Zinc in PDB 4av1: Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna

All present enzymatic activity of Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna:
2.4.2.30;

The structure of Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna, PDB code: 4av1 was solved by A.A.E.Ali, G.Timinszky, R.Arribas-Bosacoma, M.Kozlowski, P.O.Hassa, M.Hassler, A.G.Ladurner, L.H.Pearl, A.W.Oliver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.353 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.978, 59.504, 61.582, 90.00, 101.18, 90.00
R / Rfree (%)	22.95 / 24.87

The binding sites of Zinc atom in the Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna (pdb code 4av1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna, PDB code: 4av1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1600 b:84.4 occ:1.00 ND1 A:HIS53 2.0 63.4 1.0 SG A:CYS56 2.1 81.6 1.0 SG A:CYS21 2.2 82.8 1.0 SG A:CYS24 2.2 90.9 1.0 CB A:CYS21 2.7 71.8 1.0 CE1 A:HIS53 2.9 61.7 1.0 CG A:HIS53 3.1 64.3 1.0 CB A:CYS56 3.1 89.1 1.0 CB A:HIS53 3.5 65.0 1.0 CB A:CYS24 3.7 91.8 1.0 N A:CYS24 3.8 86.0 1.0 N A:HIS53 4.0 70.8 1.0 NE2 A:HIS53 4.0 60.8 1.0 CD2 A:HIS53 4.1 57.6 1.0 CA A:CYS21 4.2 69.3 1.0 CA A:CYS24 4.3 82.9 1.0 CA A:HIS53 4.4 71.4 1.0 CB A:LYS23 4.4 80.4 1.0 CA A:CYS56 4.5 84.1 1.0 C A:CYS21 4.8 67.9 1.0 C A:LYS23 4.9 90.7 1.0 N A:LYS23 4.9 77.1 1.0 C A:CYS24 5.0 76.6 1.0 N A:SER25 5.0 79.2 1.0 CA A:LYS23 5.0 80.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1600 b:63.2 occ:1.00 ND1 B:HIS159 1.9 48.7 1.0 SG B:CYS125 2.1 43.8 1.0 SG B:CYS128 2.2 44.5 1.0 SG B:CYS162 2.2 51.5 1.0 CE1 B:HIS159 2.8 50.1 1.0 CG B:HIS159 3.0 44.6 1.0 CB B:CYS125 3.1 49.0 1.0 CB B:CYS162 3.2 50.8 1.0 CB B:HIS159 3.4 45.6 1.0 CB B:CYS128 3.5 54.3 1.0 N B:HIS159 3.7 40.2 1.0 NE2 B:HIS159 3.9 45.2 1.0 N B:CYS128 4.0 62.0 1.0 CD2 B:HIS159 4.0 47.5 1.0 CA B:HIS159 4.2 41.9 1.0 CA B:CYS128 4.4 53.9 1.0 C B:GLY127 4.4 62.4 1.0 CA B:CYS125 4.5 43.9 1.0 CA B:CYS162 4.6 49.1 1.0 CA B:GLY127 4.7 53.7 1.0 N B:GLY127 4.7 61.1 1.0 O B:CYS125 4.8 53.0 1.0 C B:CYS125 4.8 49.0 1.0 C B:TYR158 4.8 49.0 1.0 CG B:GLU130 4.9 72.4 1.0 OE2 B:GLU130 4.9 81.7 1.0 N B:CYS162 4.9 53.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1600 b:0.5 occ:1.00 ND1 C:HIS53 2.0 59.4 1.0 SG C:CYS56 2.2 89.5 1.0 SG C:CYS24 2.2 84.4 1.0 SG C:CYS21 2.2 79.0 1.0 CB C:CYS21 2.7 73.4 1.0 CE1 C:HIS53 2.9 62.2 1.0 CG C:HIS53 3.1 61.4 1.0 CB C:CYS56 3.2 88.1 1.0 CB C:HIS53 3.5 63.9 1.0 CB C:CYS24 3.6 92.8 1.0 N C:CYS24 3.8 90.3 1.0 N C:HIS53 4.0 72.1 1.0 NE2 C:HIS53 4.0 64.4 1.0 CD2 C:HIS53 4.1 58.0 1.0 CA C:CYS21 4.2 67.0 1.0 CA C:CYS24 4.3 86.7 1.0 CA C:HIS53 4.4 75.4 1.0 CB C:LYS23 4.5 86.8 1.0 CA C:CYS56 4.6 82.8 1.0 C C:CYS21 4.8 66.7 1.0 C C:LYS23 4.9 89.5 1.0 N C:LYS23 4.9 77.8 1.0 C C:CYS24 4.9 76.0 1.0 CG C:LYS23 4.9 0.6 1.0 N C:SER25 4.9 77.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Human Parp-1 Dna Binding Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1600 b:68.0 occ:1.00 ND1 D:HIS159 2.0 50.0 1.0 SG D:CYS125 2.1 49.6 1.0 SG D:CYS128 2.1 44.0 1.0 SG D:CYS162 2.2 60.1 1.0 CE1 D:HIS159 2.8 49.1 1.0 CG D:HIS159 3.0 45.7 1.0 CB D:CYS125 3.0 52.5 1.0 CB D:CYS162 3.2 53.7 1.0 CB D:HIS159 3.5 43.5 1.0 CB D:CYS128 3.5 55.7 1.0 N D:HIS159 3.7 40.1 1.0 N D:CYS128 3.9 63.6 1.0 NE2 D:HIS159 4.0 45.9 1.0 CD2 D:HIS159 4.1 51.5 1.0 CA D:HIS159 4.2 38.8 1.0 CA D:CYS128 4.3 55.4 1.0 C D:GLY127 4.3 61.6 1.0 CA D:CYS125 4.4 43.6 1.0 CA D:GLY127 4.6 57.7 1.0 CA D:CYS162 4.6 51.7 1.0 N D:GLY127 4.7 63.6 1.0 O D:CYS125 4.7 53.8 1.0 C D:CYS125 4.7 47.9 1.0 C D:TYR158 4.8 52.6 1.0 CG D:GLU130 4.8 71.1 1.0 OE2 D:GLU130 4.9 81.7 1.0 N D:CYS162 5.0 52.8 1.0

A.A.E.Ali, G.Timinszky, R.Arribas-Bosacoma, M.Kozlowski, P.O.Hassa, M.Hassler, A.G.Ladurner, L.H.Pearl, A.W.Oliver. The Zinc-Finger Domains of PARP1 Cooperate to Recognise Dna Strand-Breaks Nat.Struct.Mol.Biol. V. 19 685 2012.
ISSN: ISSN 1072-8368
PubMed: 22683995
DOI: 10.1038/NSMB.2335