Magnesium in PDB 8yo4: Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna

All present enzymatic activity of Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna:
5.6.2.2;

The binding sites of Magnesium atom in the Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna (pdb code 8yo4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna, PDB code: 8yo4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:50.0 occ:1.00 CB C:ALA419 3.3 44.5 1.0 OH B:TYR117 3.6 27.7 1.0 N C:ALA419 3.7 40.4 1.0 OD1 C:ASP557 3.8 59.6 1.0 O C:GLU415 3.9 44.5 1.0 C5' F:DA12 4.0 48.9 1.0 OD2 C:ASP557 4.1 47.7 1.0 CA C:ALA419 4.1 45.4 1.0 O5' F:DA12 4.1 46.8 1.0 CA C:GLY416 4.1 48.9 1.0 OP1 F:DA12 4.2 52.6 1.0 CZ B:TYR117 4.2 32.8 1.0 C C:GLU415 4.3 41.2 1.0 N C:GLY416 4.4 43.6 1.0 CG C:ASP557 4.4 58.4 1.0 CB C:SER418 4.4 38.6 1.0 C C:GLY416 4.6 44.0 1.0 CE2 B:TYR117 4.6 33.8 1.0 C C:SER418 4.6 38.5 1.0 O C:GLY416 4.7 45.5 1.0 C4' F:DA12 4.7 38.2 1.0 N C:LEU629 4.8 45.6 1.0 CG C:GLU415 4.8 54.7 1.0 N C:SER418 4.8 50.8 1.0 P F:DA12 4.8 49.4 1.0 CA C:SER418 4.9 41.9 1.0 CA C:GLY628 5.0 45.0 1.0

Magnesium binding site 2 out of 4 in the Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:33.7 occ:1.00 OD2 C:ASP559 2.0 48.5 1.0 OD1 C:ASP559 2.5 47.4 1.0 CG C:ASP559 2.6 43.6 1.0 OD2 C:ASP557 2.8 47.7 1.0 CB C:ASP557 3.1 55.1 1.0 CG C:ASP557 3.3 58.4 1.0 O C:LYS627 3.4 50.7 1.0 O3' F:DT11 3.9 51.8 1.0 OP1 F:DA12 3.9 52.6 1.0 OE2 C:GLU415 4.0 55.5 1.0 CB C:ASP559 4.0 36.7 1.0 N C:GLY562 4.3 37.1 1.0 OD1 C:ASP557 4.4 59.6 1.0 CA C:ASP557 4.5 52.3 1.0 C C:LYS627 4.5 43.7 1.0 OE1 C:GLU415 4.5 63.7 1.0 CD C:GLU415 4.5 59.5 1.0 P F:DA12 4.6 49.4 1.0 CA C:GLY562 4.6 36.5 1.0 C4' F:DT11 4.7 53.2 1.0 CG C:LYS627 4.7 39.1 1.0 C5' F:DT11 4.7 51.3 1.0 CB C:ASP561 4.8 37.3 1.0 OP1 F:DT11 4.8 56.7 1.0 C C:ASP557 4.9 50.0 1.0 N C:ASP559 4.9 41.7 1.0 C3' F:DT11 4.9 50.6 1.0 CA C:ASP559 5.0 39.6 1.0

Magnesium binding site 3 out of 4 in the Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:40.3 occ:1.00 OD2 D:ASP557 2.2 60.5 1.0 CG D:ASP557 2.9 65.9 1.0 OD1 D:ASP557 3.0 65.7 1.0 CB D:ALA419 3.6 44.9 1.0 N D:LEU629 3.8 46.6 1.0 OH A:TYR117 4.1 47.9 1.0 OP1 E:DA11 4.1 57.1 1.0 CA D:GLY628 4.3 39.2 1.0 CB D:ASP557 4.4 56.8 1.0 C5' E:DA11 4.4 53.0 1.0 CB D:LEU629 4.4 37.8 1.0 CZ A:TYR117 4.5 40.0 1.0 C D:GLY628 4.6 38.1 1.0 CA D:LEU629 4.6 44.6 1.0 CA D:ALA419 4.7 44.0 1.0 N D:GLY630 4.7 43.5 1.0 CE1 A:TYR117 4.7 34.3 1.0 N D:GLY416 4.7 49.9 1.0 N D:ALA419 4.7 46.0 1.0 CB D:GLU415 4.9 54.9 1.0

Magnesium binding site 4 out of 4 in the Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:35.0 occ:1.00 OE1 D:GLU415 2.5 61.1 1.0 OD1 D:ASP559 3.4 58.1 1.0 OD2 D:ASP559 3.5 50.3 1.0 CD D:GLU415 3.6 67.3 1.0 CG D:ASP559 3.8 55.4 1.0 N D:GLY562 3.8 42.0 1.0 OD2 D:ASP557 3.8 60.5 1.0 CA D:GLY562 3.8 40.7 1.0 O3' E:DT10 3.9 50.1 1.0 OE2 D:GLU415 4.1 72.3 1.0 CB D:ASP557 4.1 56.8 1.0 C4' E:DT10 4.2 53.6 1.0 CG D:ASP557 4.3 65.9 1.0 CD1 D:ILE566 4.6 45.0 1.0 CB D:ASP561 4.6 51.0 1.0 C D:ASP561 4.6 49.8 1.0 C3' E:DT10 4.6 51.3 1.0 O D:ASP557 4.7 62.0 1.0 OP1 E:DA11 4.7 57.1 1.0 N D:ASP557 4.7 51.3 1.0 CG D:GLU415 4.8 59.8 1.0 CB D:GLU415 4.9 54.9 1.0 CA D:ASP557 4.9 55.2 1.0 C5' E:DT10 4.9 48.7 1.0 C2' E:DT10 5.0 48.3 1.0

Y.T.Chen, Y.H.Xin, R.Q.Xian. Structure of Phage T4 Topoisomerase II Central Domain Bound with Dna To Be Published.