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Zinc in PDB 7s81: Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break.

Enzymatic activity of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break.

All present enzymatic activity of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break.:
2.4.2.30;

Protein crystallography data

The structure of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break., PDB code: 7s81 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) 49.35 / 3.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.759, 128.552, 227.379, 90, 90, 90
R / Rfree (%) 25.2 / 31.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. (pdb code 7s81). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break., PDB code: 7s81:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7s81

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Zinc binding site 1 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn200

b:161.3
occ:1.00
ND1 N:HIS53 2.0 186.7 1.0
SG N:CYS24 2.3 181.2 1.0
SG N:CYS56 2.3 168.5 1.0
SG N:CYS21 2.3 167.8 1.0
HB2 N:HIS53 2.8 160.4 1.0
HB2 N:CYS21 2.9 279.2 1.0
CE1 N:HIS53 3.0 192.5 1.0
CG N:HIS53 3.0 211.1 1.0
CB N:CYS21 3.0 231.2 1.0
HB3 N:CYS21 3.1 279.2 1.0
HB2 N:CYS56 3.2 262.0 1.0
H N:HIS53 3.2 135.2 1.0
HE1 N:HIS53 3.2 232.7 1.0
H N:CYS24 3.3 184.6 1.0
CB N:CYS56 3.3 216.9 1.0
CB N:HIS53 3.4 132.2 1.0
HB3 N:CYS56 3.6 262.0 1.0
CB N:CYS24 3.7 158.4 1.0
HB3 N:CYS24 3.7 191.8 1.0
N N:HIS53 3.9 119.9 1.0
HB3 N:LYS23 4.0 218.4 1.0
NE2 N:HIS53 4.0 175.9 1.0
CD2 N:HIS53 4.0 248.5 1.0
N N:CYS24 4.1 152.4 1.0
HB3 N:HIS53 4.1 160.4 1.0
CA N:HIS53 4.3 140.8 1.0
H N:LYS23 4.3 162.6 1.0
H N:CYS56 4.4 139.5 1.0
HB2 N:CYS24 4.4 191.8 1.0
CA N:CYS21 4.5 143.6 1.0
CA N:CYS24 4.5 229.0 1.0
HA N:TYR52 4.6 176.3 1.0
CA N:CYS56 4.7 153.8 1.0
HA N:CYS21 4.7 174.0 1.0
HE2 N:HIS53 4.8 212.8 1.0
H N:GLU26 4.8 193.8 1.0
H N:SER25 4.8 203.2 1.0
HD2 N:HIS53 4.9 300.0 1.0
N N:CYS56 4.9 123.5 1.0
CB N:LYS23 4.9 180.6 1.0
HA N:HIS53 4.9 170.7 1.0
H N:LYS22 5.0 212.9 1.0

Zinc binding site 2 out of 8 in 7s81

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Zinc binding site 2 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:227.9
occ:1.00
ND1 I:HIS53 2.0 131.8 1.0
SG I:CYS24 2.3 133.3 1.0
SG I:CYS56 2.3 213.3 1.0
SG I:CYS21 2.3 145.5 1.0
HB2 I:HIS53 2.8 228.6 1.0
HB2 I:CYS21 2.9 291.4 1.0
CE1 I:HIS53 2.9 230.4 1.0
CG I:HIS53 3.0 153.0 1.0
CB I:CYS21 3.0 241.4 1.0
HB3 I:CYS21 3.1 291.4 1.0
HE1 I:HIS53 3.1 278.3 1.0
H I:HIS53 3.2 190.9 1.0
HB2 I:CYS56 3.2 291.4 1.0
H I:CYS24 3.3 273.9 1.0
CB I:CYS56 3.3 241.4 1.0
CB I:HIS53 3.4 189.1 1.0
HB3 I:CYS56 3.6 291.4 1.0
CB I:CYS24 3.7 211.1 1.0
HB3 I:CYS24 3.7 255.1 1.0
N I:HIS53 3.9 157.7 1.0
NE2 I:HIS53 4.0 237.1 1.0
HB3 I:LYS23 4.0 165.8 1.0
CD2 I:HIS53 4.0 184.8 1.0
N I:CYS24 4.1 226.8 1.0
HB3 I:HIS53 4.1 228.6 1.0
CA I:HIS53 4.3 141.7 1.0
H I:LYS23 4.4 148.4 1.0
H I:CYS56 4.4 220.8 1.0
HB2 I:CYS24 4.4 255.1 1.0
CA I:CYS21 4.5 199.5 1.0
CA I:CYS24 4.5 135.1 1.0
HA I:TYR52 4.6 143.9 1.0
CA I:CYS56 4.7 223.2 1.0
HA I:CYS21 4.7 241.1 1.0
HE2 I:HIS53 4.8 286.2 1.0
H I:GLU26 4.8 160.8 1.0
H I:SER25 4.8 234.3 1.0
HD2 I:HIS53 4.9 223.5 1.0
N I:CYS56 4.9 182.6 1.0
HA I:HIS53 4.9 171.8 1.0
CB I:LYS23 4.9 136.8 1.0
H I:LYS22 5.0 167.2 1.0
HB2 I:GLU26 5.0 264.5 1.0

