Magnesium in PDB 1z5c: Topoisomerase VI-B, Adp Pi Bound Dimer Form

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

The structure of Topoisomerase VI-B, Adp Pi Bound Dimer Form, PDB code: 1z5c 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 (°)	74.503, 74.503, 346.458, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 23.2

The binding sites of Magnesium atom in the Topoisomerase VI-B, Adp Pi Bound Dimer Form (pdb code 1z5c). 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 Pi Bound Dimer Form, PDB code: 1z5c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Topoisomerase VI-B, Adp Pi 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 Pi Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:37.7 occ:1.00 O1B A:ADP1001 2.1 32.4 1.0 O A:HOH3028 2.1 38.5 1.0 O2A A:ADP1001 2.1 31.8 1.0 O4 A:PO43001 2.2 51.3 1.0 OD1 A:ASN42 2.2 15.7 1.0 O A:HOH3041 2.3 38.8 1.0 CG A:ASN42 3.1 16.1 1.0 PB A:ADP1001 3.2 33.1 1.0 PA A:ADP1001 3.3 33.5 1.0 ND2 A:ASN42 3.4 10.8 1.0 O3A A:ADP1001 3.4 33.2 1.0 P A:PO43001 3.8 60.2 1.0 O2B A:ADP1001 3.8 30.3 1.0 OE2 A:GLU38 3.9 21.6 1.0 O5' A:ADP1001 4.0 33.5 1.0 CA A:GLY106 4.0 21.3 1.0 NZ A:LYS98 4.1 16.9 1.0 O1 A:PO43001 4.3 59.1 1.0 O2 A:PO43001 4.4 54.6 1.0 O3B A:ADP1001 4.5 33.9 1.0 O1A A:ADP1001 4.5 31.9 1.0 CB A:ASN42 4.5 15.7 1.0 O A:GLU38 4.6 19.3 1.0 O3 A:PO43001 4.6 55.9 1.0 CA A:ASN42 4.8 16.1 1.0 CA A:GLY111 4.8 20.3 1.0 N A:GLY106 4.9 19.1 1.0 N A:ASN42 4.9 15.7 1.0 N A:VAL112 4.9 18.9 1.0

Magnesium binding site 2 out of 2 in the Topoisomerase VI-B, Adp Pi 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 Pi Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:37.6 occ:1.00 O1B B:ADP1002 2.2 34.2 1.0 O B:HOH3096 2.2 44.8 1.0 OD1 B:ASN42 2.2 13.5 1.0 O2A B:ADP1002 2.2 30.0 1.0 O3 B:PO43002 2.2 47.0 1.0 O B:HOH3030 2.4 35.2 1.0 CG B:ASN42 3.1 12.4 1.0 PA B:ADP1002 3.2 30.6 1.0 PB B:ADP1002 3.2 29.5 1.0 O3A B:ADP1002 3.4 31.7 1.0 ND2 B:ASN42 3.4 10.8 1.0 O2B B:ADP1002 3.7 30.5 1.0 P B:PO43002 3.8 57.1 1.0 O B:HOH3024 3.9 36.6 1.0 OE2 B:GLU38 3.9 21.6 1.0 NZ B:LYS98 3.9 16.0 1.0 O5' B:ADP1002 4.0 33.1 1.0 CA B:GLY106 4.2 19.1 1.0 O4 B:PO43002 4.4 54.0 1.0 O1A B:ADP1002 4.5 34.0 1.0 CB B:ASN42 4.5 12.1 1.0 O B:GLU38 4.5 16.2 1.0 O3B B:ADP1002 4.6 30.2 1.0 O1 B:PO43002 4.6 55.6 1.0 O2 B:PO43002 4.6 55.7 1.0 CA B:ASN42 4.8 13.7 1.0 CA B:GLY111 4.8 18.6 1.0 N B:ASN42 4.8 13.6 1.0 N B:VAL112 4.9 18.1 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