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Magnesium in PDB 4j3n: Human Topoisomerase Iibeta in Complex with Dna

Enzymatic activity of Human Topoisomerase Iibeta in Complex with Dna

All present enzymatic activity of Human Topoisomerase Iibeta in Complex with Dna:
5.99.1.3;

Protein crystallography data

The structure of Human Topoisomerase Iibeta in Complex with Dna, PDB code: 4j3n was solved by C.C.Wu, T.K.Li, Y.C.Li, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.31 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.953, 176.368, 94.225, 90.00, 112.06, 90.00
R / Rfree (%) 17.6 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Topoisomerase Iibeta in Complex with Dna (pdb code 4j3n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Human Topoisomerase Iibeta in Complex with Dna, PDB code: 4j3n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4j3n

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Magnesium binding site 1 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:46.4
occ:1.00
 O A:HOH1401 2.1 39.0 1.0
O A:HOH1615 2.1 46.0 1.0
O A:HOH1614 2.2 42.0 1.0
OD2 A:ASP557 2.2 45.6 1.0
O C:HOH103 2.2 37.4 1.0
OD2 A:ASP559 2.2 36.5 1.0
CG A:ASP559 3.1 38.8 1.0
CG A:ASP557 3.2 49.0 1.0
OD1 A:ASP559 3.4 38.1 1.0
CB A:ASP557 3.5 44.1 1.0
O A:HOH1443 4.1 38.5 1.0
OP1 C:DC8 4.2 41.0 1.0
OE2 A:GLU477 4.2 52.5 1.0
OD1 A:ASP557 4.3 48.8 1.0
C5' C:DC8 4.5 37.2 1.0
CB A:ASP559 4.5 36.5 1.0
O3' C:DC8 4.6 50.6 1.0
OE1 A:GLU477 4.8 49.1 1.0
CD A:GLU477 4.9 47.3 1.0

Magnesium binding site 2 out of 7 in 4j3n

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Magnesium binding site 2 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:67.1
occ:1.00
 O C:HOH123 2.0 54.4 1.0
O A:HOH1624 2.0 46.8 1.0
O C:HOH122 2.1 54.3 1.0
O A:ASN867 3.0 40.2 1.0
O A:GLY868 3.5 54.6 1.0
OE2 A:GLU870 3.9 56.4 1.0
OP1 C:DG5 4.1 49.7 1.0
O A:HOH1625 4.2 45.8 1.0
C A:ASN867 4.2 33.5 1.0
O A:SER794 4.3 29.3 1.0
C A:GLY868 4.3 39.0 1.0
OD1 A:ASN795 4.4 26.1 1.0
NH2 A:ARG945 4.6 58.4 1.0
O A:HOH1623 4.6 47.6 1.0
C A:SER794 4.7 29.2 1.0
CA A:GLY868 4.8 40.2 1.0
O A:HOH1464 4.8 34.9 1.0
ND2 A:ASN882 4.9 22.5 1.0
O C:HOH111 5.0 45.5 1.0
N A:GLY868 5.0 38.2 1.0

Magnesium binding site 3 out of 7 in 4j3n

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Magnesium binding site 3 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:56.7
occ:1.00
 O F:HOH213 2.6 50.3 1.0
OD2 A:ASP726 3.0 37.0 1.0
O A:HOH1430 3.0 41.2 1.0
O4' F:DC16 3.0 35.5 1.0
CG A:ASP726 3.4 38.7 1.0
OD1 A:ASP726 3.5 35.9 1.0
CZ A:PHE722 3.6 38.4 1.0
C4' F:DC16 3.6 39.2 1.0
O2 F:DC16 3.8 34.1 1.0
O2 F:DT15 3.9 39.4 1.0
C5' F:DC16 3.9 38.2 1.0
C1' F:DC16 3.9 37.8 1.0
CE2 A:PHE722 4.0 31.6 1.0
OG1 A:THR874 4.3 36.7 1.0
CE1 A:HIS564 4.3 31.7 1.0
C1' F:DT15 4.4 36.6 1.0
C2 F:DC16 4.5 36.3 1.0
N1 F:DC16 4.6 33.8 1.0
O3' F:DT15 4.6 40.4 1.0
CB A:ASP726 4.6 33.4 1.0
O A:GLY873 4.6 34.2 1.0
O A:HOH1423 4.7 36.6 1.0
CE1 A:PHE722 4.7 33.6 1.0
C2 F:DT15 4.8 39.3 1.0
O5' F:DC16 4.8 38.9 1.0
C2' F:DT15 4.8 35.8 1.0
ND1 A:HIS564 4.9 33.7 1.0
O C:HOH104 4.9 42.6 1.0
NE2 A:HIS564 4.9 34.5 1.0

