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Magnesium in PDB 3qx3: Human Topoisomerase Iibeta in Complex with Dna and Etoposide

Enzymatic activity of Human Topoisomerase Iibeta in Complex with Dna and Etoposide

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

Protein crystallography data

The structure of Human Topoisomerase Iibeta in Complex with Dna and Etoposide, PDB code: 3qx3 was solved by C.C.Wu, T.K.Li, L.Farh, L.Y.Lin, T.S.Lin, Y.J.Yu, T.J.Yen, C.W.Chiang, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.54 / 2.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.149, 176.801, 94.067, 90.00, 111.58, 90.00
R / Rfree (%) 16.8 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide (pdb code 3qx3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide, PDB code: 3qx3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3qx3

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Magnesium binding site 1 out of 6 in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide


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 and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1222

b:31.1
occ:1.00
 O A:HOH1333 2.2 22.1 1.0
OD2 A:ASP559 2.2 25.0 1.0
OD2 A:ASP557 2.3 33.7 1.0
O C:HOH795 2.3 32.2 1.0
O A:HOH1348 2.3 41.2 1.0
O C:HOH633 2.4 28.8 1.0
CG A:ASP559 3.2 26.9 1.0
CG A:ASP557 3.3 40.4 1.0
CB A:ASP557 3.5 32.8 1.0
OD1 A:ASP559 3.5 25.0 1.0
O A:HOH1247 3.9 46.1 1.0
OE2 A:GLU477 4.1 35.2 1.0
O C:HOH402 4.2 40.5 1.0
OP1 C:DC8 4.3 26.2 1.0
OD1 A:ASP557 4.4 47.6 1.0
O A:HOH68 4.4 26.8 1.0
O3' C:DC8 4.5 36.2 1.0
C5' C:DC8 4.5 21.8 1.0
CB A:ASP559 4.6 26.3 1.0
OE1 A:GLU477 4.7 37.2 1.0
CD A:GLU477 4.8 38.7 1.0
O A:HOH1255 5.0 48.5 1.0

Magnesium binding site 2 out of 6 in 3qx3

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Magnesium binding site 2 out of 6 in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide


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 and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1223

b:46.0
occ:1.00
 O C:HOH1143 2.1 51.9 1.0
O A:HOH1467 2.2 31.1 1.0
O C:HOH1145 2.2 35.2 1.0
O A:HOH1466 2.5 38.8 1.0
O A:HOH1465 3.0 39.8 1.0
O A:GLY868 3.1 45.9 1.0
O A:ASN867 3.1 34.7 1.0
OE2 A:GLU870 3.6 54.0 1.0
OP1 C:DG5 3.9 42.1 1.0
C A:GLY868 4.0 30.7 1.0
C A:ASN867 4.3 29.6 1.0
NH2 A:ARG945 4.3 54.6 1.0
O A:HOH1242 4.4 43.1 1.0
CA A:GLY868 4.4 33.0 1.0
O A:HOH186 4.5 29.1 1.0
O A:HOH1319 4.6 38.6 1.0
CD A:GLU870 4.7 47.8 1.0
O A:SER794 4.8 21.5 1.0
O A:HOH257 4.9 30.4 1.0
N A:GLY868 4.9 29.0 1.0
ND2 A:ASN882 4.9 15.6 1.0
CB A:GLU870 4.9 37.6 1.0
O A:HOH1427 4.9 36.0 1.0

Magnesium binding site 3 out of 6 in 3qx3

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Magnesium binding site 3 out of 6 in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide


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 and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:30.9
occ:1.00
 OD2 B:ASP559 2.1 28.9 1.0
O B:HOH46 2.2 22.8 1.0
O B:HOH1250 2.3 28.5 1.0
OD2 B:ASP557 2.3 36.1 1.0
O B:HOH1291 2.3 30.6 1.0
O E:HOH64 2.4 22.0 1.0
CG B:ASP559 3.1 30.8 1.0
CG B:ASP557 3.3 45.1 1.0
OD1 B:ASP559 3.5 24.9 1.0
CB B:ASP557 3.5 25.6 1.0
OE2 B:GLU477 4.1 24.6 1.0
O B:HOH1347 4.2 52.6 1.0
O B:HOH80 4.3 29.0 1.0
OP1 E:DC8 4.3 25.2 1.0
OD1 B:ASP557 4.4 44.4 1.0
CB B:ASP559 4.4 26.0 1.0
O E:HOH682 4.5 38.4 1.0
C5' E:DC8 4.6 20.2 1.0
O3' E:DC8 4.7 35.8 1.0
CD B:GLU477 4.8 27.5 1.0
OE1 B:GLU477 4.8 26.2 1.0

