Magnesium in PDB 1zxn: Human Dna Topoisomerase Iia Atpase/Adp

All present enzymatic activity of Human Dna Topoisomerase Iia Atpase/Adp:
5.99.1.3;

The structure of Human Dna Topoisomerase Iia Atpase/Adp, PDB code: 1zxn was solved by H.Wei, A.J.Ruthenburg, S.K.Bechis, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.015, 90.492, 148.293, 90.00, 89.97, 90.00
R / Rfree (%)	23.5 / 28.1

The binding sites of Magnesium atom in the Human Dna Topoisomerase Iia Atpase/Adp (pdb code 1zxn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Dna Topoisomerase Iia Atpase/Adp, PDB code: 1zxn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Dna Topoisomerase Iia Atpase/Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Topoisomerase Iia Atpase/Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg900 b:33.1 occ:1.00 OD1 A:ASN91 2.0 42.3 1.0 O2A A:ADP901 2.0 44.5 1.0 O A:HOH902 2.0 29.8 1.0 O3B A:ADP901 2.1 43.0 1.0 O A:HOH958 2.2 37.0 1.0 O A:HOH960 2.9 86.4 1.0 CG A:ASN91 3.0 42.6 1.0 PB A:ADP901 3.3 39.0 1.0 PA A:ADP901 3.3 45.7 1.0 ND2 A:ASN91 3.4 42.6 1.0 O3A A:ADP901 3.6 40.3 1.0 O2B A:ADP901 3.8 37.0 1.0 CA A:GLY161 4.2 50.5 1.0 O A:GLU87 4.2 39.7 1.0 OE2 A:GLU87 4.3 50.1 1.0 O1A A:ADP901 4.3 46.4 1.0 O5' A:ADP901 4.4 57.6 1.0 CB A:ASN91 4.4 42.1 1.0 C5' A:ADP901 4.4 57.6 1.0 O1B A:ADP901 4.5 41.0 1.0 OD2 A:ASP94 4.5 48.9 1.0 CA A:GLY166 4.6 37.1 1.0 CA A:ASN91 4.7 41.9 1.0 N A:GLY161 4.8 51.2 1.0 N A:ALA167 4.9 39.9 1.0 N A:ASN91 4.9 40.5 1.0

Magnesium binding site 2 out of 4 in the Human Dna Topoisomerase Iia Atpase/Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Topoisomerase Iia Atpase/Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:36.5 occ:1.00 O2A B:ADP903 2.0 32.5 1.0 O B:HOH981 2.1 29.9 1.0 OD1 B:ASN91 2.1 27.3 1.0 O B:HOH980 2.1 29.8 1.0 O B:HOH979 2.2 41.6 1.0 O3B B:ADP903 2.3 28.7 1.0 CG B:ASN91 2.9 30.2 1.0 ND2 B:ASN91 3.2 28.4 1.0 PA B:ADP903 3.3 38.9 1.0 PB B:ADP903 3.4 33.8 1.0 O3A B:ADP903 3.6 32.3 1.0 O B:HOH916 3.9 28.0 1.0 O2B B:ADP903 3.9 28.9 1.0 O B:GLU87 4.1 33.0 1.0 CA B:GLY161 4.1 47.4 1.0 OE2 B:GLU87 4.2 56.9 1.0 O1A B:ADP903 4.3 37.7 1.0 CB B:ASN91 4.3 32.5 1.0 O5' B:ADP903 4.4 57.6 1.0 OD2 B:ASP94 4.4 40.2 1.0 C5' B:ADP903 4.5 57.6 1.0 CA B:GLY166 4.5 37.9 1.0 O1B B:ADP903 4.6 32.5 1.0 CA B:ASN91 4.6 33.2 1.0 N B:GLY161 4.7 47.3 1.0 N B:ALA167 4.8 39.4 1.0 O1 B:SO4909 4.8 87.6 1.0 N B:ASN91 4.9 34.7 1.0 N B:GLY166 5.0 36.8 1.0