Zinc binding site 3 out of 8 in 7s81

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Zinc binding site 3 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:154.5
occ:1.00
ND1 A:HIS53 2.0 133.8 1.0
SG A:CYS24 2.3 136.3 1.0
SG A:CYS21 2.3 160.6 1.0
SG A:CYS56 2.3 144.1 1.0
HB2 A:HIS53 2.8 241.9 1.0
HB2 A:CYS21 2.9 153.2 1.0
CE1 A:HIS53 2.9 173.3 1.0
CG A:HIS53 3.0 132.8 1.0
CB A:CYS21 3.0 134.9 1.0
HB3 A:CYS21 3.1 153.2 1.0
HE1 A:HIS53 3.1 209.7 1.0
H A:HIS53 3.2 164.0 1.0
HB2 A:CYS56 3.2 175.0 1.0
H A:CYS24 3.3 223.0 1.0
CB A:CYS56 3.3 144.4 1.0
CB A:HIS53 3.4 200.2 1.0
HB3 A:CYS56 3.6 175.0 1.0
CB A:CYS24 3.7 238.0 1.0
HB3 A:CYS24 3.7 287.4 1.0
N A:HIS53 3.9 135.2 1.0
NE2 A:HIS53 4.0 135.3 1.0
HB3 A:LYS23 4.0 161.4 1.0
CD2 A:HIS53 4.0 133.8 1.0
N A:CYS24 4.1 184.4 1.0
HB3 A:HIS53 4.1 241.9 1.0
CA A:HIS53 4.3 130.6 1.0
H A:LYS23 4.4 200.7 1.0
H A:CYS56 4.4 147.7 1.0
HB2 A:CYS24 4.4 287.4 1.0
CA A:CYS21 4.5 135.4 1.0
CA A:CYS24 4.5 241.9 1.0
HA A:TYR52 4.6 175.3 1.0
CA A:CYS56 4.7 159.5 1.0
HA A:CYS21 4.7 153.8 1.0
HE2 A:HIS53 4.8 153.7 1.0
H A:GLU26 4.8 240.1 1.0
H A:SER25 4.8 159.0 1.0
HD2 A:HIS53 4.9 151.8 1.0
N A:CYS56 4.9 130.3 1.0
HA A:HIS53 4.9 148.0 1.0
CB A:LYS23 5.0 135.4 1.0
H A:LYS22 5.0 224.8 1.0
HB2 A:GLU26 5.0 221.5 1.0

