Zinc in the structure of Co-Complex of Backtracked Rna Polymerase II With Tfiis (pdb 3gtm)

The binding sites of Zinc atom in the structure of Co-Complex of Backtracked Rna Polymerase II With Tfiis (pdb code 3gtm). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3gtm structure was solved by D.WANG, D.A.BUSHNELL, X.HUANG, K.D.WESTOVER, M.LEVITT, R.D.KORNBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-3.8 Space group C121 a (A) 172.329 b (A) 218.530 c (A) 193.913 alpha (°) 90.00 beta (°) 100.32 gamma (°) 90.00 Rfactor (%) 23.4 Rfree (%) 28.9 Zinc Binding Sites: Zinc binding site 1 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3gtm. 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, conact list: Atom Atom Distance (A) Zn O A:Cys107 4.72 Zn CB A:Cys107 3.77 Zn SG A:Cys107 2.98 Zn C A:Cys107 4.47 Zn CA A:Cys107 4.78 Zn O A:Met108 2.74 Zn N A:Met108 4.51 Zn C A:Met108 3.97 Zn CA A:Met108 4.90 Zn N A:His109 4.86 Zn CB A:His109 4.29 Zn CD2 A:His109 4.66 Zn C A:His109 4.78 Zn CG A:His109 4.87 Zn CA A:His109 4.85 Zn N A:Cys110 3.97 Zn CB A:Cys110 4.08 Zn SG A:Cys110 2.98 Zn CA A:Cys110 4.59 Zn N A:Gly111 4.99 Zn CB A:Cys148 3.45 Zn SG A:Cys148 2.77 Zn CA A:Cys148 4.90 Zn O A:Cys167 3.38 Zn SG A:Cys167 4.98 Zn C A:Cys167 4.61 interactive model: Zinc binding site 2 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3gtm. 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: Leu58, A: Cys67, A: Gln68, A: Cys70, A: Gln71, A: Cys77, A: His80, conact list: Atom Atom Distance (A) Zn O A:Leu58 4.42 Zn O A:Cys67 3.41 Zn CB A:Cys67 3.18 Zn SG A:Cys67 2.47 Zn C A:Cys67 4.23 Zn CA A:Cys67 4.30 Zn NE2 A:Gln68 4.44 Zn OE1 A:Gln68 4.01 Zn CD A:Gln68 4.39 Zn CB A:Cys70 3.41 Zn SG A:Cys70 3.07 Zn CA A:Cys70 4.84 Zn O A:Gln71 5.00 Zn CB A:Cys77 3.79 Zn SG A:Cys77 2.71 Zn NE2 A:His80 2.21 Zn ND1 A:His80 4.35 Zn CD2 A:His80 2.85 Zn CE1 A:His80 3.41 Zn CG A:His80 4.12 interactive model: Zinc binding site 3 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3gtm. 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: Cys1182, B: Cys1185, conact list: Atom Atom Distance (A) Zn O B:Cys1163 4.85 Zn CB B:Cys1163 2.94 Zn SG B:Cys1163 2.58 Zn C B:Cys1163 4.85 Zn CA B:Cys1163 4.40 Zn O B:Cys1166 3.82 Zn N B:Cys1166 3.85 Zn CB B:Cys1166 3.75 Zn SG B:Cys1166 2.36 Zn C B:Cys1166 4.26 Zn CA B:Cys1166 4.14 Zn CB B:Cys1182 4.07 Zn SG B:Cys1182 2.71 Zn O B:Cys1185 4.38 Zn N B:Cys1185 4.43 Zn CB B:Cys1185 2.76 Zn SG B:Cys1185 2.68 Zn C B:Cys1185 4.60 Zn CA B:Cys1185 4.08 interactive model: Zinc binding site 4 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3gtm. 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: Ser83, C: Cys86, C: Cys88, C: Asp90, C: His91, C: Cys92, C: Cys95, conact list: Atom Atom Distance (A) Zn O C:Ser83 4.89 Zn O C:Cys86 3.96 Zn N C:Cys86 4.84 Zn CB C:Cys86 2.73 Zn SG C:Cys86 2.34 Zn C C:Cys86 4.17 Zn CA C:Cys86 4.01 Zn N C:Cys88 4.59 Zn CB C:Cys88 3.91 Zn SG C:Cys88 2.70 Zn CA C:Cys88 4.85 Zn C C:Asp90 4.67 Zn O C:His91 4.29 Zn N C:His91 3.88 Zn C C:His91 3.34 Zn CA C:His91 3.58 Zn O C:Cys92 4.71 Zn N C:Cys92 2.63 Zn CB C:Cys92 2.93 Zn SG C:Cys92 2.37 Zn C C:Cys92 4.27 Zn CA C:Cys92 3.33 Zn N C:Cys95 4.72 Zn CB C:Cys95 3.85 Zn SG C:Cys95 2.49 Zn CA C:Cys95 4.85 interactive model: Zinc binding site 5 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3gtm. 