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Zinc in PDB 4oqb: Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide, PDB code: 4oqb 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 / 3.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.100, 113.080, 296.230, 90.00, 90.00, 90.00
R / Rfree (%) 32.2 / 34.9

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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide (pdb code 4oqb). 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide, PDB code: 4oqb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4oqb

Go back to Zinc Binding Sites List in 4oqb
Zinc binding site 1 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:78.1
occ:1.00
 ND1 A:HIS53 2.1 0.1 1.0
SG A:CYS24 2.3 0.9 1.0
SG A:CYS56 2.3 0.4 1.0
SG A:CYS21 2.3 0.5 1.0
CG A:HIS53 3.0 0.3 1.0
CE1 A:HIS53 3.1 0.5 1.0
CB A:HIS53 3.2 0.3 1.0
CB A:CYS21 3.4 0.3 1.0
CB A:CYS56 3.4 0.4 1.0
CB A:CYS24 3.4 0.5 1.0
N A:HIS53 4.0 0.7 1.0
CD2 A:HIS53 4.1 0.5 1.0
N A:CYS24 4.1 0.4 1.0
NE2 A:HIS53 4.2 0.1 1.0
CA A:HIS53 4.2 0.2 1.0
CA A:CYS24 4.3 0.9 1.0
CA A:CYS56 4.7 0.9 1.0
CA A:CYS21 4.8 1.0 1.0
N A:CYS56 4.9 0.3 1.0

Zinc binding site 2 out of 4 in 4oqb

Go back to Zinc Binding Sites List in 4oqb
Zinc binding site 2 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:62.7
occ:1.00
 SG A:CYS321 2.3 0.8 1.0
SG A:CYS295 2.3 0.7 1.0
SG A:CYS298 2.3 0.3 1.0
SG A:CYS311 2.3 0.4 1.0
CB A:CYS295 3.4 0.4 1.0
CB A:CYS321 3.4 0.5 1.0
CB A:CYS311 3.4 0.1 1.0
CB A:CYS298 3.4 0.2 1.0
CG2 A:VAL323 3.8 0.6 1.0
N A:CYS298 4.0 0.5 1.0
CB A:VAL323 4.1 0.5 1.0
OE1 A:GLU297 4.2 0.0 1.0
CA A:CYS298 4.2 0.2 1.0
CA A:CYS295 4.8 0.3 1.0
CA A:CYS321 4.8 0.4 1.0
CA A:CYS311 4.8 0.5 1.0
C A:CYS298 4.9 0.4 1.0
N A:SER299 4.9 1.0 1.0
CG1 A:VAL323 4.9 1.0 1.0
N A:VAL323 5.0 0.5 1.0
N A:GLY300 5.0 0.4 1.0

Zinc binding site 3 out of 4 in 4oqb

Go back to Zinc Binding Sites List in 4oqb
Zinc binding site 3 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:0.5
occ:1.00
 ND1 D:HIS53 2.1 0.3 1.0
SG D:CYS56 2.3 1.0 1.0
SG D:CYS24 2.3 0.2 1.0
SG D:CYS21 2.3 0.2 1.0
CG D:HIS53 3.0 0.5 1.0
CE1 D:HIS53 3.1 0.7 1.0
CB D:HIS53 3.2 0.1 1.0
CB D:CYS21 3.4 0.5 1.0
CB D:CYS56 3.4 0.6 1.0
CB D:CYS24 3.4 0.5 1.0
N D:HIS53 4.0 0.8 1.0
CD2 D:HIS53 4.1 0.1 1.0
N D:CYS24 4.1 0.9 1.0
NE2 D:HIS53 4.2 0.9 1.0
CA D:HIS53 4.2 0.3 1.0
CA D:CYS24 4.3 0.9 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 0.8 1.0

Zinc binding site 4 out of 4 in 4oqb

Go back to Zinc Binding Sites List in 4oqb
Zinc binding site 4 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break in Complex with (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 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 (2Z)-2-{4-[2-(Morpholin-4-Yl)Ethoxy]Benzylidene}-3-Oxo- 2,3-Dihydro-1-Benzofuran-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:0.6
occ:1.00
 SG D:CYS321 2.3 0.3 1.0
SG D:CYS295 2.3 0.5 1.0
SG D:CYS311 2.3 0.4 1.0
SG D:CYS298 2.3 0.2 1.0
CB D:CYS295 3.4 0.6 1.0
CB D:CYS321 3.4 0.6 1.0
CB D:CYS311 3.4 0.7 1.0
CB D:CYS298 3.4 0.1 1.0
CG2 D:VAL323 3.8 0.4 1.0
N D:CYS298 4.0 0.1 1.0
CB D:VAL323 4.1 0.4 1.0
OE1 D:GLU297 4.2 0.5 1.0
CA D:CYS298 4.3 0.9 1.0
CA D:CYS295 4.8 0.6 1.0
CA D:CYS321 4.8 0.2 1.0
CA D:CYS311 4.8 0.9 1.0
C D:CYS298 4.9 0.7 1.0
N D:SER299 4.9 0.8 1.0
CG1 D:VAL323 4.9 0.6 1.0
N D:VAL323 5.0 0.3 1.0
N D:GLY300 5.0 0.4 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 03:56:47 2024

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