Zinc binding site 4 out of 8 in 7s81

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Zinc binding site 4 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn400

b:224.5
occ:1.00
SG G:CYS295 2.3 187.6 1.0
SG G:CYS298 2.3 188.3 1.0
SG G:CYS311 2.3 190.8 1.0
SG G:CYS321 2.3 210.9 1.0
HG21 G:VAL323 2.9 214.2 1.0
HB3 G:CYS321 3.1 217.7 1.0
CB G:CYS321 3.3 188.7 1.0
HB3 G:CYS311 3.3 231.5 1.0
HB G:VAL323 3.3 215.6 1.0
CB G:CYS311 3.3 191.5 1.0
H G:CYS298 3.4 213.8 1.0
HB2 G:CYS295 3.5 217.7 1.0
HB2 G:CYS311 3.5 231.5 1.0
CB G:CYS295 3.5 188.7 1.0
HB2 G:CYS321 3.5 217.7 1.0
CG2 G:VAL323 3.6 185.8 1.0
HG23 G:VAL323 3.6 214.2 1.0
HB3 G:CYS295 3.8 217.7 1.0
CB G:CYS298 3.8 192.8 1.0
HB3 G:CYS298 3.8 233.0 1.0
CB G:VAL323 4.0 186.9 1.0
H G:VAL323 4.0 216.3 1.0
H G:GLY313 4.1 222.7 1.0
N G:CYS298 4.2 185.4 1.0
H G:GLY300 4.3 222.2 1.0
HA3 G:GLY313 4.3 221.3 1.0
H G:GLU297 4.3 223.7 1.0
HB2 G:CYS298 4.4 233.0 1.0
HG22 G:VAL323 4.4 214.2 1.0
HB2 G:GLU297 4.6 259.4 1.0
H G:GLU296 4.6 214.4 1.0
CA G:CYS298 4.6 197.2 1.0
CA G:CYS321 4.6 188.8 1.0
HG11 G:VAL323 4.7 215.0 1.0
CA G:CYS311 4.7 193.0 1.0
N G:VAL323 4.8 187.5 1.0
H G:SER299 4.8 322.1 1.0
CA G:CYS295 4.8 198.1 1.0
N G:GLY313 4.9 192.8 1.0
CG1 G:VAL323 4.9 186.4 1.0
HA G:CYS295 4.9 239.5 1.0
C G:CYS321 4.9 231.6 1.0
HA3 G:GLY300 5.0 220.5 1.0
CA G:GLY313 5.0 191.7 1.0

Zinc binding site 5 out of 8 in 7s81

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Zinc binding site 5 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 5 of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn400

b:267.7
occ:1.00
SG O:CYS295 2.3 149.3 1.0
SG O:CYS298 2.3 128.6 1.0
SG O:CYS311 2.3 125.6 1.0
SG O:CYS321 2.3 185.9 1.0
HG21 O:VAL323 2.8 284.7 1.0
HB3 O:CYS321 3.1 226.8 1.0
CB O:CYS321 3.3 187.5 1.0
HB3 O:CYS311 3.3 252.0 1.0
CB O:CYS311 3.3 208.5 1.0
HB O:VAL323 3.3 143.5 1.0
H O:CYS298 3.4 207.5 1.0
HB2 O:CYS311 3.5 252.0 1.0
HB2 O:CYS295 3.5 305.1 1.0
CB O:CYS295 3.5 252.8 1.0
HB2 O:CYS321 3.5 226.8 1.0
CG2 O:VAL323 3.6 235.8 1.0
HG23 O:VAL323 3.6 284.7 1.0
HB3 O:CYS295 3.8 305.1 1.0
CB O:CYS298 3.8 225.4 1.0
HB3 O:CYS298 3.8 272.2 1.0
CB O:VAL323 3.9 123.6 1.0
H O:VAL323 4.0 165.9 1.0
H O:GLY313 4.1 144.4 1.0
N O:CYS298 4.2 171.5 1.0
HA3 O:GLY313 4.3 204.9 1.0
H O:GLY300 4.3 257.7 1.0
H O:GLU297 4.3 259.8 1.0
HG22 O:VAL323 4.4 284.7 1.0
HB2 O:CYS298 4.4 272.2 1.0
HB2 O:GLU297 4.6 286.8 1.0
H O:GLU296 4.6 240.9 1.0
CA O:CYS298 4.6 222.9 1.0
CA O:CYS321 4.6 130.0 1.0
HG11 O:VAL323 4.7 162.9 1.0
CA O:CYS311 4.7 139.8 1.0
N O:VAL323 4.8 136.8 1.0
H O:SER299 4.8 292.2 1.0
CA O:CYS295 4.8 245.0 1.0
N O:GLY313 4.8 127.6 1.0
CG1 O:VAL323 4.9 134.3 1.0
HA O:CYS295 4.9 295.7 1.0
C O:CYS321 4.9 168.8 1.0
CA O:GLY313 5.0 169.3 1.0

