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Zinc in PDB 3oda: Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna

Enzymatic activity of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna

All present enzymatic activity of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna:
2.4.2.30;

Protein crystallography data

The structure of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna, PDB code: 3oda was solved by J.M.Pascal, M.-F.Langelier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.42 / 2.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.812, 107.334, 86.998, 90.00, 100.61, 90.00
R / Rfree (%) 19.6 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna (pdb code 3oda). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna, PDB code: 3oda:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3oda

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Zinc binding site 1 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:15.4
occ:1.00
 ND1 A:HIS53 2.1 21.8 1.0
SG A:CYS56 2.1 16.9 1.0
SG A:CYS21 2.2 21.7 1.0
SG A:CYS24 2.3 19.0 1.0
CB A:CYS21 2.9 17.2 1.0
CE1 A:HIS53 3.1 20.7 1.0
CB A:CYS56 3.1 19.9 1.0
CG A:HIS53 3.1 23.1 1.0
CB A:CYS24 3.4 26.8 1.0
CB A:HIS53 3.4 20.1 1.0
N A:CYS24 3.8 23.5 1.0
N A:HIS53 3.9 18.1 1.0
CA A:CYS24 4.2 20.8 1.0
NE2 A:HIS53 4.2 20.3 1.0
CD2 A:HIS53 4.2 22.9 1.0
CA A:HIS53 4.3 20.7 1.0
CA A:CYS21 4.4 15.2 1.0
CA A:CYS56 4.5 20.2 1.0
O A:HOH210 4.7 34.8 1.0
CB A:LYS23 4.7 17.5 1.0
C A:CYS24 4.9 19.1 1.0
C A:LYS23 4.9 25.8 1.0
O A:HOH213 4.9 26.2 1.0
N A:SER25 4.9 17.7 1.0
N A:CYS56 5.0 22.0 1.0

Zinc binding site 2 out of 8 in 3oda

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Zinc binding site 2 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:18.9
occ:1.00
 SG B:CYS56 2.1 17.5 1.0
SG B:CYS21 2.2 17.3 1.0
ND1 B:HIS53 2.3 18.0 1.0
SG B:CYS24 2.3 25.7 1.0
CB B:CYS21 3.0 15.8 1.0
CB B:CYS56 3.2 16.2 1.0
CE1 B:HIS53 3.2 24.4 1.0
CB B:CYS24 3.3 17.6 1.0
CG B:HIS53 3.3 18.3 1.0
CB B:HIS53 3.6 17.2 1.0
N B:CYS24 3.8 27.4 1.0
N B:HIS53 4.1 13.4 1.0
CA B:CYS24 4.1 17.4 1.0
O B:HOH220 4.3 39.7 1.0
NE2 B:HIS53 4.3 23.9 1.0
CD2 B:HIS53 4.4 23.3 1.0
O B:HOH102 4.4 31.1 1.0
CA B:HIS53 4.5 15.9 1.0
CA B:CYS21 4.5 15.0 1.0
CA B:CYS56 4.6 18.3 1.0
O B:HOH103 4.6 36.5 1.0
CB B:LYS23 4.7 15.3 1.0
C B:CYS24 4.9 21.0 1.0
C B:LYS23 4.9 28.5 1.0
N B:CYS56 4.9 24.5 1.0
N B:SER25 4.9 18.9 1.0

