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Iodine 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:

Magnesium (Mg) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 6 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 5zrf

Go back to Iodine Binding Sites List in 5zrf
Iodine 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 Iodine with other atoms in the I 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
D:I9

b:85.6
occ:1.00
 I5 D:IU9 0.0 85.6 1.0
C5 D:IU9 2.1 46.0 1.0
C6 D:IU9 3.1 39.3 1.0
C4 D:IU9 3.2 36.8 1.0
O4 D:IU9 3.3 37.0 1.0
O F:HOH1417 3.8 48.1 1.0
CZ B:ARG820 4.0 82.2 1.0
O B:HOH1631 4.0 60.1 1.0
NH2 B:ARG820 4.1 83.0 1.0
NE B:ARG820 4.1 77.6 1.0
C24 F:EVP1301 4.1 41.3 1.0
NH1 B:ARG820 4.3 82.6 1.0
CB A:GLN778 4.4 39.6 1.0
N1 D:IU9 4.5 43.7 1.0
N3 D:IU9 4.5 43.5 1.0
CD B:ARG820 4.7 71.4 1.0
O6 D:DG10 4.7 42.1 1.0
O10 F:EVP1301 4.8 40.5 1.0
OP2 D:IU9 4.9 69.8 1.0

Iodine binding site 2 out of 6 in 5zrf

Go back to Iodine Binding Sites List in 5zrf
Iodine 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 Iodine with other atoms in the I 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
D:I15

b:55.5
occ:1.00
 I5 D:IU15 0.0 55.5 1.0
C5 D:IU15 2.1 38.8 1.0
O D:HOH513 2.9 27.9 1.0
C6 D:IU15 3.1 31.5 1.0
C4 D:IU15 3.2 30.6 1.0
O4 D:IU15 3.3 28.6 1.0
O D:HOH506 3.4 35.8 1.0
OP2 D:IU15 3.7 60.6 1.0
C6 D:DC14 3.8 31.8 1.0
C5 D:DC14 3.8 33.8 1.0
N1 D:DC14 4.0 33.1 1.0
N4 D:DC16 4.0 29.3 1.0
O E:HOH110 4.1 41.4 1.0
C4 D:DC14 4.1 30.4 1.0
C3' D:DC14 4.2 32.6 1.0
C2' D:DC14 4.2 30.3 1.0
C2 D:DC14 4.3 32.7 1.0
N3 D:DC14 4.3 31.5 1.0
N1 D:IU15 4.5 33.6 1.0
N3 D:IU15 4.5 34.1 1.0
C1' D:DC14 4.6 33.1 1.0
P D:IU15 4.7 49.2 1.0
N4 D:DC14 4.8 28.6 1.0
O5' D:IU15 4.8 40.1 1.0
O2 D:DC14 4.9 31.9 1.0
C4 D:DC16 4.9 34.5 1.0
O3' D:DC14 5.0 42.3 1.0
O5' D:DC14 5.0 42.6 1.0

Iodine binding site 3 out of 6 in 5zrf

Go back to Iodine Binding Sites List in 5zrf
Iodine 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 Iodine with other atoms in the I 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
D:I20

b:82.9
occ:1.00
 I5 D:IU20 0.0 82.9 1.0
C5 D:IU20 2.1 30.9 1.0
C4 D:IU20 3.2 45.3 1.0
C6 D:IU20 3.2 33.9 1.0
O4 D:IU20 3.3 55.7 1.0
C6 D:DC19 4.2 43.5 1.0
C5 D:DC19 4.3 37.6 1.0
N3 D:IU20 4.6 33.1 1.0
N1 D:IU20 4.6 33.8 1.0
O D:HOH501 4.6 51.2 1.0
C2' D:DC19 4.7 62.5 1.0
N1 D:DC19 4.9 47.0 1.0

Iodine binding site 4 out of 6 in 5zrf

Go back to Iodine Binding Sites List in 5zrf
Iodine 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 Iodine with other atoms in the I 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
F:I9

b:86.8
occ:1.00
 I5 F:IU9 0.0 86.8 1.0
C5 F:IU9 2.1 39.6 1.0
C6 F:IU9 3.1 34.8 1.0
C4 F:IU9 3.2 32.0 1.0
O4 F:IU9 3.3 33.4 1.0
CB B:GLN778 4.3 41.3 1.0
C24 D:EVP101 4.3 39.6 1.0
N1 F:IU9 4.5 36.8 1.0
N3 F:IU9 4.5 33.4 1.0
CG B:GLN778 4.7 47.8 1.0
O6 F:DG10 4.7 41.2 1.0
CD A:ARG820 4.8 64.2 1.0
O10 D:EVP101 4.9 41.3 1.0
OP2 F:IU9 5.0 52.9 1.0

Iodine binding site 5 out of 6 in 5zrf

Go back to Iodine Binding Sites List in 5zrf
Iodine 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 Iodine with other atoms in the I 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
F:I15

b:52.8
occ:1.00
 I5 F:IU15 0.0 52.8 1.0
C5 F:IU15 2.1 34.9 1.0
O F:HOH1419 2.9 32.3 1.0
C4 F:IU15 3.1 33.2 1.0
C6 F:IU15 3.1 36.6 1.0
O4 F:IU15 3.3 32.9 1.0
O F:HOH1406 3.4 41.7 1.0
OP2 F:IU15 3.6 41.4 1.0
C6 F:DC14 3.7 36.8 1.0
C5 F:DC14 3.7 41.3 1.0
O F:HOH1421 3.8 51.1 1.0
N4 F:DC16 4.0 34.0 1.0
N1 F:DC14 4.0 38.7 1.0
O C:HOH118 4.0 42.0 1.0
C4 F:DC14 4.0 38.9 1.0
C3' F:DC14 4.2 38.8 1.0
C2' F:DC14 4.3 35.3 1.0
C2 F:DC14 4.3 36.3 1.0
N3 F:DC14 4.3 34.9 1.0
N3 F:IU15 4.5 33.1 1.0
N1 F:IU15 4.5 38.4 1.0
N4 F:DC14 4.7 36.2 1.0
C1' F:DC14 4.7 38.9 1.0
P F:IU15 4.7 36.6 1.0
O5' F:IU15 4.8 39.4 1.0
C4 F:DC16 4.9 36.5 1.0
O3' F:DC14 5.0 36.9 1.0

Iodine binding site 6 out of 6 in 5zrf

Go back to Iodine Binding Sites List in 5zrf
Iodine 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 Iodine with other atoms in the I 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:I20

b:0.2
occ:1.00
 I5 F:IU20 0.0 0.2 1.0
C5 F:IU20 2.1 61.8 1.0
C6 F:IU20 3.1 63.5 1.0
C4 F:IU20 3.2 59.7 1.0
O4 F:IU20 3.4 62.2 1.0
C2' F:DC19 3.8 73.3 1.0
C6 F:DC19 4.0 53.2 1.0
N1 F:DC19 4.3 57.7 1.0
C5 F:DC19 4.3 50.1 1.0
N1 F:IU20 4.5 65.3 1.0
N3 F:IU20 4.6 56.0 1.0
C1' F:DC19 4.6 66.5 1.0
C3' F:DC19 4.8 81.3 1.0
C2 F:DC19 4.9 51.7 1.0
C4 F:DC19 4.9 51.9 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: Fri Aug 8 20:52:26 2025

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