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Zinc in PDB 3l4k: Topoisomerase II-Dna Cleavage Complex, Metal-Bound

Enzymatic activity of Topoisomerase II-Dna Cleavage Complex, Metal-Bound

All present enzymatic activity of Topoisomerase II-Dna Cleavage Complex, Metal-Bound:
5.99.1.3;

Protein crystallography data

The structure of Topoisomerase II-Dna Cleavage Complex, Metal-Bound, PDB code: 3l4k was solved by B.H.Schmidt, A.B.Burgin, J.E.Deweese, N.Osheroff, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 2.98
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 86.064, 91.851, 115.939, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound (pdb code 3l4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound, PDB code: 3l4k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3l4k

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Zinc binding site 1 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:0.8
occ:1.00
 NE2 A:HIS735 1.9 83.3 1.0
OE2 A:GLU808 2.1 0.7 1.0
CD A:GLU808 2.4 0.3 1.0
CG A:GLU808 2.4 1.0 1.0
CE1 A:HIS735 2.8 83.4 1.0
CD2 A:HIS735 3.0 82.3 1.0
OD1 A:ASP809 3.3 0.4 1.0
OE1 A:GLU808 3.4 0.1 1.0
CB A:GLU808 3.9 0.8 1.0
ND1 A:HIS735 4.0 83.3 1.0
CG A:ASP809 4.1 0.8 1.0
CG A:HIS735 4.1 81.8 1.0
OD2 A:ASP809 4.4 0.6 1.0
O A:ALA733 4.5 54.0 1.0
N A:ASP809 4.6 0.3 1.0
CA A:GLU808 4.7 0.6 1.0
CB A:ALA733 4.8 48.0 1.0
C A:GLU808 4.8 0.9 1.0

Zinc binding site 2 out of 8 in 3l4k

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Zinc binding site 2 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:0.1
occ:1.00
 S3' D:TSP11 2.0 60.5 0.5
O3' B:DC11 2.1 59.8 0.5
OD2 A:ASP526 2.2 80.1 1.0
CD A:GLU449 2.6 90.5 1.0
OE2 A:GLU449 2.7 92.6 1.0
OE1 A:GLU449 2.9 91.7 1.0
CG A:ASP526 3.2 77.9 1.0
CG A:GLU449 3.3 86.5 1.0
C3' B:DC11 3.4 58.0 0.5
C3' D:TSP11 3.4 58.2 0.5
ZN A:ZN4 3.4 0.0 1.0
OD1 A:ASP526 3.7 78.0 1.0
C4' B:DC11 4.3 57.1 0.5
C2' D:TSP11 4.3 57.2 0.5
C4' D:TSP11 4.3 57.1 0.5
C2' B:DC11 4.4 57.0 0.5
CB A:ASP526 4.4 74.0 1.0
OD2 A:ASP528 4.5 75.5 1.0
CB A:GLU449 4.6 83.4 1.0
C5' B:DC11 4.7 56.1 0.5
C5' D:TSP11 4.8 56.1 0.5
O A:GLU449 4.9 89.2 1.0

Zinc binding site 3 out of 8 in 3l4k

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Zinc binding site 3 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:0.0
occ:1.00
 OD2 A:ASP528 2.1 75.5 1.0
OD2 A:ASP526 2.3 80.1 1.0
CG A:ASP526 3.2 77.9 1.0
CG A:ASP528 3.3 74.0 1.0
CE A:LYS603 3.4 0.2 1.0
ZN A:ZN3 3.4 0.1 1.0
CB A:ASP526 3.7 74.0 1.0
CG A:LYS603 3.8 0.8 1.0
OD1 A:ASP528 4.0 76.2 1.0
CD A:LYS603 4.2 0.1 1.0
OP1 B:DC11 4.2 53.5 0.5
OD1 A:ASP526 4.2 78.0 1.0
CB A:ASP528 4.3 69.8 1.0
S3' D:TSP11 4.3 60.5 0.5
OP1 D:TSP11 4.3 53.6 0.5
O3' B:DC11 4.4 59.8 0.5
NZ A:LYS603 4.5 0.5 1.0
C5' B:DC11 4.6 56.1 0.5
OE2 A:GLU449 4.6 92.6 1.0
C5' D:TSP11 4.7 56.1 0.5
N A:GLY604 4.8 0.2 1.0