Zinc binding site 3 out of 8 in 3oda

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Zinc binding site 3 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:16.9
occ:1.00
 ND1 C:HIS53 2.1 20.0 1.0
SG C:CYS56 2.2 15.2 1.0
SG C:CYS21 2.3 16.5 1.0
SG C:CYS24 2.4 20.1 1.0
CB C:CYS21 3.0 15.9 1.0
CE1 C:HIS53 3.1 20.9 1.0
CB C:CYS56 3.1 19.6 1.0
CG C:HIS53 3.1 23.2 1.0
CB C:CYS24 3.3 23.1 1.0
CB C:HIS53 3.5 19.4 1.0
N C:CYS24 3.8 22.0 1.0
N C:HIS53 4.0 18.8 1.0
CA C:CYS24 4.1 18.4 1.0
NE2 C:HIS53 4.2 22.1 1.0
CD2 C:HIS53 4.3 23.4 1.0
CA C:HIS53 4.4 23.2 1.0
CA C:CYS21 4.4 13.6 1.0
CA C:CYS56 4.6 21.9 1.0
CB C:LYS23 4.7 18.4 1.0
C C:CYS24 4.8 19.5 1.0
N C:SER25 4.9 19.5 1.0
C C:LYS23 4.9 24.9 1.0

Zinc binding site 4 out of 8 in 3oda

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Zinc binding site 4 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:16.3
occ:1.00
 SG D:CYS21 2.2 14.9 1.0
ND1 D:HIS53 2.2 19.4 1.0
SG D:CYS56 2.2 15.5 1.0
SG D:CYS24 2.3 22.0 1.0
CB D:CYS21 3.0 13.6 1.0
CE1 D:HIS53 3.1 23.9 1.0
CG D:HIS53 3.2 18.6 1.0
CB D:CYS56 3.3 15.6 1.0
CB D:CYS24 3.3 15.6 1.0
CB D:HIS53 3.6 16.4 1.0
N D:CYS24 3.8 23.1 1.0
N D:HIS53 4.1 13.7 1.0
CA D:CYS24 4.1 17.1 1.0
NE2 D:HIS53 4.2 21.9 1.0
CD2 D:HIS53 4.3 25.7 1.0
CA D:HIS53 4.5 16.5 1.0
CA D:CYS21 4.5 15.8 1.0
O D:HOH130 4.6 30.0 1.0
O D:HOH148 4.6 24.2 1.0
CA D:CYS56 4.7 16.4 1.0
CB D:LYS23 4.8 16.5 1.0
C D:CYS24 4.8 18.6 1.0
N D:SER25 4.9 15.7 1.0
C D:LYS23 5.0 26.6 1.0

Zinc binding site 5 out of 8 in 3oda

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Zinc binding site 5 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:34.4
occ:1.00
 ND1 E:HIS53 2.1 28.5 1.0
SG E:CYS24 2.2 29.5 1.0
SG E:CYS56 2.2 23.9 1.0
SG E:CYS21 2.3 32.2 1.0
CB E:CYS21 3.0 20.8 1.0
CE1 E:HIS53 3.0 28.3 1.0
CG E:HIS53 3.2 24.9 1.0
CB E:CYS24 3.2 26.7 1.0
CB E:CYS56 3.3 20.1 1.0
CB E:HIS53 3.6 24.2 1.0
N E:CYS24 3.7 24.4 1.0
CA E:CYS24 4.0 19.7 1.0
N E:HIS53 4.1 25.8 1.0
NE2 E:HIS53 4.1 30.6 1.0
CD2 E:HIS53 4.2 27.4 1.0
O E:HOH103 4.4 31.8 1.0
CA E:CYS21 4.4 17.5 1.0
CA E:HIS53 4.5 27.2 1.0
CA E:CYS56 4.7 20.5 1.0
C E:CYS24 4.7 22.3 1.0
CB E:LYS23 4.8 18.4 1.0
N E:SER25 4.8 21.9 1.0
C E:LYS23 4.9 31.1 1.0

