Magnesium in PDB 6ca4: Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations

The structure of Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations, PDB code: 6ca4 was solved by K.Shi, H.Aihrara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.39 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.034, 98.260, 134.740, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations (pdb code 6ca4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations, PDB code: 6ca4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:38.5 occ:1.00 OD1 A:ASP131 2.2 31.9 1.0 OE1 A:GLU161 2.2 24.1 1.0 O A:HOH652 2.3 55.8 1.0 O A:HOH553 2.4 27.2 1.0 O A:HOH526 2.4 36.4 1.0 O A:HOH513 2.6 40.5 1.0 CD A:GLU161 3.0 25.8 1.0 HA A:ASP131 3.0 29.2 1.0 OE2 A:GLU161 3.0 24.3 1.0 CG A:ASP131 3.3 29.3 1.0 HB2 A:LEU133 3.3 32.4 1.0 CA A:ASP131 3.8 24.4 1.0 O A:HOH554 3.9 43.0 1.0 H A:LEU133 4.0 30.9 1.0 HD11 A:LEU133 4.0 38.3 1.0 CB A:ASP131 4.0 20.9 1.0 OD2 A:ASP131 4.2 33.8 1.0 HB2 A:ASP131 4.2 25.1 1.0 CB A:LEU133 4.3 27.0 1.0 OD2 A:ASP359 4.3 34.8 1.0 OD1 A:ASP359 4.3 30.1 1.0 CG A:GLU161 4.5 25.5 1.0 C A:ASP131 4.5 27.9 1.0 OD1 A:ASN129 4.6 23.0 1.0 CG A:ASP359 4.6 37.9 1.0 HG2 A:GLU161 4.6 30.6 1.0 H A:ASP134 4.7 38.7 1.0 HD21 A:ASN129 4.7 26.1 1.0 HG A:LEU133 4.7 31.7 1.0 N A:LEU133 4.7 25.8 1.0 HB3 A:LEU133 4.7 32.4 1.0 HB2 A:ASP134 4.8 46.5 1.0 H A:ASP131 4.8 28.6 1.0 CD1 A:LEU133 4.8 32.0 1.0 O A:ASP131 4.9 29.4 1.0 CG A:LEU133 4.9 26.5 1.0 HB3 A:ASP131 4.9 25.1 1.0 N A:ASP131 4.9 23.9 1.0 CA A:LEU133 4.9 25.0 1.0 HG3 A:GLU161 5.0 30.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:32.4 occ:1.00 OE1 B:GLU161 2.2 27.8 1.0 O B:HOH505 2.2 42.5 1.0 O B:HOH575 2.3 30.1 1.0 OD1 B:ASP131 2.4 29.6 1.0 O B:HOH525 2.5 50.3 1.0 OE2 B:GLU161 2.5 23.3 1.0 CD B:GLU161 2.7 25.5 1.0 HA B:ASP131 2.9 28.0 1.0 HB2 B:LEU133 3.3 33.4 1.0 O B:HOH613 3.3 41.6 1.0 O B:HOH621 3.3 76.7 1.0 CG B:ASP131 3.4 34.8 1.0 CA B:ASP131 3.8 23.4 1.0 HD11 B:LEU133 3.9 46.0 1.0 H B:LEU133 3.9 34.8 1.0 O B:HOH544 4.1 42.5 1.0 CB B:ASP131 4.1 27.9 1.0 CG B:GLU161 4.2 26.9 1.0 CB B:LEU133 4.2 27.9 1.0 HB2 B:ASP131 4.3 33.5 1.0 HD21 B:ASN129 4.3 24.6 1.0 OD2 B:ASP131 4.4 37.3 1.0 OD1 B:ASP359 4.4 32.2 1.0 OD2 B:ASP359 4.4 33.9 1.0 OD1 B:ASN129 4.4 22.0 1.0 C B:ASP131 4.5 25.6 1.0 HG2 B:GLU161 4.5 32.2 1.0 HG B:LEU133 4.6 38.2 1.0 HG3 B:GLU161 4.6 32.2 1.0 N B:LEU133 4.7 29.0 1.0 H B:ASP131 4.7 27.7 1.0 CD1 B:LEU133 4.7 38.4 1.0 H B:ASP134 4.7 33.6 1.0 HB3 B:LEU133 4.7 33.4 1.0 CG B:LEU133 4.8 31.9 1.0 CG B:ASP359 4.8 33.7 1.0 N B:ASP131 4.8 23.1 1.0 O B:ASP131 4.9 25.5 1.0 HB3 B:GLU161 4.9 29.6 1.0 CA B:LEU133 5.0 29.3 1.0 HB3 B:ASP131 5.0 33.5 1.0 HB2 B:GLU161 5.0 29.6 1.0 ND2 B:ASN129 5.0 20.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Humanized D. Rerio TDP2 By 14 Mutations within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:34.7 occ:1.00 OD1 C:ASP131 2.2 38.9 1.0 O C:HOH629 2.3 71.1 1.0 OE1 C:GLU161 2.3 31.1 1.0 O C:HOH592 2.3 29.5 1.0 O C:HOH524 2.5 41.8 1.0 HA C:ASP131 2.9 30.0 1.0 O C:HOH510 3.0 60.1 1.0 CD C:GLU161 3.0 34.1 1.0 OE2 C:GLU161 3.0 31.2 1.0 CG C:ASP131 3.3 35.9 1.0 HB2 C:LEU133 3.6 36.3 1.0 CA C:ASP131 3.8 25.1 1.0 CB C:ASP131 4.0 27.4 1.0 H C:LEU133 4.1 43.2 1.0 HB2 C:ASP131 4.2 32.9 1.0 OD2 C:ASP131 4.2 40.9 1.0 O C:HOH537 4.2 47.6 1.0 OD1 C:ASP359 4.3 39.7 1.0 OD2 C:ASP359 4.3 42.5 1.0 HD12 C:LEU133 4.3 37.2 1.0 C C:ASP131 4.4 27.6 1.0 CG C:GLU161 4.5 39.3 1.0 CB C:LEU133 4.5 30.3 1.0 H C:ASP134 4.6 40.7 1.0 OD1 C:ASN129 4.6 24.0 1.0 HD21 C:ASN129 4.6 30.6 1.0 CG C:ASP359 4.6 42.5 1.0 HB2 C:ASP134 4.7 59.1 1.0 HG2 C:GLU161 4.7 47.1 1.0 O C:ASP131 4.7 33.0 1.0 H C:ASP131 4.8 30.9 1.0 N C:LEU133 4.8 36.1 1.0 N C:ASP131 4.9 25.8 1.0 HB3 C:ASP131 4.9 32.9 1.0 HG C:LEU133 5.0 38.0 1.0

C.J.A.Ribeiro, J.Kankanala, K.Shi, K.Kurahashi, E.Kiselev, A.Ravji, Y.Pommier, H.Aihara, Z.Wang. New Fluorescence-Based High-Throughput Screening Assay For Small Molecule Inhibitors of Tyrosyl-Dna Phosphodiesterase 2 (TDP2). Eur J Pharm Sci V. 118 67 2018.
ISSN: ISSN 1879-0720
PubMed: 29574079
DOI: 10.1016/J.EJPS.2018.03.021