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Manganese in PDB 5zen: Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate

Enzymatic activity of Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate

All present enzymatic activity of Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate, PDB code: 5zen was solved by S.F.Chen, Y.R.Wang, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.760, 95.760, 231.055, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 26.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate (pdb code 5zen). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate, PDB code: 5zen:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5zen

Go back to Manganese Binding Sites List in 5zen
Manganese binding site 1 out of 2 in the Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1301

b:0.6
occ:1.00
 OD2 A:ASP559 2.2 61.6 1.0
OD2 A:ASP557 2.4 77.6 1.0
O A:HOH1403 3.1 0.3 1.0
CG A:ASP559 3.1 59.8 1.0
OD1 A:ASP559 3.4 56.6 1.0
CG A:ASP557 3.5 72.5 1.0
CB A:ASP557 3.8 68.2 1.0
OP1 B:DC8 4.1 54.2 1.0
OE2 A:GLU477 4.1 63.9 1.0
CB A:ASP559 4.4 63.4 1.0
C5' B:DC8 4.4 52.4 1.0
OD1 A:ASP557 4.6 74.2 1.0
O3' B:DC8 4.6 55.6 1.0
CA A:GLY631 4.7 0.6 1.0
N A:GLY631 4.9 0.6 1.0
CD A:GLU477 5.0 63.3 1.0

Manganese binding site 2 out of 2 in 5zen

Go back to Manganese Binding Sites List in 5zen
Manganese binding site 2 out of 2 in the Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Topoisomerase II Beta in Complex with Dna: A New Quaternary Conformation Showing Opening of the Protein-Linked Dna-Gate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1302

b:0.8
occ:1.00
 O A:ASN867 3.3 65.2 1.0
O A:SER794 3.5 59.7 1.0
OD1 A:ASN795 4.0 47.0 1.0
O A:GLY868 4.2 67.7 1.0
C A:SER794 4.2 56.3 1.0
OE1 A:GLU870 4.4 79.0 1.0
C A:ASN867 4.6 62.0 1.0
OD1 A:ASN786 4.6 67.8 1.0
CA A:SER794 4.7 55.3 1.0
OP1 B:DG5 4.8 62.7 1.0
CG A:ASN795 4.9 48.2 1.0
NH1 A:ARG945 4.9 80.6 1.0
C A:GLY868 4.9 65.0 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: Sun Oct 6 03:41:52 2024

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