Zinc binding site 6 out of 8 in 3oda

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Zinc binding site 6 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn200

b:24.2
occ:1.00
 ND1 F:HIS53 2.1 24.9 1.0
SG F:CYS21 2.2 16.9 1.0
SG F:CYS56 2.2 22.5 1.0
SG F:CYS24 2.4 33.3 1.0
CB F:CYS21 3.0 14.8 1.0
CE1 F:HIS53 3.0 27.0 1.0
CG F:HIS53 3.1 23.4 1.0
CB F:CYS56 3.2 17.9 1.0
CB F:CYS24 3.4 17.1 1.0
CB F:HIS53 3.5 18.5 1.0
N F:CYS24 4.0 25.5 1.0
N F:HIS53 4.1 13.1 1.0
NE2 F:HIS53 4.2 27.2 1.0
CD2 F:HIS53 4.2 23.7 1.0
CA F:CYS24 4.3 19.0 1.0
CA F:HIS53 4.4 15.9 1.0
CA F:CYS21 4.5 17.7 1.0
CA F:CYS56 4.6 20.4 1.0
CB F:LYS23 4.9 18.6 1.0
C F:CYS24 4.9 22.9 1.0
N F:SER25 5.0 21.9 1.0
N F:CYS56 5.0 22.5 1.0

Zinc binding site 7 out of 8 in 3oda

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Zinc binding site 7 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn200

b:27.9
occ:1.00
 ND1 G:HIS53 2.0 22.5 1.0
SG G:CYS56 2.2 22.4 1.0
SG G:CYS24 2.3 26.8 1.0
SG G:CYS21 2.3 28.2 1.0
CE1 G:HIS53 3.0 27.4 1.0
CB G:CYS21 3.0 20.0 1.0
CG G:HIS53 3.0 23.6 1.0
CB G:CYS56 3.1 20.1 1.0
CB G:HIS53 3.4 20.4 1.0
CB G:CYS24 3.4 25.1 1.0
N G:HIS53 3.9 22.9 1.0
N G:CYS24 3.9 25.9 1.0
NE2 G:HIS53 4.1 23.3 1.0
CD2 G:HIS53 4.1 24.6 1.0
CA G:CYS24 4.3 20.4 1.0
CA G:HIS53 4.3 25.3 1.0
CA G:CYS21 4.5 15.5 1.0
CA G:CYS56 4.5 20.6 1.0
O G:HOH101 4.7 19.1 1.0
CB G:LYS23 4.8 20.2 1.0
C G:CYS24 4.9 22.0 1.0
N G:CYS56 5.0 23.4 1.0

Zinc binding site 8 out of 8 in 3oda

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Zinc binding site 8 out of 8 in the Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn200

b:21.4
occ:1.00
 ND1 H:HIS53 2.1 22.0 1.0
SG H:CYS21 2.1 20.0 1.0
SG H:CYS56 2.2 18.3 1.0
SG H:CYS24 2.3 24.8 1.0
CB H:CYS21 2.9 18.0 1.0
CE1 H:HIS53 3.0 26.0 1.0
CG H:HIS53 3.1 20.8 1.0
CB H:CYS56 3.3 17.4 1.0
CB H:CYS24 3.4 15.3 1.0
CB H:HIS53 3.5 17.3 1.0
N H:CYS24 3.9 26.6 1.0
N H:HIS53 4.0 16.0 1.0
NE2 H:HIS53 4.1 21.9 1.0
CD2 H:HIS53 4.2 21.7 1.0
CA H:CYS24 4.2 17.4 1.0
CA H:HIS53 4.4 16.4 1.0
CA H:CYS21 4.4 18.9 1.0
CA H:CYS56 4.7 18.3 1.0
CB H:LYS23 4.9 16.4 1.0
C H:CYS24 4.9 21.9 1.0
N H:SER25 5.0 18.1 1.0

Reference:

M.F.Langelier, J.L.Planck, S.Roy, J.M.Pascal. Crystal Structures of Poly(Adp-Ribose) Polymerase-1 (Parp-1) Zinc Fingers Bound to Dna: Structural and Functional Insights Into Dna-Dependent Parp-1 Activity. J.Biol.Chem. V. 286 10690 2011.
ISSN: ISSN 0021-9258
PubMed: 21233213
DOI: 10.1074/JBC.M110.202507
Page generated: Sat Oct 26 10:54:05 2024

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