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: Asn11, I: Cys29, I: Cys32, I: Ser33, I: Tyr34, conact list: Atom Atom Distance (A) Zn CB I:Cys7 3.72 Zn SG I:Cys7 2.56 Zn O I:Arg8 4.16 Zn OD2 I:Asp9 3.09 Zn CG I:Asp9 4.33 Zn N I:Cys10 3.98 Zn CB I:Cys10 3.43 Zn SG I:Cys10 2.52 Zn C I:Cys10 4.51 Zn CA I:Cys10 4.13 Zn N I:Asn11 4.58 Zn CB I:Cys29 3.59 Zn SG I:Cys29 3.35 Zn N I:Cys32 4.92 Zn CB I:Cys32 3.12 Zn SG I:Cys32 2.29 Zn CA I:Cys32 4.52 Zn N I:Ser33 4.96 Zn N I:Tyr34 4.65 Zn CB I:Tyr34 3.69 Zn CD1 I:Tyr34 4.66 Zn CG I:Tyr34 4.49 Zn CA I:Tyr34 4.84 interactive model: Zinc binding site 6 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3gtm. 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: Cys103, I: Ser105, I: Cys106, I: Ser107, I: His108, conact list: Atom Atom Distance (A) Zn CB I:Cys75 3.80 Zn SG I:Cys75 2.62 Zn C I:Lys77 4.98 Zn N I:Cys78 3.74 Zn CB I:Cys78 2.89 Zn SG I:Cys78 2.47 Zn C I:Cys78 4.49 Zn CA I:Cys78 3.82 Zn N I:His79 4.67 Zn CB I:Cys103 3.42 Zn SG I:Cys103 2.53 Zn CA I:Cys103 4.80 Zn N I:Ser105 4.79 Zn CB I:Ser105 4.14 Zn OG I:Ser105 4.96 Zn C I:Ser105 4.45 Zn CA I:Ser105 4.69 Zn N I:Cys106 3.71 Zn CB I:Cys106 3.46 Zn SG I:Cys106 2.49 Zn C I:Cys106 4.80 Zn CA I:Cys106 4.14 Zn N I:Ser107 4.91 Zn N I:His108 4.97 Zn CB I:His108 4.48 interactive model: Zinc binding site 7 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3gtm. 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, J: Met49, conact list: Atom Atom Distance (A) Zn CB J:Cys7 3.08 Zn SG J:Cys7 2.47 Zn CA J:Cys7 4.59 Zn OG J:Ser9 4.22 Zn C J:Ser9 4.95 Zn N J:Cys10 3.73 Zn CB J:Cys10 2.96 Zn SG J:Cys10 2.74 Zn C J:Cys10 4.59 Zn CA J:Cys10 3.87 Zn N J:Gly11 4.21 Zn N J:Lys12 4.89 Zn CD J:Arg43 4.78 Zn CG J:Arg43 4.36 Zn NE J:Arg43 4.64 Zn O J:Cys45 4.11 Zn N J:Cys45 4.91 Zn CB J:Cys45 3.56 Zn SG J:Cys45 2.45 Zn C J:Cys45 3.52 Zn CA J:Cys45 4.14 Zn N J:Cys46 2.94 Zn CB J:Cys46 3.25 Zn SG J:Cys46 2.25 Zn C J:Cys46 4.79 Zn CA J:Cys46 3.28 Zn CE J:Met49 4.98 interactive model: Zinc binding site 8 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3gtm. 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: Ser36, L: Cys48, L: Lys49, L: Cys51, L: His53, conact list: Atom Atom Distance (A) Zn CB L:Cys31 2.99 Zn SG L:Cys31 2.58 Zn CA L:Cys31 4.32 Zn N L:Cys34 5.00 Zn CB L:Cys34 4.12 Zn SG L:Cys34 2.34 Zn OG L:Ser36 4.98 Zn CB L:Cys48 2.80 Zn SG L:Cys48 2.83 Zn C L:Cys48 4.78 Zn CA L:Cys48 4.28 Zn N L:Lys49 4.70 Zn O L:Cys51 3.46 Zn N L:Cys51 4.18 Zn CB L:Cys51 3.00 Zn SG L:Cys51 2.41 Zn C L:Cys51 3.99 Zn CA L:Cys51 3.88 Zn O L:His53 4.48 interactive model: Zinc binding site 9 out of 9 in 3gtm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 3gtm. 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: Gly272, S: Lys273, S: Cys274, S: Cys299, S: Cys302, S: Gly303, S: Asn304, conact list: Atom Atom Distance (A) Zn CA S:Cys271 4.69 Zn N S:Gly272 4.86 Zn N S:Lys273 4.45 Zn CA S:Lys273 4.63 Zn N S:Cys274 4.28 Zn O S:Cys299 4.89 Zn N S:Cys299 4.82 Zn C S:Cys299 4.77 Zn CA S:Cys299 4.01 Zn N S:Cys302 4.57 Zn C S:Cys302 4.88 Zn CA S:Cys302 4.36 Zn N S:Gly303 4.71 Zn N S:Asn304 4.83 interactive model: