Zinc in PDB 4dqy: Structure of Human Parp-1 Bound to A Dna Double Strand Break

All present enzymatic activity of Structure of Human Parp-1 Bound to A Dna Double Strand Break:
2.4.2.30;

The structure of Structure of Human Parp-1 Bound to A Dna Double Strand Break, PDB code: 4dqy was solved by M.F.Langelier, J.M.Pascal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.095, 112.965, 294.724, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 30.4

The binding sites of Zinc atom in the Structure of Human Parp-1 Bound to A Dna Double Strand Break (pdb code 4dqy). 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, PDB code: 4dqy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:0.7 occ:1.00 ND1 A:HIS53 2.2 0.6 1.0 SG A:CYS24 2.3 0.8 1.0 SG A:CYS56 2.3 0.1 1.0 SG A:CYS21 2.3 0.6 1.0 CG A:HIS53 3.0 0.4 1.0 CE1 A:HIS53 3.2 0.5 1.0 CB A:HIS53 3.3 0.8 1.0 CB A:CYS21 3.3 0.2 1.0 CB A:CYS24 3.3 0.8 1.0 CB A:CYS56 3.4 0.0 1.0 N A:CYS24 4.0 0.7 1.0 N A:HIS53 4.2 0.7 1.0 CD2 A:HIS53 4.2 0.0 1.0 CA A:CYS24 4.3 0.9 1.0 NE2 A:HIS53 4.3 0.5 1.0 CA A:HIS53 4.4 0.4 1.0 CA A:CYS21 4.7 0.8 1.0 CA A:CYS56 4.8 0.4 1.0 N A:SER25 4.8 0.7 1.0 C A:CYS24 5.0 0.2 1.0 N A:CYS56 5.0 0.8 1.0

Zinc binding site 2 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:0.2 occ:1.00 SG B:CYS298 2.3 1.0 1.0 SG B:CYS295 2.3 0.9 1.0 SG B:CYS321 2.3 0.6 1.0 SG B:CYS311 2.3 0.0 1.0 CB B:CYS295 3.3 0.8 1.0 CB B:CYS298 3.3 0.5 1.0 CB B:CYS321 3.4 0.4 1.0 CB B:CYS311 3.4 0.0 1.0 OE1 B:GLU297 3.7 0.9 1.0 N B:CYS298 3.9 0.2 1.0 CG2 B:VAL323 4.0 0.3 1.0 CA B:CYS298 4.1 0.4 1.0 CB B:VAL323 4.1 0.3 1.0 C B:CYS298 4.7 0.1 1.0 CA B:CYS295 4.8 0.1 1.0 N B:SER299 4.8 0.4 1.0 CA B:CYS321 4.8 0.5 1.0 CA B:CYS311 4.8 0.5 1.0 N B:GLY300 4.9 0.4 1.0 CD B:GLU297 4.9 0.9 1.0 N B:GLY313 5.0 0.2 1.0 CG1 B:VAL323 5.0 0.4 1.0

Zinc binding site 3 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn200 b:0.6 occ:1.00 ND1 D:HIS53 2.2 0.7 1.0 SG D:CYS56 2.3 0.6 1.0 SG D:CYS24 2.3 0.0 1.0 SG D:CYS21 2.3 0.8 1.0 CG D:HIS53 3.0 0.2 1.0 CE1 D:HIS53 3.2 0.9 1.0 CB D:HIS53 3.3 0.8 1.0 CB D:CYS21 3.3 0.6 1.0 CB D:CYS56 3.4 0.4 1.0 CB D:CYS24 3.4 0.5 1.0 N D:CYS24 4.0 0.6 1.0 N D:HIS53 4.1 0.9 1.0 CD2 D:HIS53 4.2 0.4 1.0 CA D:CYS24 4.3 0.9 1.0 NE2 D:HIS53 4.3 0.9 1.0 CA D:HIS53 4.3 0.5 1.0 CA D:CYS21 4.7 0.8 1.0 CA D:CYS56 4.7 0.8 1.0 N D:SER25 4.8 0.3 1.0 N D:CYS56 5.0 0.4 1.0 C D:CYS24 5.0 0.1 1.0

Zinc binding site 4 out of 4 in the Structure of Human Parp-1 Bound to A Dna Double Strand Break


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn400 b:0.6 occ:1.00 SG E:CYS295 2.3 0.5 1.0 SG E:CYS298 2.3 0.1 1.0 SG E:CYS311 2.3 0.5 1.0 SG E:CYS321 2.3 1.0 1.0 CB E:CYS295 3.3 0.8 1.0 CB E:CYS298 3.3 0.5 1.0 CB E:CYS321 3.4 0.5 1.0 CB E:CYS311 3.4 0.4 1.0 OE1 E:GLU297 3.8 0.2 1.0 N E:CYS298 3.9 0.8 1.0 CG2 E:VAL323 4.0 0.1 1.0 CA E:CYS298 4.2 0.4 1.0 CB E:VAL323 4.2 0.9 1.0 C E:CYS298 4.7 0.6 1.0 CA E:CYS295 4.7 0.1 1.0 N E:SER299 4.8 0.0 1.0 CA E:CYS321 4.8 0.4 1.0 CA E:CYS311 4.8 0.1 1.0 N E:GLY300 4.8 0.9 1.0 CD E:GLU297 4.9 0.9 1.0 N E:GLY313 5.0 0.9 1.0

M.F.Langelier, J.L.Planck, S.Roy, J.M.Pascal. Structural Basis For Dna Damage-Dependent Poly(Adp-Ribosyl)Ation By Human Parp-1. Science V. 336 728 2012.
ISSN: ISSN 0036-8075
PubMed: 22582261
DOI: 10.1126/SCIENCE.1216338