Magnesium binding site 4 out of 7 in 4j3n

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Magnesium binding site 4 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:38.3
occ:1.00
 O B:HOH1672 2.0 41.5 1.0
O B:HOH1402 2.0 26.6 1.0
O B:HOH1516 2.1 38.7 1.0
OD2 B:ASP559 2.1 30.1 1.0
OD2 B:ASP557 2.2 40.2 1.0
O B:HOH1434 2.2 32.4 1.0
CG B:ASP559 3.1 33.4 1.0
CG B:ASP557 3.3 48.5 1.0
OD1 B:ASP559 3.5 31.7 1.0
CB B:ASP557 3.7 35.8 1.0
OE2 B:GLU477 4.0 38.7 1.0
O E:HOH126 4.2 49.9 1.0
OP1 E:DC8 4.3 35.1 1.0
O B:HOH1407 4.3 33.7 1.0
OD1 B:ASP557 4.4 47.9 1.0
CB B:ASP559 4.5 32.9 1.0
C5' E:DC8 4.5 27.9 1.0
O3' E:DC8 4.7 41.1 1.0
CD B:GLU477 4.7 40.4 1.0
OE1 B:GLU477 4.7 37.7 1.0

Magnesium binding site 5 out of 7 in 4j3n

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Magnesium binding site 5 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:61.3
occ:1.00
 O B:HOH1679 2.0 43.1 1.0
O E:HOH125 2.0 43.9 1.0
O B:HOH1680 2.0 44.9 1.0
O E:HOH124 2.0 47.3 1.0
O B:ASN867 3.1 41.1 1.0
O B:HOH1485 3.6 43.4 1.0
OD1 B:ASN795 3.6 29.4 1.0
O B:HOH1708 3.9 49.5 1.0
O B:HOH1430 4.0 34.6 1.0
O B:HOH1709 4.0 46.0 1.0
OD1 B:ASN786 4.1 44.9 1.0
O B:SER794 4.1 32.1 1.0
OP1 E:DG5 4.2 57.2 1.0
O B:GLY868 4.3 46.9 1.0
C B:ASN867 4.4 38.4 1.0
C B:SER794 4.4 30.3 1.0
CG B:ASN795 4.5 32.0 1.0
O E:HOH115 4.5 48.4 1.0
N B:ASN795 4.8 28.2 1.0
CA B:SER794 4.9 32.3 1.0
CB B:ASN867 4.9 32.6 1.0

Magnesium binding site 6 out of 7 in 4j3n

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Magnesium binding site 6 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:55.7
occ:1.00
 O B:HOH1740 1.8 47.9 1.0
O D:HOH203 1.8 38.2 1.0
O D:HOH202 2.2 42.6 1.0
O B:HOH1612 2.2 54.1 1.0
O D:HOH208 2.2 40.0 1.0
O6 D:DG18 4.0 30.4 1.0
N4 E:DC3 4.2 34.6 1.0
O D:HOH222 4.2 49.8 1.0
O6 D:DG17 4.2 30.6 1.0
O6 E:DG2 4.3 43.8 1.0
N7 D:DG17 4.3 31.7 1.0
O D:HOH214 4.5 42.9 1.0
CE B:LYS671 4.6 63.1 1.0
O D:HOH226 4.6 47.8 1.0
O D:HOH227 4.9 57.1 1.0
C6 D:DG17 4.9 29.7 1.0
C5 D:DG17 4.9 30.9 1.0
N7 E:DG2 4.9 51.8 1.0
NZ B:LYS671 4.9 62.4 1.0
C6 E:DG2 5.0 44.1 1.0

Magnesium binding site 7 out of 7 in 4j3n

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Magnesium binding site 7 out of 7 in the Human Topoisomerase Iibeta in Complex with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Topoisomerase Iibeta in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:62.6
occ:1.00
 O A:HOH1626 2.0 57.2 1.0
O F:HOH214 2.0 52.0 1.0
O F:HOH216 2.0 49.3 1.0
O F:HOH215 2.1 48.1 1.0
O A:HOH1627 2.1 57.4 1.0
O6 F:DG18 4.2 37.0 1.0
NZ A:LYS671 4.3 65.3 0.5
O F:HOH217 4.4 46.0 1.0
N7 F:DG17 4.5 34.7 1.0
O6 F:DG17 4.5 40.3 1.0
N4 C:DC3 4.5 44.9 1.0
O6 C:DG2 4.6 55.5 1.0
O F:HOH203 4.7 44.1 1.0
CE A:LYS671 4.7 58.5 0.5

Reference:

C.C.Wu, Y.C.Li, Y.R.Wang, T.K.Li, N.L.Chan. On the Structural Basis and Design Guidelines For Type II Topoisomerase-Targeting Anticancer Drugs Nucleic Acids Res. V. 41 10630 2013.
ISSN: ISSN 0305-1048
PubMed: 24038465
DOI: 10.1093/NAR/GKT828
Page generated: Fri Aug 16 17:08:44 2024

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