Magnesium in PDB 1z5a: Topoisomerase VI-B, Adp-Bound Dimer Form

All present enzymatic activity of Topoisomerase VI-B, Adp-Bound Dimer Form:
5.99.1.3;

The structure of Topoisomerase VI-B, Adp-Bound Dimer Form, PDB code: 1z5a was solved by K.D.Corbett, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	74.569, 74.569, 345.557, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.1

The binding sites of Magnesium atom in the Topoisomerase VI-B, Adp-Bound Dimer Form (pdb code 1z5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Topoisomerase VI-B, Adp-Bound Dimer Form, PDB code: 1z5a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Topoisomerase VI-B, Adp-Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Topoisomerase VI-B, Adp-Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:63.3 occ:1.00 O1B A:ADP2001 1.8 36.3 1.0 O A:HOH2088 2.2 53.8 1.0 O A:HOH2087 2.2 46.9 1.0 O2A A:ADP2001 2.2 38.9 1.0 OD1 A:ASN42 2.2 13.6 1.0 O A:HOH2060 2.6 47.8 1.0 PB A:ADP2001 2.9 37.3 1.0 PA A:ADP2001 3.1 40.5 1.0 O3A A:ADP2001 3.1 37.9 1.0 CG A:ASN42 3.2 14.7 1.0 ND2 A:ASN42 3.4 10.8 1.0 O2B A:ADP2001 3.6 36.7 1.0 O5' A:ADP2001 3.7 40.1 1.0 NZ A:LYS98 3.9 17.2 1.0 CA A:GLY106 4.0 13.8 1.0 O A:HOH2026 4.1 41.5 1.0 O3B A:ADP2001 4.1 35.8 1.0 OE2 A:GLU38 4.3 17.5 1.0 O1A A:ADP2001 4.4 40.2 1.0 CB A:ASN42 4.6 13.6 1.0 O A:HOH2024 4.6 41.1 1.0 O A:GLU38 4.7 15.3 1.0 CA A:GLY111 4.8 16.0 1.0 N A:GLY106 4.8 13.5 1.0 CA A:ASN42 4.9 14.9 1.0 N A:VAL112 5.0 15.4 1.0

Magnesium binding site 2 out of 2 in the Topoisomerase VI-B, Adp-Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Topoisomerase VI-B, Adp-Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:55.0 occ:1.00 O1B B:ADP2002 1.8 33.5 1.0 OD1 B:ASN42 2.1 8.3 1.0 O2A B:ADP2002 2.2 35.3 1.0 O B:HOH2056 2.2 40.1 1.0 O B:HOH2119 2.6 60.0 1.0 CG B:ASN42 3.0 10.7 1.0 PB B:ADP2002 3.1 35.1 1.0 PA B:ADP2002 3.2 34.2 1.0 O3A B:ADP2002 3.3 34.4 1.0 ND2 B:ASN42 3.5 7.1 1.0 NZ B:LYS98 3.6 8.1 1.0 O2B B:ADP2002 3.8 35.7 1.0 O5' B:ADP2002 3.8 36.5 1.0 O B:HOH2021 4.1 38.5 1.0 CA B:GLY106 4.2 15.2 1.0 O3B B:ADP2002 4.3 33.9 1.0 OE2 B:GLU38 4.3 18.5 1.0 CB B:ASN42 4.4 10.8 1.0 O1A B:ADP2002 4.5 35.5 1.0 O B:GLU38 4.5 11.7 1.0 CA B:ASN42 4.7 11.3 1.0 CA B:GLY111 4.8 17.1 1.0 N B:ASN42 4.8 10.1 1.0 N B:VAL112 4.9 16.3 1.0 CE B:LYS98 4.9 11.5 1.0 N B:GLY106 5.0 15.4 1.0 O B:HOH2003 5.0 35.9 1.0

K.D.Corbett, J.M.Berger. Structural Dissection of Atp Turnover in the Prototypical Ghl Atpase Topovi. Structure V. 13 873 2005.
ISSN: ISSN 0969-2126
PubMed: 15939019
DOI: 10.1016/J.STR.2005.03.013