Zinc in the structure of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna (pdb 3od8)

The binding sites of Zinc atom in the structure of Human Parp-1 Zinc Finger 1 (ZN1) Bound to Dna (pdb code 3od8). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3od8 structure was solved by J.M.PASCAL, M.-F.LANGELIER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.6-2.4 Space group P1211 a (A) 63.219 b (A) 107.696 c (A) 86.138 alpha (°) 90.00 beta (°) 100.20 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 24.1 Zinc Binding Sites: Zinc binding site 1 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys21, A: Lys23, A: Cys24, A: His53, A: Cys56, A: Hoh208, conact list: Atom Atom Distance (A) Zn CB A:Cys21 3.01 Zn SG A:Cys21 2.27 Zn CA A:Cys21 4.48 Zn CB A:Lys23 4.71 Zn C A:Lys23 4.99 Zn N A:Cys24 3.91 Zn CB A:Cys24 3.53 Zn SG A:Cys24 2.31 Zn C A:Cys24 4.98 Zn CA A:Cys24 4.29 Zn NE2 A:His53 4.19 Zn N A:His53 3.97 Zn CB A:His53 3.50 Zn ND1 A:His53 2.12 Zn CD2 A:His53 4.26 Zn CE1 A:His53 3.05 Zn CG A:His53 3.15 Zn CA A:His53 4.37 Zn N A:Cys56 5.00 Zn CB A:Cys56 3.13 Zn SG A:Cys56 2.28 Zn CA A:Cys56 4.58 Zn O A:Hoh208 4.89 interactive model: Zinc binding site 2 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Cys21, B: Lys23, B: Cys24, B: Ser25, B: His53, B: Cys56, B: Hoh297, conact list: Atom Atom Distance (A) Zn CB B:Cys21 3.04 Zn SG B:Cys21 2.29 Zn CA B:Cys21 4.52 Zn CB B:Lys23 4.88 Zn C B:Lys23 4.87 Zn N B:Cys24 3.72 Zn CB B:Cys24 3.22 Zn SG B:Cys24 2.19 Zn C B:Cys24 4.82 Zn CA B:Cys24 4.03 Zn N B:Ser25 4.88 Zn NE2 B:His53 4.19 Zn N B:His53 4.13 Zn CB B:His53 3.65 Zn ND1 B:His53 2.16 Zn CD2 B:His53 4.32 Zn CE1 B:His53 3.02 Zn CG B:His53 3.24 Zn CA B:His53 4.52 Zn CB B:Cys56 3.20 Zn SG B:Cys56 2.22 Zn CA B:Cys56 4.63 Zn O B:Hoh297 4.01 interactive model: Zinc binding site 3 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Cys21, C: Lys23, C: Cys24, C: Ser25, C: His53, C: Cys56, C: Hoh105, conact list: Atom Atom Distance (A) Zn CB C:Cys21 3.06 Zn SG C:Cys21 2.33 Zn CA C:Cys21 4.54 Zn CB C:Lys23 4.75 Zn C C:Lys23 4.89 Zn N C:Cys24 3.77 Zn CB C:Cys24 3.28 Zn SG C:Cys24 2.32 Zn C C:Cys24 4.83 Zn CA C:Cys24 4.09 Zn N C:Ser25 4.91 Zn NE2 C:His53 4.16 Zn N C:His53 4.13 Zn CB C:His53 3.61 Zn ND1 C:His53 2.12 Zn CD2 C:His53 4.28 Zn CE1 C:His53 2.99 Zn CG C:His53 3.20 Zn CA C:His53 4.51 Zn CB C:Cys56 3.22 Zn SG C:Cys56 2.21 Zn CA C:Cys56 4.66 Zn O C:Hoh105 4.48 interactive model: Zinc binding site 4 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Cys21, D: Lys23, D: Cys24, D: Ser25, D: His53, D: Cys56, conact list: Atom Atom Distance (A) Zn CB D:Cys21 3.12 Zn SG D:Cys21 2.27 Zn CA D:Cys21 4.60 Zn CB D:Lys23 4.85 Zn C D:Lys23 4.98 Zn N D:Cys24 3.83 Zn CB D:Cys24 3.28 Zn SG D:Cys24 2.22 Zn C D:Cys24 4.87 Zn CA D:Cys24 