Zinc in the structure of Arrested Rna Polymerase II Reactivation Intermediate (pdb 3po3)

The binding sites of Zinc atom in the structure of Arrested Rna Polymerase II Reactivation Intermediate (pdb code 3po3). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3po3 structure was solved by A.C.M.CHEUNG, P.CRAMER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.3 Space group C2221 a (A) 220.019 b (A) 395.067 c (A) 280.429 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 18.9 Zinc Binding Sites: Zinc binding site 1 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3po3. 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: Cys107, A: His109, A: Cys110, A: Cys148, A: Gly166, A: Cys167, A: Gly168, A: Asn169, conact list: Atom Atom Distance (A) Zn CB A:Cys107 3.22 Zn SG A:Cys107 2.29 Zn CA A:Cys107 4.67 Zn CB A:His109 4.76 Zn ND1 A:His109 4.98 Zn C A:His109 4.89 Zn N A:Cys110 3.76 Zn CB A:Cys110 3.34 Zn SG A:Cys110 2.29 Zn C A:Cys110 4.91 Zn CA A:Cys110 4.08 Zn O A:Cys148 4.55 Zn CB A:Cys148 2.91 Zn SG A:Cys148 2.24 Zn C A:Cys148 4.97 Zn CA A:Cys148 4.39 Zn O A:Gly166 4.27 Zn C A:Gly166 4.97 Zn N A:Cys167 4.91 Zn CB A:Cys167 2.67 Zn SG A:Cys167 2.38 Zn C A:Cys167 4.56 Zn CA A:Cys167 4.10 Zn N A:Gly168 4.55 Zn N A:Asn169 4.80 interactive model: Zinc binding site 2 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3po3. 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: Cys67, A: Gln68, A: Cys70, A: Cys77, A: Pro78, A: His80, conact list: Atom Atom Distance (A) Zn O A:Cys67 3.93 Zn CB A:Cys67 3.58 Zn SG A:Cys67 2.22 Zn C A:Cys67 4.84 Zn CA A:Cys67 4.80 Zn NE2 A:Gln68 4.96 Zn OE1 A:Gln68 4.80 Zn CB A:Cys70 3.66 Zn SG A:Cys70 2.50 Zn CB A:Cys77 3.62 Zn SG A:Cys77 2.44 Zn CA A:Cys77 4.42 Zn O A:Pro78 4.06 Zn CD A:Pro78 4.65 Zn NE2 A:His80 1.98 Zn ND1 A:His80 4.08 Zn CD2 A:His80 3.04 Zn CE1 A:His80 2.91 Zn CG A:His80 4.13 interactive model: Zinc binding site 3 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3po3. 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: Ile30, B: Cys1163, B: Ile1165, B: Cys1166, B: Thr1170, B: Cys1182, B: Gly1184, B: Cys1185, conact list: Atom Atom Distance (A) Zn CD1 A:Ile30 4.97 Zn CB B:Cys1163 3.10 Zn SG B:Cys1163 2.41 Zn CA B:Cys1163 4.57 Zn N B:Ile1165 4.95 Zn CB B:Ile1165 4.59 Zn C B:Ile1165 4.70 Zn CA B:Ile1165 4.92 Zn O B:Cys1166 3.95 Zn N B:Cys1166 3.60 Zn CB B:Cys1166 3.66 Zn SG B:Cys1166 2.24 Zn C B:Cys1166 4.52 Zn CA B:Cys1166 4.15 Zn CB B:Thr1170 4.89 Zn CG2 B:Thr1170 4.82 Zn CB B:Cys1182 3.72 Zn SG B:Cys1182 2.35 Zn O B:Gly1184 4.78 Zn CB B:Cys1185 3.07 Zn SG B:Cys1185 2.20 Zn CA B:Cys1185 4.49 interactive model: Zinc binding site 4 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3po3. 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: Cys86, C: Phe87, C: Cys88, C: His91, C: Cys92, C: Asp93, C: Lys94, C: Cys95, conact list: Atom Atom Distance (A) Zn CB C:Cys86 3.08 Zn SG C:Cys86 2.37 Zn C C:Cys86 4.70 Zn CA C:Cys86 4.43 Zn N C:Phe87 4.92 Zn N C:Cys88 4.28 Zn CB C:Cys88 3.52 Zn SG C:Cys88 2.36 Zn CA C:Cys88 4.51 Zn O C:His91 4.62 Zn N C:His91 4.68 Zn C C:His91 3.82 Zn CA C:His91 4.15 Zn N C:Cys92 3.30 Zn CB C:Cys92 3.36 Zn SG C:Cys92 2.29 Zn C C:Cys92 4.66 Zn CA C:Cys92 3.86 Zn N C:Asp93 4.87 Zn N C:Lys94 4.81 Zn CB C:Lys94 4.73 Zn C C:Lys94 4.78 Zn NZ C:Lys94 4.58 Zn N C:Cys95 4.17 Zn CB C:Cys95 3.38 Zn SG C:Cys95 2.26 Zn CA C:Cys95 4.38 interactive model: Zinc binding site 5 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3po3. 