Zinc binding site 6 out of 8 in 7s81

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Zinc binding site 6 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 6 of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn400

b:143.3
occ:1.00
SG J:CYS295 2.3 134.0 1.0
SG J:CYS311 2.3 131.1 1.0
SG J:CYS298 2.3 133.0 1.0
SG J:CYS321 2.3 142.4 1.0
HG21 J:VAL323 2.9 297.1 1.0
HB3 J:CYS321 3.1 273.6 1.0
CB J:CYS321 3.3 226.5 1.0
HB3 J:CYS311 3.3 149.1 1.0
CB J:CYS311 3.3 131.5 1.0
HB J:VAL323 3.3 154.6 1.0
HB2 J:CYS295 3.4 269.2 1.0
H J:CYS298 3.4 167.6 1.0
HB2 J:CYS311 3.5 149.1 1.0
CB J:CYS295 3.5 222.9 1.0
HB2 J:CYS321 3.6 273.6 1.0
CG2 J:VAL323 3.6 246.1 1.0
HG23 J:VAL323 3.6 297.1 1.0
HB3 J:CYS295 3.7 269.2 1.0
CB J:CYS298 3.8 173.4 1.0
HB3 J:CYS298 3.8 209.9 1.0
CB J:VAL323 3.9 136.1 1.0
H J:VAL323 4.0 155.6 1.0
H J:GLY313 4.1 161.8 1.0
N J:CYS298 4.2 138.2 1.0
H J:GLY300 4.3 232.6 1.0
HA3 J:GLY313 4.3 167.7 1.0
H J:GLU297 4.3 207.1 1.0
HG22 J:VAL323 4.4 297.1 1.0
HB2 J:CYS298 4.4 209.9 1.0
H J:GLU296 4.6 253.8 1.0
HB2 J:GLU297 4.6 193.8 1.0
CA J:CYS298 4.6 158.4 1.0
CA J:CYS321 4.7 142.7 1.0
HG11 J:VAL323 4.7 235.3 1.0
CA J:CYS311 4.7 130.3 1.0
N J:VAL323 4.8 136.9 1.0
H J:SER299 4.8 280.2 1.0
CA J:CYS295 4.8 213.3 1.0
N J:GLY313 4.8 133.4 1.0
HA J:CYS295 4.9 257.7 1.0
CG1 J:VAL323 4.9 194.6 1.0
C J:CYS321 5.0 136.5 1.0
CA J:GLY313 5.0 138.3 1.0
HA3 J:GLY300 5.0 204.8 1.0

Zinc binding site 7 out of 8 in 7s81

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Zinc binding site 7 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 7 of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn200

