Zinc in PDB 7s6h: Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and to A Dna Double Strand Break.

All present enzymatic activity of Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and to A Dna Double Strand Break.:
2.4.2.30;

The structure of Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and to A Dna Double Strand Break., PDB code: 7s6h 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)	48.52 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.467, 110.651, 116.475, 90, 115.06, 90
R / Rfree (%)	21.1 / 25.1

The binding sites of Zinc atom in the Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and to A Dna Double Strand Break. (pdb code 7s6h). 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 Nad+ Analog Eb-47 and to A Dna Double Strand Break., PDB code: 7s6h:
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 Nad+ Analog Eb-47 and 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 Nad+ Analog Eb-47 and to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:155.2 occ:1.00 SG A:CYS298 2.3 108.6 1.0 SG A:CYS295 2.4 124.3 1.0 SG A:CYS321 2.4 117.7 1.0 SG A:CYS311 2.4 105.4 1.0 H A:CYS298 2.9 164.8 1.0 HB3 A:CYS321 3.0 161.9 1.0 CB A:CYS321 3.1 134.7 1.0 HB3 A:CYS298 3.2 138.1 1.0 HB2 A:CYS321 3.2 161.9 1.0 CB A:CYS295 3.2 126.4 1.0 HB3 A:CYS295 3.2 152.0 1.0 HB2 A:CYS295 3.2 152.0 1.0 CB A:CYS298 3.3 114.8 1.0 CB A:CYS311 3.4 138.8 1.0 HB3 A:CYS311 3.4 166.9 1.0 HB2 A:CYS311 3.4 166.9 1.0 HB A:VAL323 3.7 133.4 1.0 HG21 A:VAL323 3.7 159.2 1.0 N A:CYS298 3.7 137.1 1.0 HB2 A:GLU297 3.8 154.4 1.0 H A:GLY300 3.9 128.5 1.0 HG23 A:VAL323 4.0 159.2 1.0 CA A:CYS298 4.1 119.9 1.0 HB2 A:CYS298 4.1 138.1 1.0 CG2 A:VAL323 4.2 132.4 1.0 H A:GLU297 4.2 149.7 1.0 H A:VAL323 4.3 154.1 1.0 H A:SER299 4.3 131.6 1.0 H A:GLY313 4.3 120.4 1.0 CB A:VAL323 4.4 112.4 1.0 HA3 A:GLY313 4.5 146.9 1.0 CA A:CYS321 4.6 105.3 1.0 N A:SER299 4.7 109.4 1.0 HA3 A:GLY300 4.7 150.9 1.0 CA A:CYS295 4.7 107.9 1.0 N A:GLY300 4.7 106.9 1.0 C A:CYS298 4.7 103.3 1.0 CB A:GLU297 4.7 128.5 1.0 CA A:CYS311 4.8 106.9 1.0 C A:GLU297 4.8 106.4 1.0 HA A:CYS321 4.9 125.0 1.0 HA A:CYS298 4.9 144.2 1.0 N A:GLU297 4.9 124.5 1.0 HA A:CYS295 5.0 128.1 1.0

Zinc binding site 2 out of 4 in the Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and 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 Nad+ Analog Eb-47 and to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:175.9 occ:1.00 ND1 A:HIS53 2.0 125.7 1.0 SG A:CYS24 2.3 121.3 1.0 SG A:CYS56 2.3 154.7 1.0 SG A:CYS21 2.4 161.4 1.0 HB2 A:CYS21 2.8 192.2 1.0 HB2 A:HIS53 2.9 176.6 1.0 CB A:CYS21 2.9 159.9 1.0 HB3 A:CYS21 3.0 192.2 1.0 CE1 A:HIS53 3.0 141.4 1.0 HB2 A:CYS56 3.0 158.6 1.0 H A:HIS53 3.1 164.0 1.0 CG A:HIS53 3.1 140.7 1.0 H A:CYS24 3.1 191.8 1.0 HE1 A:HIS53 3.1 169.9 1.0 CB A:CYS56 3.2 131.9 1.0 HB3 A:CYS24 3.3 180.4 1.0 CB A:CYS24 3.4 150.1 1.0 CB A:HIS53 3.4 146.9 1.0 HB3 A:CYS56 3.6 158.6 1.0 N A:HIS53 3.9 136.4 1.0 N A:CYS24 3.9 159.6 1.0 HB3 A:LYS23 4.0 172.7 1.0 NE2 A:HIS53 4.1 118.9 1.0 H A:CYS56 4.1 172.7 1.0 CD2 A:HIS53 4.2 122.5 1.0 HB2 A:CYS24 4.2 180.4 1.0 HB3 A:HIS53 4.2 176.6 1.0 CA A:CYS24 4.3 131.0 1.0 CA A:HIS53 4.3 128.0 1.0 HA A:TYR52 4.4 139.5 1.0 CA A:CYS21 4.5 123.0 1.0 H A:LYS23 4.5 180.2 1.0 CA A:CYS56 4.6 157.5 1.0 H A:GLU26 4.7 177.5 1.0 HB2 A:GLU26 4.7 171.7 1.0 N A:CYS56 4.7 143.7 1.0 HA A:CYS21 4.8 147.9 1.0 HG2 A:LYS23 4.8 204.8 1.0 HE2 A:HIS53 4.9 141.2 1.0 CB A:LYS23 4.9 143.6 1.0 HA A:HIS53 4.9 153.9 1.0 H A:SER25 4.9 153.9 1.0 HD1 A:TYR52 4.9 191.7 1.0 C A:TYR52 5.0 121.8 1.0 HG12 A:ILE28 5.0 152.2 1.0 H A:CYS21 5.0 148.9 1.0 C A:CYS24 5.0 132.2 1.0