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: I: Cys7, I: Arg8, I: Asp9, I: Cys10, I: Cys29, I: Thr31, I: Cys32, I: Tyr34, conact list: Atom Atom Distance (A) Zn CB I:Cys7 3.54 Zn SG I:Cys7 2.28 Zn CA I:Cys7 4.91 Zn O I:Arg8 3.91 Zn CB I:Asp9 4.93 Zn O I:Cys10 3.87 Zn N I:Cys10 3.96 Zn CB I:Cys10 3.80 Zn SG I:Cys10 2.18 Zn C I:Cys10 4.52 Zn CA I:Cys10 4.25 Zn CB I:Cys29 3.28 Zn SG I:Cys29 2.41 Zn CA I:Cys29 4.73 Zn CB I:Thr31 4.69 Zn C I:Thr31 4.44 Zn CA I:Thr31 4.92 Zn N I:Cys32 3.83 Zn CB I:Cys32 3.35 Zn SG I:Cys32 2.27 Zn C I:Cys32 4.73 Zn CA I:Cys32 4.09 Zn N I:Tyr34 4.99 Zn CB I:Tyr34 4.28 interactive model: Zinc binding site 6 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3po3. 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: I: Cys75, I: Lys77, I: Cys78, I: His79, I: Ser80, I: Cys103, I: Ser105, I: Cys106, I: Ser107, I: His108, conact list: Atom Atom Distance (A) Zn CB I:Cys75 3.26 Zn SG I:Cys75 2.35 Zn CA I:Cys75 4.71 Zn CB I:Lys77 4.66 Zn C I:Lys77 4.92 Zn N I:Cys78 3.81 Zn CB I:Cys78 3.34 Zn SG I:Cys78 2.32 Zn C I:Cys78 4.89 Zn CA I:Cys78 4.12 Zn N I:His79 4.90 Zn CB I:Ser80 4.99 Zn CB I:Cys103 3.17 Zn SG I:Cys103 2.44 Zn CA I:Cys103 4.62 Zn CB I:Ser105 4.55 Zn C I:Ser105 4.55 Zn CA I:Ser105 4.93 Zn N I:Cys106 3.43 Zn CB I:Cys106 3.09 Zn SG I:Cys106 2.30 Zn C I:Cys106 4.45 Zn CA I:Cys106 3.74 Zn N I:Ser107 4.76 Zn CB I:His108 4.94 interactive model: Zinc binding site 7 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3po3. 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: J: Cys7, J: Ser9, J: Cys10, J: Gly11, J: Lys12, J: Arg43, J: Cys45, J: Cys46, conact list: Atom Atom Distance (A) Zn O J:Cys7 4.89 Zn CB J:Cys7 3.38 Zn SG J:Cys7 2.25 Zn C J:Cys7 4.95 Zn CA J:Cys7 4.72 Zn CB J:Ser9 4.69 Zn C J:Ser9 4.89 Zn N J:Cys10 3.78 Zn CB J:Cys10 3.45 Zn SG J:Cys10 2.31 Zn C J:Cys10 4.81 Zn CA J:Cys10 4.12 Zn N J:Gly11 4.60 Zn N J:Lys12 4.96 Zn CB J:Lys12 4.91 Zn CB J:Arg43 4.71 Zn NE J:Arg43 4.40 Zn NH2 J:Arg43 4.82 Zn O J:Cys45 4.16 Zn N J:Cys45 4.70 Zn CB J:Cys45 3.44 Zn SG J:Cys45 2.35 Zn C J:Cys45 3.52 Zn CA J:Cys45 4.03 Zn N J:Cys46 3.13 Zn CB J:Cys46 3.59 Zn SG J:Cys46 2.44 Zn CA J:Cys46 3.57 interactive model: Zinc binding site 8 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3po3. 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: L: Cys31, L: Glu33, L: Cys34, L: Ser36, L: Cys48, L: Asp50, L: Cys51, conact list: Atom Atom Distance (A) Zn CB L:Cys31 3.34 Zn SG L:Cys31 2.43 Zn CA L:Cys31 4.80 Zn CB L:Glu33 4.65 Zn O L:Cys34 3.68 Zn N L:Cys34 4.13 Zn CB L:Cys34 3.95 Zn SG L:Cys34 2.23 Zn C L:Cys34 4.51 Zn CA L:Cys34 4.47 Zn CB L:Ser36 4.79 Zn OG L:Ser36 3.45 Zn CB L:Cys48 3.19 Zn SG L:Cys48 2.27 Zn CA L:Cys48 4.63 Zn N L:Asp50 4.87 Zn CB L:Asp50 4.37 Zn OD2 L:Asp50 4.80 Zn C L:Asp50 4.77 Zn CA L:Asp50 4.95 Zn O L:Cys51 3.83 Zn N L:Cys51 3.79 Zn CB L:Cys51 3.62 Zn SG L:Cys51 2.34 Zn C L:Cys51 4.37 Zn CA L:Cys51 4.16 interactive model: Zinc binding site 9 out of 9 in 3po3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 3po3. 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: S: Cys271, S: Cys274, S: Lys275, S: Glu276, S: Cys299, S: Ala301, S: Cys302, S: Gly303, S: Asn304, conact list: Atom Atom Distance (A) Zn CB S:Cys271 3.09 Zn SG S:Cys271 2.33 Zn CA S:Cys271 4.56 Zn N S:Cys274 4.07 Zn CB S:Cys274 3.57 Zn SG S:Cys274 2.29 Zn C S:Cys274 4.85 Zn CA S:Cys274 4.30 Zn N S:Lys275 4.90 Zn N S:Glu276 4.97 Zn CB S:Cys299 3.18 Zn SG S:Cys299 2.35 Zn CA S:Cys299 4.64 Zn C S:Ala301 4.85 Zn CB S:Ala301 4.67 Zn N S:Cys302 3.66 Zn CB S:Cys302 3.09 Zn SG S:Cys302 2.30 Zn C S:Cys302 4.62 Zn CA S:Cys302 3.91 Zn N S:Gly303 4.44 Zn CB S:Asn304 4.52 interactive model: