Zinc in the structure of Rna Polymerase II Elongation Complex (pdb 1i6h)

The binding sites of Zinc atom in the structure of Rna Polymerase II Elongation Complex (pdb code 1i6h). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1i6h structure was solved by A.L.GNATT, P.CRAMER, R.D.KORNBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-3.3 Space group C121 a (A) 157.300 b (A) 220.700 c (A) 191.300 alpha (°) 90.00 beta (°) 97.50 gamma (°) 90.00 Rfactor (%) 25 Rfree (%) 29.8 Zinc Binding Sites: Zinc binding site 1 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1i6h. 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 CB J:Cys7 3.50 Zn SG J:Cys7 2.52 Zn CA J:Cys7 4.96 Zn CB J:Ser9 4.28 Zn C J:Ser9 4.84 Zn N J:Cys10 3.72 Zn CB J:Cys10 3.48 Zn SG J:Cys10 2.08 Zn C J:Cys10 4.82 Zn CA J:Cys10 4.13 Zn N J:Gly11 4.76 Zn CB J:Lys12 4.85 Zn CD J:Arg43 4.60 Zn CG J:Arg43 4.44 Zn NE J:Arg43 4.33 Zn O J:Cys45 3.84 Zn N J:Cys45 4.58 Zn CB J:Cys45 3.27 Zn SG J:Cys45 1.93 Zn C J:Cys45 3.31 Zn CA J:Cys45 3.89 Zn N J:Cys46 2.98 Zn CB J:Cys46 3.13 Zn SG J:Cys46 1.81 Zn C J:Cys46 4.81 Zn CA J:Cys46 3.30 interactive model: Zinc binding site 2 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1i6h. 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: Asp90, C: His91, C: Cys92, C: Lys94, C: Cys95, conact list: Atom Atom Distance (A) Zn O C:Cys86 4.84 Zn CB C:Cys86 2.77 Zn SG C:Cys86 1.92 Zn C C:Cys86 4.51 Zn CA C:Cys86 4.16 Zn N C:Phe87 4.98 Zn N C:Cys88 4.21 Zn CB C:Cys88 3.27 Zn SG C:Cys88 2.28 Zn CA C:Cys88 4.34 Zn O C:Asp90 4.38 Zn O C:His91 4.58 Zn C C:His91 3.94 Zn CA C:His91 4.21 Zn O C:Cys92 4.85 Zn N C:Cys92 3.61 Zn CB C:Cys92 3.49 Zn SG C:Cys92 2.16 Zn C C:Cys92 4.65 Zn CA C:Cys92 4.08 Zn N C:Lys94 4.92 Zn CB C:Lys94 4.50 Zn C C:Lys94 4.80 Zn N C:Cys95 4.12 Zn CB C:Cys95 3.38 Zn SG C:Cys95 2.20 Zn CA C:Cys95 4.39 interactive model: Zinc binding site 3 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1i6h. 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: Cys10, I: Cys29, I: Thr31, I: Cys32, I: Ser33, I: Tyr34, conact list: Atom Atom Distance (A) Zn CB I:Cys7 3.82 Zn SG I:Cys7 2.80 Zn O I:Arg8 4.97 Zn N I:Cys10 4.61 Zn CB I:Cys10 3.65 Zn SG I:Cys10 1.91 Zn CA I:Cys10 4.69 Zn O I:Cys29 3.98 Zn CB I:Cys29 2.99 Zn SG I:Cys29 1.91 Zn C I:Cys29 4.55 Zn CA I:Cys29 4.35 Zn N I:Thr31 4.88 Zn CB I:Thr31 4.40 Zn CG2 I:Thr31 3.53 Zn C I:Thr31 4.56 Zn CA I:Thr31 4.90 Zn N I:Cys32 3.69 Zn CB I:Cys32 3.08 Zn SG I:Cys32 1.89 Zn C I:Cys32 4.71 Zn CA I:Cys32 3.97 Zn N I:Ser33 4.44 Zn N I:Tyr34 4.54 Zn CB I:Tyr34 4.07 Zn CG I:Tyr34 5.00 Zn CA I:Tyr34 4.99 interactive model: Zinc binding site 4 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1i6h. 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: Ser80, I: Cys103, I: Ser105, I: Cys106, I: Ser107, I: His108, conact list: Atom Atom Distance (A) Zn O I:Cys75 4.97 Zn N I:Cys75 4.55 Zn CB I:Cys75 2.56 Zn SG I:Cys75 1.76 Zn C I:Cys75 4.84 Zn CA I:Cys75 4.01 Zn CB I:Lys77 4.60 Zn N I:Cys78 3.94 Zn CB I:Cys78 3.93 Zn SG I:Cys78 2.40 Zn C I:Cys78 4.83 Zn CA I:Cys78 4.41 Zn CB I:Ser80 4.82 Zn OG I:Ser80 4.51 Zn O I:Cys103 4.99 Zn N I:Cys103 4.91 Zn CB I:Cys103 2.53 Zn SG I:Cys103 2.07 Zn C I:Cys103 4.69 Zn CA I:Cys103 4.04 Zn CB I:Ser105 4.95 Zn C I:Ser105 4.89 Zn N I:Cys106 3.90 Zn CB I:Cys106 3.48 Zn SG I:Cys106 1.89 Zn C I:Cys106 4.84 Zn CA I:Cys106 4.25 Zn N I:Ser107 4.87 Zn N I:His108 4.58 Zn CB I:His108 3.87 Zn CD2 I:His108 4.84 Zn CG I:His108 4.75 Zn CA I:His108 4.85 interactive model: Zinc binding site 5 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1i6h. 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: Cys34, L: Cys48, L: Lys49, L: Cys51, L: His53, conact list: Atom Atom Distance (A) Zn CB L:Cys31 3.43 Zn SG L:Cys31 2.52 Zn CA L:Cys31 4.87 Zn N L:Cys34 4.02 Zn CB L:Cys34 3.46 Zn SG L:Cys34 1.72 Zn C L:Cys34 4.98 Zn CA L:Cys34 4.31 Zn CB L:Cys48 3.38 Zn SG L:Cys48 2.52 Zn CA L:Cys48 4.84 Zn O L:Lys49 4.75 Zn N L:Lys49 4.77 Zn O L:Cys51 3.96 Zn N L:Cys51 4.68 Zn CB L:Cys51 3.59 Zn SG L:Cys51 1.81 Zn C L:Cys51 4.68 Zn CA L:Cys51 4.54 Zn CD2 L:His53 4.54 interactive model: Zinc binding site 6 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1i6h. 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: Met108, A: His109, A: Cys110, A: Gly111, A: Cys148, A: Cys167, A: Asn169, conact list: Atom Atom Distance (A) Zn O A:Cys107 4.71 Zn CB A:Cys107 4.38 Zn SG A:Cys107 4.30 Zn O A:Met108 3.77 Zn C A:Met108 4.77 Zn CB A:His109 4.59 Zn C A:His109 4.67 Zn O A:Cys110 4.89 Zn N A:Cys110 3.48 Zn CB A:Cys110 3.27 Zn SG A:Cys110 2.34 Zn C A:Cys110 4.25 Zn CA A:Cys110 3.81 Zn N A:Gly111 4.47 Zn CB A:Cys148 4.56 Zn SG A:Cys148 3.79 Zn O A:Cys167 4.27 Zn CB A:Cys167 3.87 Zn SG A:Cys167 2.16 Zn CA A:Cys167 5.00 Zn ND2 A:Asn169 4.78 interactive model: Zinc binding site 7 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 1i6h. 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: Cys1163, B: Cys1166, B: Thr1170, B: Cys1182, B: Cys1185, conact list: Atom Atom Distance (A) Zn CB B:Cys1163 3.18 Zn SG B:Cys1163 2.72 Zn CA B:Cys1163 4.71 Zn O B:Cys1166 4.13 Zn N B:Cys1166 4.39 Zn CB B:Cys1166 3.75 Zn SG B:Cys1166 1.96 Zn C B:Cys1166 4.80 Zn CA B:Cys1166 4.55 Zn CB B:Thr1170 4.85 Zn O B:Cys1182 4.41 Zn CB B:Cys1182 3.99 Zn SG B:Cys1182 2.23 Zn C B:Cys1182 4.92 Zn CA B:Cys1182 4.96 Zn N B:Cys1185 4.74 Zn CB B:Cys1185 3.13 Zn SG B:Cys1185 2.93 Zn CA B:Cys1185 4.47 interactive model: Zinc binding site 8 out of 8 in 1i6h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 1i6h. 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: Gln71, A: Cys77, A: His80, conact list: Atom Atom Distance (A) Zn O A:Cys67 3.11 Zn CB A:Cys67 2.98 Zn SG A:Cys67 2.02 Zn C A:Cys67 3.64 Zn CA A:Cys67 3.93 Zn N A:Gln68 4.55 Zn CB A:Gln68 4.64 Zn O A:Cys70 4.95 Zn N A:Cys70 4.87 Zn CB A:Cys70 3.42 Zn SG A:Cys70 2.09 Zn C A:Cys70 4.64 Zn CA A:Cys70 4.50 Zn O A:Gln71 4.35 Zn N A:Gln71 4.98 Zn CB A:Cys77 4.36 Zn SG A:Cys77 3.52 Zn C A:Cys77 4.91 Zn CA A:Cys77 4.50 Zn NE2 A:His80 2.31 Zn ND1 A:His80 4.44 Zn CD2 A:His80 3.18 Zn CE1 A:His80 3.37 Zn CG A:His80 4.38 interactive model: