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Magnesium in PDB 5gwk: Human Topoisomerase Iialpha in Complex with Dna and Etoposide

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

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

Protein crystallography data

The structure of Human Topoisomerase Iialpha in Complex with Dna and Etoposide, PDB code: 5gwk was solved by 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) 27.49 / 3.15
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.113, 126.155, 198.856, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Topoisomerase Iialpha in Complex with Dna and Etoposide (pdb code 5gwk). 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 Iialpha in Complex with Dna and Etoposide, PDB code: 5gwk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5gwk

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Magnesium binding site 1 out of 6 in the Human Topoisomerase Iialpha 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 Iialpha in Complex with Dna and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:76.4
occ:1.00
 OD2 A:ASP543 2.2 97.2 1.0
OD2 A:ASP541 2.2 0.3 1.0
CG A:ASP541 3.3 0.5 1.0
CG A:ASP543 3.3 96.5 1.0
O3' C:DC8 3.7 92.6 1.0
OD1 A:ASP543 3.7 94.9 1.0
CB A:ASP541 3.8 0.0 1.0
OE2 A:GLU461 3.9 0.8 1.0
C5' C:DC8 4.0 78.0 1.0
OP1 C:DC8 4.2 84.6 1.0
O A:LYS614 4.4 0.1 1.0
OD1 A:ASP541 4.4 0.5 1.0
C4' C:DC8 4.4 83.3 1.0
CB A:ASP543 4.6 0.2 1.0
C3' C:DC8 4.6 85.9 1.0
CD A:GLU461 4.6 0.9 1.0
O5' C:DC8 4.8 61.8 1.0
OE1 A:GLU461 4.8 0.9 1.0

Magnesium binding site 2 out of 6 in 5gwk

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Magnesium binding site 2 out of 6 in the Human Topoisomerase Iialpha 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 Iialpha in Complex with Dna and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:84.9
occ:1.00
 O A:ASN851 3.6 73.2 1.0
NH2 A:ARG929 3.6 0.6 1.0
OE2 A:GLU854 3.7 0.9 1.0
OP1 C:DG5 3.8 90.3 1.0
OD1 A:ASN779 3.9 94.4 1.0
O A:SER778 4.4 84.0 1.0
CD A:GLU854 4.6 0.5 1.0
OD1 A:ASN770 4.7 0.1 1.0
C A:ASN851 4.9 73.2 1.0
C A:SER778 4.9 71.5 1.0
CZ A:ARG929 4.9 0.9 1.0

Magnesium binding site 3 out of 6 in 5gwk

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Magnesium binding site 3 out of 6 in the Human Topoisomerase Iialpha 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 Iialpha in Complex with Dna and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:83.1
occ:1.00
 OD2 B:ASP543 2.2 0.6 1.0
OD2 B:ASP541 2.2 0.0 1.0
CG B:ASP541 3.3 0.0 1.0
CG B:ASP543 3.3 96.8 1.0
CB B:ASP541 3.7 0.5 1.0
OD1 B:ASP543 3.8 99.6 1.0
OE2 B:GLU461 3.8 0.8 1.0
OP1 E:DC8 4.2 94.8 1.0
O3' E:DC8 4.2 0.7 1.0
C5' E:DC8 4.3 0.6 1.0
O B:LYS614 4.4 0.9 1.0
OD1 B:ASP541 4.4 0.7 1.0
CD B:GLU461 4.5 0.3 1.0
CB B:ASP543 4.6 0.2 1.0
OE1 B:GLU461 4.7 0.7 1.0
C4' E:DC8 4.9 96.0 1.0

Magnesium binding site 4 out of 6 in 5gwk

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Magnesium binding site 4 out of 6 in the Human Topoisomerase Iialpha 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 Iialpha in Complex with Dna and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1302

b:84.2
occ:1.00
 O B:ASN851 3.4 88.8 1.0
NH2 B:ARG929 3.6 0.9 1.0
OD1 B:ASN779 3.7 0.2 1.0
O B:SER778 3.9 83.3 1.0
OP1 E:DG5 4.0 88.5 1.0
OE2 B:GLU854 4.1 0.5 1.0
C B:SER778 4.4 68.7 1.0
C B:ASN851 4.7 81.3 1.0
CA B:SER778 4.8 69.5 1.0
CG B:ASN779 4.9 82.0 1.0
OD1 B:ASN770 4.9 94.6 1.0
CZ B:ARG929 4.9 0.5 1.0
CD B:GLU854 4.9 0.1 1.0

Magnesium binding site 5 out of 6 in 5gwk

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Magnesium binding site 5 out of 6 in the Human Topoisomerase Iialpha 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 Iialpha in Complex with Dna and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:80.5
occ:1.00
 O6 D:DG17 3.7 0.6 1.0
N7 D:DG17 3.9 0.9 1.0
CE B:LYS655 4.3 0.3 1.0
NZ B:LYS655 4.4 0.1 1.0
C6 D:DG17 4.4 0.5 1.0
O6 D:DG18 4.5 1.0 1.0
C5 D:DC16 4.5 0.1 1.0
C5 D:DG17 4.5 0.6 1.0
C8 D:DG17 4.9 0.7 1.0
C6 D:DC16 5.0 0.7 1.0

Magnesium binding site 6 out of 6 in 5gwk

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Magnesium binding site 6 out of 6 in the Human Topoisomerase Iialpha 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 Iialpha in Complex with Dna and Etoposide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:86.0
occ:1.00
 O6 F:DG17 3.6 0.8 1.0
O6 F:DG18 3.9 0.5 1.0
N7 F:DG17 4.2 0.1 1.0
C6 F:DG17 4.4 0.3 1.0
C5 F:DG17 4.6 0.1 1.0
N4 C:DC3 4.7 1.0 1.0

Reference:

Y.R.Wang, S.F.Chen, C.C.Wu, Y.W.Liao, T.S.Lin, K.T.Liu, Y.S.Chen, T.K.Li, T.C.Chien, N.L.Chan. Producing Irreversible Topoisomerase II-Mediated Dna Breaks By Site-Specific Pt(II)-Methionine Coordination Chemistry Nucleic Acids Res. V. 45 10861 2017.
ISSN: ESSN 1362-4962
PubMed: 28977631
DOI: 10.1093/NAR/GKX742
Page generated: Mon Dec 14 20:25:41 2020

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