4.12 Zn N D:Ser25 4.99 Zn NE2 D:His53 4.29 Zn N D:His53 4.13 Zn CB D:His53 3.46 Zn ND1 D:His53 2.20 Zn CD2 D:His53 4.32 Zn CE1 D:His53 3.17 Zn CG D:His53 3.18 Zn CA D:His53 4.44 Zn CB D:Cys56 3.24 Zn SG D:Cys56 2.23 Zn CA D:Cys56 4.63 interactive model: Zinc binding site 5 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Cys21, E: Lys23, E: Cys24, E: Ser25, E: His53, E: Cys56, E: Hoh100, conact list: Atom Atom Distance (A) Zn CB E:Cys21 3.05 Zn SG E:Cys21 2.28 Zn CA E:Cys21 4.51 Zn CB E:Lys23 4.86 Zn C E:Lys23 4.95 Zn N E:Cys24 3.82 Zn CB E:Cys24 3.38 Zn SG E:Cys24 2.24 Zn C E:Cys24 4.81 Zn CA E:Cys24 4.12 Zn N E:Ser25 4.93 Zn NE2 E:His53 4.34 Zn N E:His53 4.03 Zn CB E:His53 3.59 Zn ND1 E:His53 2.27 Zn CD2 E:His53 4.40 Zn CE1 E:His53 3.20 Zn CG E:His53 3.28 Zn CA E:His53 4.44 Zn CB E:Cys56 3.16 Zn SG E:Cys56 2.30 Zn CA E:Cys56 4.60 Zn O E:Hoh100 4.47 interactive model: Zinc binding site 6 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: Cys21, F: Lys23, F: Cys24, F: His53, F: Cys56, G: Hoh121, conact list: Atom Atom Distance (A) Zn CB F:Cys21 3.09 Zn SG F:Cys21 2.29 Zn CA F:Cys21 4.58 Zn CB F:Lys23 4.91 Zn CG F:Lys23 4.72 Zn N F:Cys24 3.91 Zn CB F:Cys24 3.34 Zn SG F:Cys24 2.32 Zn C F:Cys24 4.94 Zn CA F:Cys24 4.19 Zn NE2 F:His53 4.26 Zn N F:His53 4.06 Zn CB F:His53 3.54 Zn ND1 F:His53 2.19 Zn CD2 F:His53 4.33 Zn CE1 F:His53 3.12 Zn CG F:His53 3.21 Zn CA F:His53 4.42 Zn CB F:Cys56 3.22 Zn SG F:Cys56 2.28 Zn CA F:Cys56 4.67 Zn O G:Hoh121 4.35 interactive model: Zinc binding site 7 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: Cys21, G: Lys23, G: Cys24, G: Ser25, G: His53, G: Cys56, G: Hoh132, conact list: Atom Atom Distance (A) Zn CB G:Cys21 2.99 Zn SG G:Cys21 2.31 Zn CA G:Cys21 4.47 Zn CB G:Lys23 4.87 Zn C G:Lys23 4.95 Zn N G:Cys24 3.84 Zn CB G:Cys24 3.38 Zn SG G:Cys24 2.27 Zn C G:Cys24 4.78 Zn CA G:Cys24 4.14 Zn N G:Ser25 4.94 Zn NE2 G:His53 4.14 Zn N G:His53 4.03 Zn CB G:His53 3.58 Zn ND1 G:His53 2.09 Zn CD2 G:His53 4.26 Zn CE1 G:His53 2.97 Zn CG G:His53 3.18 Zn CA G:His53 4.43 Zn CB G:Cys56 3.18 Zn SG G:Cys56 2.26 Zn CA G:Cys56 4.64 Zn O G:Hoh132 4.63 interactive model: Zinc binding site 8 out of 8 in 3od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3od8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: H: Cys21, H: Lys23, H: Cys24, H: His53, H: Cys56, conact list: Atom Atom Distance (A) Zn CB H:Cys21 3.04 Zn SG H:Cys21 2.28 Zn CA H:Cys21 4.51 Zn CB H:Lys23 4.61 Zn CG H:Lys23 4.70 Zn N H:Cys24 3.91 Zn CB H:Cys24 3.35 Zn SG H:Cys24 2.30 Zn C H:Cys24 4.93 Zn CA H:Cys24 4.20 Zn NE2 H:His53 4.03 Zn N H:His53 4.01 Zn CB H:His53 3.59 Zn ND1 H:His53 2.03 Zn CD2 H:His53 4.18 Zn CE1 H:His53 2.87 Zn CG H:His53 3.13 Zn CA H:His53 4.43 Zn CB H:Cys56 3.19 Zn SG H:Cys56 2.25 Zn CA H:Cys56 4.65 interactive model: