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Zinc in PDB 3ode: Human Parp-1 Zinc Finger 2 (ZN2) Bound to Dna

Enzymatic activity of Human Parp-1 Zinc Finger 2 (ZN2) Bound to Dna

All present enzymatic activity of Human Parp-1 Zinc Finger 2 (ZN2) Bound to Dna:
2.4.2.30;

Protein crystallography data

The structure of Human Parp-1 Zinc Finger 2 (ZN2) Bound to Dna, PDB code: 3ode 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) 41.81 / 2.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.804, 62.804, 196.049, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Parp-1 Zinc Finger 2 (ZN2) Bound to Dna (pdb code 3ode). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Parp-1 Zinc Finger 2 (ZN2) Bound to Dna, PDB code: 3ode:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ode

Go back to Zinc Binding Sites List in 3ode
Zinc binding site 1 out of 2 in the Human Parp-1 Zinc Finger 2 (ZN2) 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 2 (ZN2) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:44.7
occ:1.00
ND1 A:HIS159 2.1 40.4 1.0
SG A:CYS162 2.2 40.2 1.0
SG A:CYS128 2.2 35.2 1.0
SG A:CYS125 2.2 36.6 1.0
CG A:HIS159 3.0 38.2 1.0
CE1 A:HIS159 3.1 39.6 1.0
CB A:CYS125 3.1 39.1 1.0
CB A:CYS128 3.2 49.6 1.0
CB A:CYS162 3.2 38.9 1.0
N A:CYS128 3.3 54.9 1.0
CB A:HIS159 3.4 37.9 1.0
CA A:CYS128 3.9 49.3 1.0
N A:HIS159 3.9 41.1 1.0
NE2 A:HIS159 4.1 35.4 1.0
CD2 A:HIS159 4.1 36.5 1.0
CA A:HIS159 4.2 38.3 1.0
C A:GLY127 4.4 57.5 1.0
CA A:CYS125 4.6 45.9 1.0
CA A:GLY127 4.6 52.5 1.0
CA A:CYS162 4.6 46.4 1.0
C A:CYS128 4.7 47.1 1.0
N A:GLY127 4.8 52.7 1.0
N A:MET129 4.9 48.8 1.0
N A:CYS162 4.9 46.3 1.0
C A:CYS125 4.9 49.3 1.0
O A:CYS125 4.9 51.4 1.0

Zinc binding site 2 out of 2 in 3ode

Go back to Zinc Binding Sites List in 3ode
Zinc binding site 2 out of 2 in the Human Parp-1 Zinc Finger 2 (ZN2) 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 2 (ZN2) Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:57.6
occ:1.00
SG B:CYS128 2.1 48.0 1.0
ND1 B:HIS159 2.1 37.8 1.0
SG B:CYS162 2.3 49.6 1.0
SG B:CYS125 2.4 55.5 1.0
CB B:CYS128 2.8 49.1 1.0
CE1 B:HIS159 3.0 44.0 1.0
N B:CYS128 3.1 55.5 1.0
CG B:HIS159 3.2 39.1 1.0
CB B:CYS162 3.3 51.2 1.0
CB B:CYS125 3.3 49.6 1.0
CA B:CYS128 3.6 51.0 1.0
CB B:HIS159 3.6 39.3 1.0
C B:GLY127 4.1 58.9 1.0
NE2 B:HIS159 4.2 40.4 1.0
N B:HIS159 4.2 45.6 1.0
CD2 B:HIS159 4.3 37.2 1.0
CA B:GLY127 4.3 53.1 1.0
C B:CYS128 4.5 49.1 1.0
CA B:HIS159 4.6 40.6 1.0
N B:GLY127 4.6 54.5 1.0
CA B:CYS162 4.6 48.6 1.0
CA B:CYS125 4.7 48.8 1.0
N B:MET129 4.7 51.5 1.0
O B:CYS125 4.9 53.4 1.0
C B:CYS125 4.9 51.6 1.0
N B:CYS162 4.9 47.7 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 Sep 26 12:12:43 2020
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