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Magnesium in PDB 5gwj: Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

Enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

All present enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S:
5.99.1.3;

Protein crystallography data

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S, PDB code: 5gwj was solved by Y.R.Wang, S.F.Chen, 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) 29.68 / 2.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.178, 176.990, 94.414, 90.00, 111.50, 90.00
R / Rfree (%) 18.3 / 22.6

Other elements in 5gwj:

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S also contains other interesting chemical elements:

Platinum (Pt) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S (pdb code 5gwj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S, PDB code: 5gwj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5gwj

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Magnesium binding site 1 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:47.3
occ:1.00
OD2 A:ASP559 2.4 39.2 1.0
OD2 A:ASP557 2.6 56.4 1.0
O C:HOH104 2.6 33.0 1.0
CG A:ASP559 3.5 43.0 1.0
CG A:ASP557 3.6 50.7 1.0
O C:HOH101 3.7 50.9 1.0
OD1 A:ASP559 3.8 43.5 1.0
CB A:ASP557 3.9 40.5 1.0
OE2 A:GLU477 4.0 55.4 1.0
OP1 C:DC8 4.1 32.2 1.0
O3' C:DC8 4.3 46.7 1.0
C5' C:DC8 4.4 29.5 1.0
O A:HOH1403 4.6 39.6 1.0
OD1 A:ASP557 4.7 68.5 1.0
CB A:ASP559 4.8 32.7 1.0
CD A:GLU477 4.8 54.5 1.0
OE1 A:GLU477 4.9 49.4 1.0

Magnesium binding site 2 out of 6 in 5gwj

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Magnesium binding site 2 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:59.7
occ:1.00
O A:ASN867 2.8 46.1 1.0
O A:GLY868 3.3 51.6 1.0
C A:ASN867 4.0 37.6 1.0
OD1 A:ASN795 4.0 37.7 1.0
OP1 C:DG5 4.1 65.4 1.0
O A:HOH1474 4.2 47.3 1.0
C A:GLY868 4.3 45.0 1.0
O A:SER794 4.4 38.4 1.0
NH2 A:ARG945 4.6 54.8 1.0
OD1 A:ASN786 4.7 54.8 1.0
CA A:GLY868 4.7 39.3 1.0
CB A:ASN867 4.8 22.6 1.0
C A:SER794 4.8 29.1 1.0
N A:GLY868 4.9 38.6 1.0
CA A:ASN867 5.0 30.9 1.0

Magnesium binding site 3 out of 6 in 5gwj

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Magnesium binding site 3 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:60.1
occ:1.00
O B:ASN867 3.1 43.1 1.0
O B:GLY868 3.6 51.9 1.0
OP1 E:DG5 3.8 58.5 1.0
NH2 B:ARG945 4.2 79.7 1.0
OD1 B:ASN795 4.2 34.0 1.0
C B:ASN867 4.3 39.3 1.0
ND2 B:ASN786 4.5 55.3 1.0
O B:SER794 4.5 35.4 1.0
C B:GLY868 4.5 41.8 1.0
OE2 B:GLU870 4.8 51.3 1.0
C B:SER794 4.9 23.1 1.0
OD1 B:ASN786 5.0 51.9 1.0
CA B:GLY868 5.0 43.6 1.0

Magnesium binding site 4 out of 6 in 5gwj

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Magnesium binding site 4 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:47.8
occ:1.00
OD2 B:ASP559 2.0 36.7 1.0
O B:HOH1521 2.4 36.5 1.0
OD1 B:ASP557 2.4 56.0 1.0
O B:HOH1482 2.6 35.5 1.0
CG B:ASP559 3.1 36.1 1.0
CG B:ASP557 3.4 49.9 1.0
OD1 B:ASP559 3.5 41.2 1.0
CB B:ASP557 3.5 33.0 1.0
OE2 B:GLU477 4.2 40.8 1.0
CB B:ASP559 4.4 34.4 1.0
O B:HOH1533 4.5 45.0 1.0
OD2 B:ASP557 4.5 72.5 1.0
OP1 E:DC8 4.5 34.3 1.0
O B:HOH1411 4.6 31.0 1.0
C5' E:DC8 4.8 19.1 1.0
O3' E:DC8 4.8 49.5 1.0
CD B:GLU477 4.9 42.3 1.0
OE1 B:GLU477 5.0 37.7 1.0

Magnesium binding site 5 out of 6 in 5gwj

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Magnesium binding site 5 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:57.6
occ:1.00
O D:HOH113 2.0 36.8 1.0
O D:HOH101 2.5 37.6 1.0
O6 E:DG2 4.1 38.1 1.0
O6 D:DG18 4.2 37.6 1.0
O D:HOH104 4.5 37.9 1.0
N4 E:DC3 4.7 27.1 1.0
O6 D:DG17 4.8 31.9 1.0
N7 E:DG2 4.9 48.0 1.0
C6 E:DG2 4.9 43.4 1.0
N7 D:DG17 4.9 30.5 1.0
O D:HOH108 4.9 41.7 1.0

Magnesium binding site 6 out of 6 in 5gwj

Go back to Magnesium Binding Sites List in 5gwj
Magnesium binding site 6 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:57.0
occ:1.00
O F:HOH206 2.4 57.1 1.0
O6 F:DG17 4.0 47.9 1.0
N7 F:DG17 4.1 31.2 1.0
C5 F:DC16 4.4 28.9 1.0
O6 F:DG18 4.5 35.3 1.0
C6 F:DG17 4.7 36.0 1.0
C5 F:DG17 4.8 36.6 1.0
N4 C:DC3 4.8 42.8 1.0
C6 F:DC16 5.0 32.6 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 20:25:37 2020

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