Magnesium binding site 4 out of 6 in 3qx3

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Magnesium binding site 4 out of 6 in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide


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 and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1222

b:49.0
occ:1.00
 O B:HOH1470 1.9 41.9 1.0
O E:HOH1150 2.0 37.9 1.0
O E:HOH1148 2.2 38.5 1.0
O B:ASN867 3.1 28.0 1.0
OD1 B:ASN795 3.7 19.8 1.0
O B:HOH355 3.8 42.6 1.0
O B:HOH1329 3.8 37.0 1.0
O B:GLY868 4.2 40.9 1.0
OP1 E:DG5 4.2 37.4 1.0
O B:HOH41 4.2 26.1 1.0
O B:SER794 4.3 20.5 1.0
C B:ASN867 4.3 25.6 1.0
OD1 B:ASN786 4.4 33.8 1.0
O E:HOH138 4.5 30.9 1.0
C B:SER794 4.5 20.7 1.0
CG B:ASN795 4.6 23.5 1.0
CB B:ASN867 4.8 23.9 1.0
ND2 B:ASN786 4.9 23.7 1.0
C B:GLY868 4.9 36.6 1.0
N B:ASN795 5.0 18.4 1.0

Magnesium binding site 5 out of 6 in 3qx3

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Magnesium binding site 5 out of 6 in the Human Topoisomerase Iibeta in Complex with Dna and Etoposide


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 and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg21

b:45.0
occ:1.00
 O D:HOH553 2.1 36.1 1.0
O D:HOH768 2.2 41.1 1.0
O D:HOH765 2.4 32.4 1.0
O D:HOH766 2.4 47.0 1.0
O D:HOH767 2.4 32.3 1.0
O E:HOH1224 2.5 51.8 1.0
N7 D:DG17 4.0 20.6 1.0
O D:HOH799 4.0 41.9 1.0
O E:HOH1273 4.1 46.7 1.0
O6 D:DG17 4.2 24.8 1.0
O6 D:DG18 4.3 22.7 1.0
CE B:LYS671 4.3 61.0 1.0
O D:HOH802 4.3 38.8 1.0
O D:HOH499 4.3 36.5 1.0
N4 E:DC3 4.6 22.9 1.0
C5 D:DG17 4.7 19.6 1.0
C5 D:DC16 4.8 18.7 1.0
C6 D:DG17 4.8 18.8 1.0
O D:HOH476 4.9 40.8 1.0
O6 E:DG2 4.9 28.7 1.0
C8 D:DG17 5.0 17.9 1.0

Magnesium binding site 6 out of 6 in 3qx3

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


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 and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1

b:50.4
occ:1.00
 O F:HOH871 1.6 43.2 1.0
O F:HOH1123 2.0 53.8 1.0
O F:HOH763 2.2 37.7 1.0
O F:HOH764 2.3 42.5 1.0
O F:HOH866 2.4 36.8 1.0
O F:HOH877 4.0 46.0 1.0
N7 F:DG17 4.3 24.4 1.0
O F:HOH597 4.3 37.1 1.0
O F:HOH715 4.4 46.3 1.0
O6 F:DG18 4.5 23.2 1.0
O6 F:DG17 4.6 28.1 1.0
O F:HOH870 4.7 35.4 1.0
O C:HOH829 4.8 49.6 1.0
NZ A:LYS671 4.8 55.2 1.0
CE A:LYS671 4.8 56.2 1.0
O F:HOH734 4.9 46.8 1.0
O A:HOH1462 5.0 44.3 1.0
N4 C:DC3 5.0 29.3 1.0
C5 F:DC16 5.0 21.9 1.0

Reference:

C.C.Wu, T.K.Li, L.Farh, L.Y.Lin, T.S.Lin, Y.J.Yu, T.J.Yen, C.W.Chiang, N.L.Chan. Structural Basis of Type II Topoisomerase Inhibition By the Anticancer Drug Etoposide Science V. 333 459 2011.
ISSN: ISSN 0036-8075
PubMed: 21778401
DOI: 10.1126/SCIENCE.1204117
Page generated: Thu Aug 15 10:12:11 2024

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