Zinc binding site 3 out of 4 in the Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and 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 Nad+ Analog Eb-47 and to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:185.9 occ:1.00 SG C:CYS298 2.3 104.6 1.0 SG C:CYS321 2.4 137.1 1.0 SG C:CYS295 2.4 142.7 1.0 SG C:CYS311 2.4 105.9 1.0 H C:CYS298 2.9 150.6 1.0 HB3 C:CYS321 3.0 153.4 1.0 CB C:CYS321 3.1 127.6 1.0 HB3 C:CYS298 3.2 127.5 1.0 HB2 C:CYS321 3.2 153.4 1.0 HB3 C:CYS295 3.2 142.8 1.0 CB C:CYS295 3.2 118.7 1.0 HB2 C:CYS295 3.2 142.8 1.0 CB C:CYS298 3.3 106.0 1.0 CB C:CYS311 3.4 142.5 1.0 HB3 C:CYS311 3.4 171.3 1.0 HB2 C:CYS311 3.4 171.3 1.0 N C:CYS298 3.7 125.3 1.0 HB C:VAL323 3.7 133.1 1.0 HG21 C:VAL323 3.7 139.4 1.0 HB2 C:GLU297 3.8 141.2 1.0 H C:GLY300 3.8 123.6 1.0 HG23 C:VAL323 4.0 139.4 1.0 CA C:CYS298 4.0 117.7 1.0 HB2 C:CYS298 4.1 127.5 1.0 CG2 C:VAL323 4.2 116.0 1.0 H C:GLU297 4.2 149.2 1.0 H C:SER299 4.3 146.1 1.0 H C:VAL323 4.3 140.0 1.0 H C:GLY313 4.3 121.2 1.0 HA3 C:GLY313 4.4 144.5 1.0 CB C:VAL323 4.4 112.1 1.0 CA C:CYS321 4.6 115.8 1.0 N C:SER299 4.6 121.5 1.0 HA3 C:GLY300 4.7 136.7 1.0 N C:GLY300 4.7 104.2 1.0 C C:CYS298 4.7 111.4 1.0 CA C:CYS295 4.7 109.6 1.0 CB C:GLU297 4.7 117.5 1.0 CA C:CYS311 4.8 108.2 1.0 C C:GLU297 4.8 117.1 1.0 HA C:CYS298 4.9 141.5 1.0 HA C:CYS321 4.9 139.2 1.0 N C:GLU297 4.9 124.1 1.0 HA C:CYS295 5.0 130.1 1.0

Zinc binding site 4 out of 4 in the Human PARP1 DELTAV687-E688 Bound to Nad+ Analog Eb-47 and 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 Nad+ Analog Eb-47 and to A Dna Double Strand Break. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:220.0 occ:1.00 ND1 C:HIS53 2.0 127.2 1.0 SG C:CYS24 2.3 129.0 1.0 SG C:CYS56 2.3 179.2 1.0 SG C:CYS21 2.4 157.9 1.0 HB2 C:CYS21 2.8 188.2 1.0 HB2 C:HIS53 2.9 168.0 1.0 CB C:CYS21 3.0 156.6 1.0 HB3 C:CYS21 3.0 188.2 1.0 CE1 C:HIS53 3.0 138.1 1.0 HB2 C:CYS56 3.0 166.0 1.0 H C:HIS53 3.1 182.5 1.0 CG C:HIS53 3.1 136.0 1.0 HE1 C:HIS53 3.1 166.0 1.0 H C:CYS24 3.1 167.6 1.0 CB C:CYS56 3.2 138.1 1.0 HB3 C:CYS24 3.3 179.8 1.0 CB C:HIS53 3.4 139.7 1.0 CB C:CYS24 3.5 149.6 1.0 HB3 C:CYS56 3.6 166.0 1.0 N C:HIS53 3.8 151.8 1.0 N C:CYS24 3.9 139.5 1.0 HB3 C:LYS23 4.0 167.6 1.0 NE2 C:HIS53 4.1 125.5 1.0 H C:CYS56 4.1 176.9 1.0 CD2 C:HIS53 4.2 125.9 1.0 HB3 C:HIS53 4.2 168.0 1.0 HB2 C:CYS24 4.2 179.8 1.0 CA C:HIS53 4.3 142.7 1.0 CA C:CYS24 4.3 130.4 1.0 HA C:TYR52 4.4 145.5 1.0 CA C:CYS21 4.5 121.3 1.0 H C:LYS23 4.6 181.2 1.0 CA C:CYS56 4.6 157.9 1.0 H C:GLU26 4.7 172.8 1.0 HB2 C:GLU26 4.7 188.6 1.0 N C:CYS56 4.7 147.2 1.0 HA C:CYS21 4.8 144.1 1.0 HG2 C:LYS23 4.8 184.5 1.0 HE2 C:HIS53 4.9 149.2 1.0 HA C:HIS53 4.9 171.5 1.0 CB C:LYS23 4.9 139.4 1.0 H C:SER25 4.9 150.3 1.0 HD1 C:TYR52 4.9 197.9 1.0 C C:TYR52 5.0 123.2 1.0 HG12 C:ILE28 5.0 155.5 1.0 H C:CYS21 5.0 157.3 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