD21 A:ASN130 3.3 15.7 1.0 HE2 A:HIS359 3.5 15.6 1.0 OP2 D:EDA1 3.7 16.8 1.0 O5' D:EDA1 3.9 15.3 1.0 ND2 A:ASN130 4.0 13.1 1.0 OD2 A:ASP358 4.1 14.9 1.0 HE1 A:HIS236 4.2 18.3 1.0 NE2 A:HIS359 4.2 13.0 1.0 OD1 A:ASN130 4.3 11.8 1.0 C8 D:EDA1 4.3 19.5 1.0 OD1 A:ASP358 4.3 13.2 1.0 O D:HOH111 4.4 32.2 1.0 HE2 A:HIS236 4.4 17.5 1.0 OD1 A:ASP132 4.4 19.1 1.0 HD2 A:HIS359 4.4 15.3 1.0 CG A:GLU162 4.4 14.3 1.0 HA A:ASP132 4.5 15.1 1.0 HG3 A:GLU162 4.5 17.2 1.0 CG A:ASN130 4.5 12.2 1.0 O D:HOH128 4.5 34.7 0.6 C5' D:EDA1 4.5 16.1 1.0 HD22 A:ASN130 4.5 15.7 1.0 HD12 A:LEU134 4.6 23.3 1.0 OP3 D:EDA1 4.6 16.9 1.0 CG A:ASP358 4.6 13.8 1.0 O4' D:EDA1 4.7 16.6 1.0 CD2 A:HIS359 4.7 12.7 1.0 N7 D:EDA1 4.8 21.2 1.0 CE1 A:HIS236 4.8 15.2 1.0 HG2 A:GLU162 4.8 17.2 1.0 NE2 A:HIS236 4.9 14.6 1.0 CG A:ASP132 4.9 17.4 1.0 O A:HOH563 5.0 37.7 1.0

Magnesium binding site 2 out of 3 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with 1-N6-Etheno-Adenine


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 1-N6-Etheno-Adenine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:18.8 occ:1.00 O B:HOH526 2.0 20.5 1.0 O B:HOH557 2.1 17.9 1.0 O B:HOH538 2.1 19.6 1.0 OP3 C:EDA1 2.1 18.3 1.0 OE2 B:GLU162 2.1 18.3 1.0 O C:HOH117 2.1 20.6 1.0 CD B:GLU162 3.0 19.4 1.0 HD21 B:ASN130 3.3 19.8 1.0 OE1 B:GLU162 3.3 20.7 1.0 P C:EDA1 3.3 19.4 1.0 HE2 B:HIS359 3.5 22.9 1.0 OP1 C:EDA1 3.7 20.6 1.0 O5' C:EDA1 3.9 19.7 1.0 ND2 B:ASN130 4.0 16.5 1.0 OD2 B:ASP358 4.1 20.3 1.0 C8 C:EDA1 4.2 21.0 1.0 OD1 B:ASN130 4.2 16.8 1.0 NE2 B:HIS359 4.2 19.1 1.0 OD1 B:ASP358 4.3 19.3 1.0 HE1 B:HIS236 4.3 21.6 1.0 HD2 B:HIS359 4.3 22.2 1.0 OD1 B:ASP132 4.4 24.5 1.0 HE2 B:HIS236 4.4 20.9 1.0 HA B:ASP132 4.4 21.9 1.0 O C:HOH132 4.4 47.2 1.0 CG B:GLU162 4.4 17.2 1.0 CG B:ASN130 4.4 16.1 1.0 O C:HOH115 4.5 41.2 1.0 HD22 B:ASN130 4.5 19.8 1.0 HD12 B:LEU134 4.5 30.0 1.0 HG3 B:GLU162 4.5 20.6 1.0 OP2 C:EDA1 4.5 20.5 1.0 C5' C:EDA1 4.5 19.4 1.0 CG B:ASP358 4.6 19.8 1.0 O4' C:EDA1 4.6 20.2 1.0 CD2 B:HIS359 4.7 18.5 1.0 N7 C:EDA1 4.7 23.8 1.0 CG B:ASP132 4.8 23.8 1.0 HG2 B:GLU162 4.9 20.6 1.0 CE1 B:HIS236 4.9 18.0 1.0 NE2 B:HIS236 4.9 17.5 1.0 O B:HOH614 4.9 57.3 1.0 HB2 B:ASP132 4.9 23.4 1.0

Magnesium binding site 3 out of 3 in the Mouse TDP2 Reaction Product (5'-Phosphorylated Dna)-MG2+ Complex with 1-N6-Etheno-Adenine


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 1-N6-Etheno-Adenine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:30.7 occ:0.24 O B:HOH661 2.0 42.6 0.5 O B:GLN340 2.1 31.8 1.0 O B:HOH506 2.2 39.8 0.6 O B:HOH710 2.3 57.3 1.0 O B:HOH765 2.7 56.5 1.0 O B:HOH661 2.7 38.8 0.5 O B:HOH506 2.8 26.1 0.4 C B:GLN340 3.2 29.5 1.0 HB3 B:GLN340 3.4 40.2 1.0 OE1 B:GLN340 3.6 50.6 1.0 HB3 B:SER341 3.6 38.1 1.0 HA B:GLN340 3.7 34.3 1.0 CA B:GLN340 3.9 28.6 1.0 HA B:SER341 4.0 35.0 1.0 CB B:GLN340 4.1 33.5 1.0 N B:SER341 4.2 27.6 1.0 CB B:SER341 4.4 31.8 1.0 CA B:SER341 4.4 29.2 1.0 CD B:GLN340 4.6 49.2 1.0 HB2 B:GLN340 4.8 40.2 1.0 HB2 B:SER341 4.8 38.1 1.0 CG B:GLN340 4.9 40.9 1.0 H B:SER341 4.9 33.1 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