b:246.8
occ:1.00
ND1 F:HIS53 2.0 250.2 1.0
SG F:CYS24 2.3 280.3 1.0
SG F:CYS56 2.3 305.0 1.0
SG F:CYS21 2.3 216.8 1.0
HB2 F:HIS53 2.8 314.2 1.0
HB2 F:CYS21 2.9 323.5 1.0
CE1 F:HIS53 3.0 258.5 1.0
CG F:HIS53 3.0 246.5 1.0
CB F:CYS21 3.0 268.1 1.0
HB3 F:CYS21 3.1 323.5 1.0
HE1 F:HIS53 3.2 312.0 1.0
HB2 F:CYS56 3.2 377.4 1.0
H F:HIS53 3.2 307.6 1.0
H F:CYS24 3.3 332.0 1.0
CB F:CYS56 3.3 313.1 1.0
CB F:HIS53 3.4 260.4 1.0
HB3 F:CYS56 3.6 377.4 1.0
CB F:CYS24 3.7 279.1 1.0
HB3 F:CYS24 3.7 336.6 1.0
N F:HIS53 3.9 254.9 1.0
HB3 F:LYS23 4.0 255.4 1.0
NE2 F:HIS53 4.0 254.0 1.0
CD2 F:HIS53 4.0 249.9 1.0
N F:CYS24 4.1 275.2 1.0
HB3 F:HIS53 4.1 314.2 1.0
CA F:HIS53 4.3 239.2 1.0
H F:LYS23 4.3 254.2 1.0
H F:CYS56 4.4 369.2 1.0
HB2 F:CYS24 4.4 336.6 1.0
CA F:CYS24 4.5 279.3 1.0
CA F:CYS21 4.5 229.1 1.0
HA F:TYR52 4.6 249.1 1.0
CA F:CYS56 4.7 305.0 1.0
HA F:CYS21 4.7 276.7 1.0
HE2 F:HIS53 4.8 306.6 1.0
H F:GLU26 4.8 341.3 1.0
H F:SER25 4.8 285.0 1.0
HD2 F:HIS53 4.9 301.7 1.0
N F:CYS56 4.9 306.2 1.0
CB F:LYS23 4.9 220.1 1.0
HA F:HIS53 4.9 288.8 1.0
H F:LYS22 5.0 311.0 1.0

Zinc binding site 8 out of 8 in 7s81

Go back to Zinc Binding Sites List in 7s81
Zinc binding site 8 out of 8 in the Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) 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 8 of Structure of Human PARP1 Domains (ZN1, ZN3, Wgr, Hd) Bound to A Dna Double Strand Break. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:198.6
occ:1.00
SG B:CYS311 2.3 191.0 1.0
SG B:CYS295 2.3 188.7 1.0
SG B:CYS321 2.3 227.0 1.0
SG B:CYS298 2.3 148.6 1.0
HG21 B:VAL323 2.8 223.8 1.0
HB3 B:CYS321 3.1 204.5 1.0
CB B:CYS321 3.3 168.9 1.0
HB3 B:CYS311 3.3 189.9 1.0
HB B:VAL323 3.3 151.8 1.0
CB B:CYS311 3.3 156.8 1.0
HB2 B:CYS311 3.4 189.9 1.0
H B:CYS298 3.4 162.3 1.0
HB2 B:CYS295 3.5 249.6 1.0
CB B:CYS295 3.5 206.5 1.0
HB2 B:CYS321 3.6 204.5 1.0
CG2 B:VAL323 3.6 185.0 1.0
HG23 B:VAL323 3.6 223.8 1.0
HB3 B:CYS295 3.8 249.6 1.0
CB B:CYS298 3.8 182.3 1.0
HB3 B:CYS298 3.8 220.5 1.0
CB B:VAL323 3.9 125.9 1.0
H B:VAL323 4.0 201.0 1.0
H B:GLY313 4.1 151.1 1.0
N B:CYS298 4.2 142.5 1.0
HA3 B:GLY313 4.3 198.6 1.0
H B:GLY300 4.3 308.1 1.0
H B:GLU297 4.3 283.6 1.0
HG22 B:VAL323 4.4 223.8 1.0
HB2 B:CYS298 4.5 220.5 1.0
H B:GLU296 4.6 321.4 1.0
HB2 B:GLU297 4.6 291.3 1.0
CA B:CYS298 4.6 185.2 1.0
CA B:CYS321 4.6 133.8 1.0
HG11 B:VAL323 4.7 241.4 1.0
CA B:CYS311 4.7 165.9 1.0
N B:VAL323 4.8 166.1 1.0
CA B:CYS295 4.8 228.3 1.0
H B:SER299 4.8 303.3 1.0
N B:GLY313 4.8 133.2 1.0
CG1 B:VAL323 4.9 199.7 1.0
HA B:CYS295 4.9 275.7 1.0
C B:CYS321 4.9 165.0 1.0
CA B:GLY313 5.0 164.1 1.0
HA3 B:GLY300 5.0 256.0 1.0
CA B:VAL323 5.0 171.0 1.0

Reference:

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
Page generated: Sat Apr 8 03:06:59 2023

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