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Magnesium in PDB 5zrf: Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21

Enzymatic activity of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21

All present enzymatic activity of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21, PDB code: 5zrf was solved by S.F.Chen, Y.R.Wang, C.C.Wu, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.147, 176.270, 94.331, 90.00, 111.44, 90.00
R / Rfree (%) 18.9 / 22.7

Other elements in 5zrf:

The structure of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 also contains other interesting chemical elements:

Iodine (I) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 (pdb code 5zrf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21, PDB code: 5zrf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5zrf

Go back to Magnesium Binding Sites List in 5zrf
Magnesium binding site 1 out of 6 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:27.9
occ:1.00
 O A:HOH1496 2.0 33.0 1.0
OD2 A:ASP559 2.1 36.0 1.0
O A:HOH1577 2.1 40.7 1.0
O A:HOH1462 2.2 30.8 1.0
OD1 A:ASP557 2.2 29.7 1.0
O C:HOH102 2.2 37.2 1.0
CG A:ASP559 3.1 39.5 1.0
CG A:ASP557 3.2 37.8 1.0
OD1 A:ASP559 3.5 38.8 1.0
CB A:ASP557 3.6 36.2 1.0
OE1 A:GLU477 4.3 44.1 1.0
OP1 C:DC8 4.3 36.1 1.0
OD2 A:ASP557 4.4 36.9 1.0
CB A:ASP559 4.4 35.5 1.0
O A:HOH1427 4.5 33.6 1.0
O3' C:DC8 4.7 47.2 1.0
C5' C:DC8 4.8 31.3 1.0
O A:HOH1602 4.8 50.8 1.0
CD A:GLU477 5.0 44.1 1.0

Magnesium binding site 2 out of 6 in 5zrf

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:73.0
occ:1.00
 O A:ASN867 2.9 39.4 1.0
O A:GLY868 3.1 52.9 1.0
O A:HOH1415 3.1 40.7 1.0
O C:HOH114 3.4 49.5 1.0
C A:GLY868 3.9 47.1 1.0
OP1 C:DG5 4.1 46.8 1.0
C A:ASN867 4.1 40.3 1.0
O A:SER794 4.1 42.7 1.0
CA A:GLY868 4.4 43.6 1.0
O A:HOH1408 4.6 44.6 1.0
OD1 A:ASN795 4.6 31.6 1.0
O C:HOH108 4.7 41.9 1.0
N A:GLY868 4.8 44.4 1.0
O A:HOH1557 4.8 35.0 1.0
OD1 A:ASN882 4.8 34.3 1.0
N A:ALA869 4.9 43.9 1.0
C A:SER794 4.9 35.4 1.0

Magnesium binding site 3 out of 6 in 5zrf

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Magnesium binding site 3 out of 6 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:64.7
occ:1.00
 O B:HOH1557 2.2 44.1 1.0
O E:HOH101 2.2 54.9 1.0
O B:ASN867 2.6 43.0 1.0
O B:GLY868 3.4 55.9 1.0
O B:HOH1549 3.4 44.3 1.0
C B:ASN867 3.8 43.4 1.0
O B:SER794 4.0 37.5 1.0
OD1 B:ASN795 4.0 33.2 1.0
C B:GLY868 4.1 52.3 1.0
OP1 E:DG5 4.2 50.0 1.0
CA B:GLY868 4.5 54.5 1.0
O E:HOH108 4.6 35.5 1.0
N B:GLY868 4.7 47.7 1.0
C B:SER794 4.7 32.6 1.0
CB B:ASN867 4.7 34.7 1.0
CA B:ASN867 4.8 35.7 1.0
O B:HOH1536 4.9 41.1 1.0
O B:HOH1530 4.9 41.4 1.0
OE2 B:GLU870 4.9 54.6 1.0
OD1 B:ASN882 5.0 36.9 1.0
CG B:ASN795 5.0 35.3 1.0
OD1 B:ASN786 5.0 41.8 1.0

Magnesium binding site 4 out of 6 in 5zrf

Go back to Magnesium Binding Sites List in 5zrf
Magnesium binding site 4 out of 6 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:36.4
occ:1.00
 O B:HOH1531 2.0 38.1 1.0
OD2 B:ASP559 2.1 32.9 1.0
OD2 B:ASP557 2.1 44.1 1.0
O E:HOH114 2.1 37.8 1.0
O B:HOH1424 2.2 34.7 1.0
O E:HOH104 2.3 34.9 1.0
CG B:ASP559 3.1 33.6 1.0
CG B:ASP557 3.2 44.5 1.0
OD1 B:ASP559 3.4 31.2 1.0
CB B:ASP557 3.5 38.2 1.0
OE1 B:GLU477 4.1 33.2 1.0
O B:HOH1456 4.3 38.3 1.0
OP1 E:DC8 4.3 32.7 1.0
OD1 B:ASP557 4.3 43.4 1.0
O3' E:DC8 4.4 50.2 1.0
CB B:ASP559 4.4 35.2 1.0
C5' E:DC8 4.6 29.9 1.0
CD B:GLU477 4.7 36.3 1.0
OE2 B:GLU477 4.8 43.9 1.0

Magnesium binding site 5 out of 6 in 5zrf

Go back to Magnesium Binding Sites List in 5zrf
Magnesium binding site 5 out of 6 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:63.0
occ:1.00
 O D:HOH507 2.3 38.2 1.0
O D:HOH509 4.0 48.3 1.0
O6 D:DG18 4.2 42.7 1.0
N7 D:DG17 4.4 35.0 1.0
O6 D:DG17 4.6 33.9 1.0
O6 E:DG2 4.8 45.9 1.0
N4 E:DC3 4.8 34.7 1.0

Magnesium binding site 6 out of 6 in 5zrf

Go back to Magnesium Binding Sites List in 5zrf
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna and Etoposide in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1302

b:54.1
occ:1.00
 O A:HOH1604 2.1 37.0 1.0
O F:HOH1402 2.1 48.5 1.0
O F:HOH1409 2.2 38.1 1.0
O F:HOH1415 2.3 43.7 1.0
O6 F:DG18 4.4 39.3 1.0
N7 F:DG17 4.6 35.8 1.0
O6 F:DG17 4.7 38.2 1.0
CE A:LYS671 4.8 69.1 1.0
N4 C:DC3 4.9 38.7 1.0
O6 C:DG2 5.0 46.1 1.0

Reference:

S.F.Chen, N.L.Huang, J.H.Lin, C.C.Wu, Y.R.Wang, Y.J.Yu, M.K.Gilson, N.L.Chan. Structural Insights Into the Gating of Dna Passage By the Topoisomerase II Dna-Gate. Nat Commun V. 9 3085 2018.
ISSN: ESSN 2041-1723
PubMed: 30082834
DOI: 10.1038/S41467-018-05406-Y
Page generated: Mon Sep 30 18:43:16 2024

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