Zinc binding site 4 out of 8 in 3l4k

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Zinc binding site 4 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5

b:0.7
occ:1.00
 NE2 A:HIS981 2.4 80.8 1.0
CD2 A:HIS981 2.8 79.7 1.0
CE1 A:HIS981 3.6 80.9 1.0
CG A:HIS981 4.1 78.2 1.0
ND1 A:HIS981 4.4 80.0 1.0
CG A:PRO980 4.7 61.6 1.0
CB A:PRO980 4.7 62.4 1.0
CD A:PRO980 4.9 60.7 1.0
OE1 A:GLU996 5.0 67.3 1.0

Zinc binding site 5 out of 8 in 3l4k

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Zinc binding site 5 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn6

b:0.1
occ:1.00
 CE1 A:HIS623 2.3 76.1 1.0
NE2 A:HIS623 2.5 74.2 1.0
OE1 A:GLU615 3.2 1.0 1.0
ND1 A:HIS623 3.6 78.1 1.0
CD2 A:HIS623 3.8 73.5 1.0
CD A:GLU615 4.0 0.1 1.0
OE2 A:GLU615 4.0 1.0 1.0
OH A:TYR579 4.1 98.5 1.0
CG A:HIS623 4.4 76.8 1.0
CE1 A:TYR616 4.5 0.1 1.0
CD1 A:TYR616 4.6 0.9 1.0
OD1 A:ASN619 4.8 0.5 1.0

Zinc binding site 6 out of 8 in 3l4k

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Zinc binding site 6 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn7

b:0.6
occ:1.00
 NE2 A:HIS628 2.7 90.7 1.0
CD2 A:HIS628 3.0 88.7 1.0
CE1 A:HIS628 3.7 91.1 1.0
CG A:HIS628 4.2 89.2 1.0
ND1 A:HIS628 4.5 90.5 1.0
NE2 A:GLN553 4.7 1.0 1.0
NE2 A:GLN631 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 3l4k

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Zinc binding site 7 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn8

b:0.3
occ:1.00
 NE2 A:HIS736 2.5 81.0 1.0
CE1 A:HIS736 2.8 81.1 1.0
CD2 A:HIS736 3.8 79.6 1.0
ND1 A:HIS736 4.1 79.5 1.0
NH1 A:ARG690 4.1 42.2 1.0
CD A:ARG690 4.5 48.8 1.0
CG A:HIS736 4.6 78.0 1.0
CB A:ALA686 4.8 54.6 1.0

Zinc binding site 8 out of 8 in 3l4k

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Zinc binding site 8 out of 8 in the Topoisomerase II-Dna Cleavage Complex, Metal-Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Topoisomerase II-Dna Cleavage Complex, Metal-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn16

b:0.4
occ:1.00
 N7 E:DG4 1.9 77.5 0.5
N7 C:DG4 2.0 77.5 0.5
C8 C:DG4 2.9 78.2 0.5
C8 E:DG4 2.9 78.2 0.5
C5 E:DG4 2.9 76.3 0.5
C5 C:DG4 3.0 76.2 0.5
O6 E:DG4 3.3 74.3 0.5
O6 C:DG4 3.4 74.4 0.5
C6 E:DG4 3.4 75.1 0.5
C6 C:DG4 3.6 75.0 0.5
N9 C:DG4 4.1 78.0 0.5
N9 E:DG4 4.1 78.0 0.5
C4 E:DG4 4.1 76.3 0.5
C4 C:DG4 4.1 76.3 0.5
OP2 E:DG4 4.5 86.5 0.5
OP2 C:DG4 4.6 86.5 0.5
C4 E:DC3 4.7 65.1 0.5
C5 E:DC3 4.7 67.6 0.5
N1 E:DG4 4.8 74.5 0.5
N4 E:DC3 4.9 64.1 0.5
N1 C:DG4 4.9 74.2 0.5
C4 C:DC3 5.0 64.7 0.5

Reference:

B.H.Schmidt, A.B.Burgin, J.E.Deweese, N.Osheroff, J.M.Berger. A Novel and Unified Two-Metal Mechanism For Dna Cleavage By Type II and Ia Topoisomerases. Nature V. 465 641 2010.
ISSN: ISSN 0028-0836
PubMed: 20485342
DOI: 10.1038/NATURE08974
Page generated: Wed Dec 16 04:31:50 2020

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