Magnesium in PDB 1z5b: Topoisomerase VI-B, Adp ALF4- Bound Dimer Form

All present enzymatic activity of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form:
5.99.1.3;

The structure of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form, PDB code: 1z5b 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)	30.00 / 2.00
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	74.077, 74.077, 344.381, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 20.8

The structure of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form (pdb code 1z5b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form, PDB code: 1z5b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Topoisomerase VI-B, Adp ALF4- 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 ALF4- Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:20.1 occ:1.00 O1B A:ADP1001 2.0 16.2 1.0 F1 A:ALF3001 2.0 20.6 1.0 O A:HOH4038 2.1 20.8 1.0 O A:HOH4136 2.1 28.3 1.0 OD1 A:ASN42 2.1 6.0 1.0 O1A A:ADP1001 2.2 18.6 1.0 F3 A:ALF3001 2.6 20.7 1.0 PB A:ADP1001 3.0 18.1 1.0 CG A:ASN42 3.0 6.3 1.0 PA A:ADP1001 3.2 18.6 1.0 AL A:ALF3001 3.2 19.4 1.0 O3A A:ADP1001 3.3 17.7 1.0 ND2 A:ASN42 3.3 4.8 1.0 O3B A:ADP1001 3.4 15.9 1.0 OE2 A:GLU38 4.0 9.5 1.0 NZ A:LYS98 4.0 5.2 1.0 O5' A:ADP1001 4.1 19.9 1.0 O A:HOH4002 4.2 14.1 1.0 O A:HOH4137 4.2 26.4 1.0 O A:GLU38 4.3 7.0 1.0 O2A A:ADP1001 4.4 15.5 1.0 O2B A:ADP1001 4.4 15.2 1.0 CB A:ASN42 4.4 8.0 1.0 F4 A:ALF3001 4.4 18.7 1.0 CA A:GLY106 4.7 7.7 1.0 F2 A:ALF3001 4.7 19.4 1.0 CA A:GLY111 4.8 7.2 1.0 CA A:ASN42 4.8 7.6 1.0 N A:VAL112 4.8 7.5 1.0 N A:GLY111 4.8 7.7 1.0 N A:ASN42 4.8 8.2 1.0

Magnesium binding site 2 out of 3 in the Topoisomerase VI-B, Adp ALF4- 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 ALF4- Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:18.4 occ:1.00 O1B B:ADP1002 2.0 16.4 1.0 F4 B:ALF3002 2.0 20.9 1.0 O1A B:ADP1002 2.0 17.9 1.0 OD1 B:ASN42 2.1 7.4 1.0 O B:HOH3008 2.2 15.3 1.0 O B:HOH3165 2.2 31.3 1.0 PB B:ADP1002 2.9 17.4 1.0 CG B:ASN42 3.0 7.7 1.0 PA B:ADP1002 3.0 17.4 1.0 F2 B:ALF3002 3.1 24.1 1.0 O3A B:ADP1002 3.2 15.6 1.0 ND2 B:ASN42 3.3 4.0 1.0 AL B:ALF3002 3.3 21.2 1.0 O3B B:ADP1002 3.4 18.6 1.0 O5' B:ADP1002 3.9 18.2 1.0 NZ B:LYS98 4.0 9.3 1.0 OE2 B:GLU38 4.2 9.9 1.0 O2A B:ADP1002 4.3 16.0 1.0 O2B B:ADP1002 4.3 16.7 1.0 O B:HOH3003 4.4 15.8 1.0 O B:GLU38 4.4 5.8 1.0 O B:HOH3089 4.4 27.3 1.0 CB B:ASN42 4.4 6.5 1.0 F1 B:ALF3002 4.4 19.2 1.0 N B:VAL112 4.7 7.2 1.0 CA B:GLY111 4.8 7.4 1.0 CA B:ASN42 4.8 7.2 1.0 CA B:GLY106 4.8 7.7 1.0 N B:GLY111 4.8 7.1 1.0 N B:ASN42 4.9 6.9 1.0 F3 B:ALF3002 5.0 21.2 1.0

Magnesium binding site 3 out of 3 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:29.6 occ:1.00 O B:THR418 2.1 9.7 1.0 O B:HOH3069 2.1 20.6 1.0 O B:HOH3030 2.3 17.9 1.0 O B:ARG102 2.4 8.0 1.0 O B:HOH3053 3.2 20.6 1.0 C B:THR418 3.2 8.9 1.0 C B:ARG102 3.5 8.5 1.0 N B:ARG102 3.9 9.1 1.0 CA B:THR418 4.0 9.2 1.0 N B:LYS419 4.2 8.8 1.0 O B:VAL100 4.2 12.3 1.0 O B:HOH3011 4.3 19.2 1.0 O B:HOH3017 4.3 20.0 1.0 CA B:ARG102 4.4 8.9 1.0 OG1 B:THR104 4.4 7.0 1.0 N B:THR104 4.4 7.6 1.0 O B:LYS98 4.4 8.2 1.0 CA B:LYS419 4.4 8.9 1.0 O B:HOH3116 4.5 17.9 1.0 N B:GLN103 4.5 8.1 1.0 CA B:GLN103 4.6 8.1 1.0 CB B:THR418 4.6 9.2 1.0 O B:GLY106 4.7 6.9 1.0 O B:THR104 4.8 8.7 1.0 CB B:MET107 4.9 7.5 1.0 O B:SER417 4.9 7.7 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