Magnesium binding site 3 out of 4 in the Human Dna Topoisomerase Iia Atpase/Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Topoisomerase Iia Atpase/Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg904 b:36.1 occ:1.00 O C:HOH975 2.1 40.3 1.0 OD1 C:ASN91 2.1 32.0 1.0 O2A C:ADP905 2.2 47.2 1.0 O3B C:ADP905 2.3 42.1 1.0 O C:HOH919 2.4 52.6 1.0 O C:HOH908 2.4 39.4 1.0 CG C:ASN91 3.1 32.7 1.0 PB C:ADP905 3.4 47.1 1.0 PA C:ADP905 3.5 46.1 1.0 ND2 C:ASN91 3.6 27.4 1.0 O3A C:ADP905 3.7 42.4 1.0 O2B C:ADP905 3.8 49.2 1.0 O C:HOH976 4.0 53.4 1.0 CA C:GLY161 4.1 53.7 1.0 O C:HOH922 4.2 53.3 1.0 OE2 C:GLU87 4.2 58.7 1.0 O C:GLU87 4.2 42.9 1.0 OD2 C:ASP94 4.4 49.2 1.0 CB C:ASN91 4.5 31.9 1.0 O1A C:ADP905 4.5 43.4 1.0 CA C:GLY166 4.5 42.9 1.0 N C:GLY161 4.6 53.3 1.0 O5' C:ADP905 4.6 57.6 1.0 O1B C:ADP905 4.6 48.9 1.0 CD C:GLU87 4.6 56.2 1.0 C5' C:ADP905 4.7 57.6 1.0 CA C:ASN91 4.7 35.1 1.0 OE1 C:GLU87 4.8 57.2 1.0 N C:ASN91 4.9 36.5 1.0 N C:GLY166 4.9 44.9 1.0

Magnesium binding site 4 out of 4 in the Human Dna Topoisomerase Iia Atpase/Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dna Topoisomerase Iia Atpase/Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg906 b:42.0 occ:1.00 O D:HOH941 2.0 51.2 1.0 O D:HOH940 2.0 71.9 1.0 O D:HOH942 2.0 55.2 1.0 O2A D:ADP907 2.3 53.7 1.0 O3B D:ADP907 2.4 52.6 1.0 OD1 D:ASN91 2.5 57.0 1.0 CG D:ASN91 3.4 58.3 1.0 PB D:ADP907 3.4 55.4 1.0 PA D:ADP907 3.6 53.2 1.0 O2B D:ADP907 3.7 54.8 1.0 ND2 D:ASN91 3.7 56.8 1.0 O3A D:ADP907 3.8 52.9 1.0 CA D:GLY161 4.0 63.8 1.0 OE2 D:GLU87 4.1 69.2 1.0 O D:GLU87 4.1 54.0 1.0 OD2 D:ASP94 4.5 67.6 1.0 O1A D:ADP907 4.6 53.8 1.0 CB D:ASN91 4.6 56.7 1.0 N D:GLY161 4.7 65.8 1.0 CA D:ASN91 4.7 55.9 1.0 O1B D:ADP907 4.7 53.9 1.0 O5' D:ADP907 4.7 57.6 1.0 O2 D:SO4908 4.8 0.6 1.0 C5' D:ADP907 4.8 57.6 1.0 N D:ASN91 4.8 55.6 1.0 O D:GLY160 4.9 68.1 1.0 CA D:GLY166 4.9 50.5 1.0 O3 D:SO4908 4.9 0.4 1.0

H.Wei, A.J.Ruthenburg, S.K.Bechis, G.L.Verdine. Nucleotide-Dependent Domain Movement in the Atpase Domain of A Human Type Iia Dna Topoisomerase. J.Biol.Chem. V. 280 37041 2005.
ISSN: ISSN 0021-9258
PubMed: 16100112
DOI: 10.1074/JBC.M506520200