Atomistry » Zinc » PDB 4ojp-4owf » 4opx
Atomistry »
  Zinc »
    PDB 4ojp-4owf »
      4opx »

Zinc in PDB 4opx: Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide

Enzymatic activity of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide

All present enzymatic activity of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide:
2.4.2.30;

Protein crystallography data

The structure of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide, PDB code: 4opx was solved by J.M.Pascal, J.D.Steffen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.150, 112.910, 295.290, 90.00, 90.00, 90.00
R / Rfree (%) 30.3 / 32.5

Other elements in 4opx:

The structure of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide also contains other interesting chemical elements:

Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide (pdb code 4opx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide, PDB code: 4opx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4opx

Go back to Zinc Binding Sites List in 4opx
Zinc binding site 1 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:83.8
occ:1.00
 ND1 A:HIS53 2.1 0.5 1.0
SG A:CYS24 2.3 0.3 1.0
SG A:CYS56 2.3 0.9 1.0
SG A:CYS21 2.3 0.1 1.0
CG A:HIS53 3.0 1.0 1.0
CE1 A:HIS53 3.1 0.5 1.0
CB A:HIS53 3.2 0.6 1.0
CB A:CYS21 3.4 0.8 1.0
CB A:CYS56 3.4 0.2 1.0
CB A:CYS24 3.4 0.1 1.0
N A:HIS53 4.1 0.1 1.0
CD2 A:HIS53 4.1 0.7 1.0
N A:CYS24 4.1 0.1 1.0
NE2 A:HIS53 4.2 0.6 1.0
CA A:HIS53 4.2 0.7 1.0
CA A:CYS24 4.3 0.4 1.0
CA A:CYS56 4.7 0.3 1.0
CA A:CYS21 4.8 0.8 1.0
N A:CYS56 4.9 0.2 1.0

Zinc binding site 2 out of 4 in 4opx

Go back to Zinc Binding Sites List in 4opx
Zinc binding site 2 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:71.4
occ:1.00
 SG A:CYS295 2.3 0.3 1.0
SG A:CYS321 2.3 0.2 1.0
SG A:CYS298 2.3 0.5 1.0
SG A:CYS311 2.3 0.1 1.0
CB A:CYS295 3.4 0.7 1.0
CB A:CYS321 3.4 0.6 1.0
CB A:CYS298 3.4 0.8 1.0
CB A:CYS311 3.4 0.5 1.0
CG2 A:VAL323 3.9 0.4 1.0
N A:CYS298 4.0 0.2 1.0
CB A:VAL323 4.1 0.7 1.0
OE1 A:GLU297 4.2 0.9 1.0
CA A:CYS298 4.2 0.8 1.0
CA A:CYS295 4.8 0.5 1.0
CA A:CYS321 4.8 0.9 1.0
CA A:CYS311 4.8 0.0 1.0
C A:CYS298 4.8 0.5 1.0
N A:SER299 4.9 0.9 1.0
CG1 A:VAL323 4.9 0.2 1.0
N A:VAL323 5.0 0.7 1.0
N A:GLY300 5.0 0.3 1.0

Zinc binding site 3 out of 4 in 4opx

Go back to Zinc Binding Sites List in 4opx
Zinc binding site 3 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:0.3
occ:1.00
 ND1 D:HIS53 2.1 1.0 1.0
SG D:CYS24 2.3 0.2 1.0
SG D:CYS56 2.3 0.3 1.0
SG D:CYS21 2.3 0.7 1.0
CG D:HIS53 3.0 0.2 1.0
CE1 D:HIS53 3.1 0.4 1.0
CB D:HIS53 3.2 0.3 1.0
CB D:CYS21 3.3 0.3 1.0
CB D:CYS56 3.4 0.6 1.0
CB D:CYS24 3.4 0.2 1.0
N D:HIS53 4.1 0.6 1.0
CD2 D:HIS53 4.1 0.0 1.0
N D:CYS24 4.1 0.7 1.0
NE2 D:HIS53 4.2 0.7 1.0
CA D:HIS53 4.2 0.9 1.0
CA D:CYS24 4.3 0.6 1.0
CA D:CYS56 4.7 0.8 1.0
CA D:CYS21 4.8 0.3 1.0
N D:CYS56 4.9 0.9 1.0

Zinc binding site 4 out of 4 in 4opx

Go back to Zinc Binding Sites List in 4opx
Zinc binding site 4 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2R)-5-Fluoro-2-Methyl-2,3-Dihydro-1-Benzofuran-7- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:0.8
occ:1.00
 SG D:CYS321 2.3 0.5 1.0
SG D:CYS295 2.3 0.7 1.0
SG D:CYS298 2.3 0.6 1.0
SG D:CYS311 2.3 0.4 1.0
CB D:CYS295 3.4 0.3 1.0
CB D:CYS321 3.4 0.3 1.0
CB D:CYS311 3.4 0.2 1.0
CB D:CYS298 3.4 0.1 1.0
CG2 D:VAL323 3.9 0.3 1.0
N D:CYS298 4.0 0.8 1.0
CB D:VAL323 4.1 0.2 1.0
OE1 D:GLU297 4.2 0.0 1.0
CA D:CYS298 4.2 0.3 1.0
CA D:CYS295 4.8 0.6 1.0
CA D:CYS321 4.8 0.4 1.0
CA D:CYS311 4.8 0.9 1.0
C D:CYS298 4.8 0.4 1.0
N D:SER299 4.9 0.7 1.0
CG1 D:VAL323 4.9 0.8 1.0
N D:VAL323 5.0 0.1 1.0
N D:GLY300 5.0 0.3 1.0

Reference:

M.R.Patel, A.Bhatt, J.D.Steffen, A.Chergui, J.Murai, Y.Pommier, J.M.Pascal, L.D.Trombetta, F.R.Fronczek, T.T.Talele. Discovery and Structure-Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-Carboxamide and 2,3-Dihydrobenzofuran-3(2H)-One-7-Carboxamide Derivatives As Poly(Adp-Ribose)Polymerase-1 Inhibitors. J.Med.Chem. V. 57 5579 2014.
ISSN: ISSN 0022-2623
PubMed: 24922587
DOI: 10.1021/JM5002502
Page generated: Sun Oct 27 03:55:57 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy