Atomistry » Zinc » PDB 3o70-3okd » 3oda
Atomistry »
  Zinc »
    PDB 3o70-3okd »
      3oda »

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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Go back to Zinc Binding Sites List in 3oda
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy