Zinc in PDB 7s6m: Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break.

All present enzymatic activity of Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break.:
2.4.2.30;

The structure of Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break., PDB code: 7s6m was solved by E.Rouleau-Turcotte, J.M.Pascal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.15 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.705, 112.074, 116.482, 90, 114.83, 90
R / Rfree (%)	20.6 / 23.9

The binding sites of Zinc atom in the Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break. (pdb code 7s6m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break., PDB code: 7s6m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human PARP1 DELTAV687-E688 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 Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:125.2 occ:1.00 SG A:CYS298 2.2 101.4 1.0 SG A:CYS321 2.3 120.0 1.0 SG A:CYS311 2.4 110.6 1.0 SG A:CYS295 2.4 128.6 1.0 H A:CYS298 3.1 145.8 1.0 HB3 A:CYS321 3.1 144.5 1.0 HB3 A:CYS298 3.2 122.5 1.0 CB A:CYS321 3.3 120.4 1.0 HB3 A:CYS311 3.3 150.3 1.0 HB2 A:CYS295 3.4 141.8 1.0 CB A:CYS298 3.4 102.1 1.0 CB A:CYS311 3.4 125.2 1.0 CB A:CYS295 3.4 118.1 1.0 HB2 A:CYS321 3.4 144.5 1.0 HB2 A:CYS311 3.5 150.3 1.0 HB3 A:CYS295 3.5 141.8 1.0 HB A:VAL323 3.5 128.2 1.0 HG21 A:VAL323 3.7 148.8 1.0 N A:CYS298 3.9 121.5 1.0 HG23 A:VAL323 4.0 148.8 1.0 H A:VAL323 4.1 130.9 1.0 HB2 A:GLU297 4.1 133.5 1.0 HB2 A:CYS298 4.1 122.5 1.0 CG2 A:VAL323 4.1 124.0 1.0 CA A:CYS298 4.2 103.5 1.0 H A:GLY313 4.3 116.0 1.0 H A:GLY300 4.3 120.3 1.0 CB A:VAL323 4.3 106.8 1.0 H A:GLU297 4.4 181.3 1.0 H A:SER299 4.5 139.2 1.0 HA3 A:GLY313 4.6 161.3 1.0 CA A:CYS321 4.7 115.5 1.0 CA A:CYS311 4.8 100.3 1.0 CA A:CYS295 4.8 105.6 1.0 N A:VAL323 4.9 109.0 1.0 C A:CYS298 4.9 122.7 1.0 N A:SER299 4.9 116.0 1.0 H A:MET322 4.9 161.3 1.0 CB A:GLU297 5.0 111.3 1.0 HA A:CYS298 5.0 124.3 1.0

Zinc binding site 2 out of 4 in the Human PARP1 DELTAV687-E688 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 Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:255.6 occ:1.00 ND1 A:HIS53 2.0 132.1 1.0 SG A:CYS24 2.0 119.3 1.0 SG A:CYS56 2.2 111.1 1.0 SG A:CYS21 2.6 152.6 1.0 CE1 A:HIS53 2.8 150.8 1.0 HE1 A:HIS53 2.9 181.0 1.0 HB2 A:CYS21 3.0 147.1 1.0 HB3 A:CYS21 3.0 147.1 1.0 CB A:CYS21 3.1 122.6 1.0 HB2 A:HIS53 3.1 175.3 1.0 CG A:HIS53 3.1 163.3 1.0 H A:HIS53 3.3 125.5 1.0 H A:CYS24 3.3 157.4 1.0 HB2 A:CYS56 3.4 182.9 1.0 CB A:CYS56 3.4 152.4 1.0 CB A:CYS24 3.5 124.5 1.0 HB3 A:CYS24 3.5 149.4 1.0 CB A:HIS53 3.6 146.1 1.0 HB3 A:CYS56 3.7 182.9 1.0 NE2 A:HIS53 4.0 124.2 1.0 HB3 A:LYS23 4.0 132.5 1.0 H11 A:EDO402 4.0 174.2 1.0 N A:CYS24 4.1 131.2 1.0 N A:HIS53 4.1 104.6 1.0 CD2 A:HIS53 4.1 112.2 1.0 HB2 A:CYS24 4.1 149.4 1.0 CA A:CYS24 4.4 104.6 1.0 HB3 A:HIS53 4.4 175.3 1.0 CA A:HIS53 4.5 126.2 1.0 H A:CYS56 4.5 142.6 1.0 CA A:CYS21 4.6 97.5 1.0 HA A:TYR52 4.6 145.7 1.0 H A:LYS23 4.7 172.0 1.0 HE2 A:HIS53 4.7 149.0 1.0 HB2 A:GLU26 4.7 169.6 1.0 H A:GLU26 4.7 183.9 1.0 CA A:CYS56 4.8 138.1 1.0 H12 A:EDO402 4.9 174.2 1.0 CB A:LYS23 4.9 110.4 1.0 C1 A:EDO402 4.9 145.2 1.0 H A:SER25 4.9 157.3 1.0 HA A:CYS21 5.0 117.0 1.0

Zinc binding site 3 out of 4 in the Human PARP1 DELTAV687-E688 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 Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:229.5 occ:1.00 ND1 C:HIS53 2.1 112.0 1.0 SG C:CYS21 2.1 156.3 1.0 SG C:CYS56 2.3 116.9 1.0 SG C:CYS24 2.5 123.8 1.0 HB2 C:CYS21 2.7 163.1 1.0 H C:HIS53 2.7 122.8 1.0 CB C:CYS21 2.8 135.9 1.0 HB2 C:CYS56 2.9 168.9 1.0 HB2 C:HIS53 2.9 186.2 1.0 HB3 C:CYS21 2.9 163.1 1.0 CE1 C:HIS53 3.0 154.8 1.0 CG C:HIS53 3.1 159.5 1.0 CB C:CYS56 3.1 140.8 1.0 HE1 C:HIS53 3.2 185.7 1.0 H C:CYS24 3.3 151.1 1.0 HB3 C:CYS56 3.3 168.9 1.0 CB C:HIS53 3.4 155.2 1.0 N C:HIS53 3.5 102.3 1.0 HB3 C:LYS23 3.7 149.4 1.0 CB C:CYS24 3.9 140.4 1.0 HA C:TYR52 4.0 156.6 1.0 HB3 C:CYS24 4.0 168.5 1.0 CA C:HIS53 4.1 121.4 1.0 NE2 C:HIS53 4.1 123.3 1.0 N C:CYS24 4.2 125.9 1.0 CD2 C:HIS53 4.2 101.0 1.0 HB3 C:HIS53 4.3 186.2 1.0 H C:CYS56 4.3 135.8 1.0 CA C:CYS21 4.3 116.2 1.0 H C:LYS23 4.3 164.2 1.0 HB3 C:TYR52 4.4 127.2 1.0 HD1 C:TYR52 4.5 165.8 1.0 CA C:CYS56 4.5 133.8 1.0 HA C:CYS21 4.5 139.4 1.0 C C:TYR52 4.6 101.3 1.0 CA C:CYS24 4.6 107.4 1.0 CA C:TYR52 4.6 130.5 1.0 HB2 C:CYS24 4.7 168.5 1.0 CB C:LYS23 4.7 124.5 1.0 HA C:HIS53 4.8 145.6 1.0 HG12 C:ILE28 4.8 118.2 1.0 N C:CYS56 4.8 113.2 1.0 HE2 C:HIS53 4.9 148.0 1.0 H C:CYS21 4.9 137.5 1.0 HA C:CYS56 5.0 160.5 1.0 H C:GLU26 5.0 180.7 1.0 O C:HIS53 5.0 116.4 1.0 H C:SER25 5.0 150.1 1.0

Zinc binding site 4 out of 4 in the Human PARP1 DELTAV687-E688 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 Human PARP1 DELTAV687-E688 Bound to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:187.8 occ:1.00 SG C:CYS298 2.2 98.3 1.0 SG C:CYS321 2.4 126.7 1.0 SG C:CYS295 2.4 117.3 1.0 SG C:CYS311 2.4 99.8 1.0 H C:CYS298 3.0 157.2 1.0 HB3 C:CYS321 3.2 150.6 1.0 HB3 C:CYS298 3.2 118.6 1.0 CB C:CYS321 3.3 125.5 1.0 CB C:CYS298 3.3 98.9 1.0 HB2 C:CYS295 3.3 153.0 1.0 HB3 C:CYS311 3.4 189.6 1.0 CB C:CYS295 3.4 127.5 1.0 CB C:CYS311 3.4 158.0 1.0 HB2 C:CYS321 3.5 150.6 1.0 HB3 C:CYS295 3.5 153.0 1.0 HB2 C:CYS311 3.5 189.6 1.0 HB C:VAL323 3.6 125.7 1.0 HG21 C:VAL323 3.6 151.8 1.0 N C:CYS298 3.8 131.0 1.0 HG23 C:VAL323 4.0 151.8 1.0 HB2 C:GLU297 4.0 126.3 1.0 HB2 C:CYS298 4.1 118.6 1.0 H C:VAL323 4.1 132.7 1.0 CA C:CYS298 4.1 99.5 1.0 CG2 C:VAL323 4.1 126.5 1.0 H C:GLY300 4.3 115.1 1.0 H C:GLY313 4.3 114.2 1.0 H C:GLU297 4.3 168.8 1.0 CB C:VAL323 4.3 104.8 1.0 H C:SER299 4.5 128.2 1.0 HA3 C:GLY313 4.6 126.6 1.0 CA C:CYS321 4.7 101.3 1.0 CA C:CYS295 4.8 100.5 1.0 CA C:CYS311 4.9 98.4 1.0 C C:CYS298 4.9 106.2 1.0 N C:SER299 4.9 106.8 1.0 N C:VAL323 4.9 110.6 1.0 CB C:GLU297 4.9 105.2 1.0 HA C:CYS298 4.9 119.4 1.0 C C:GLU297 5.0 110.0 1.0 H C:MET322 5.0 139.5 1.0

E.Rouleau-Turcotte, D.B.Krastev, S.J.Pettitt, C.J.Lord, J.M.Pascal. Captured Snapshots of PARP1 in the Active State Reveal the Mechanics of PARP1 Allostery. Mol.Cell V. 82 2939 2022.
ISSN: ISSN 1097-2765
PubMed: 35793673
DOI: 10.1016/J.MOLCEL.2022.06.011