Zinc in the structure of Crystal Structure of An Rna Polymerase II-Tfiib Complex (pdb 3k7a)

The binding sites of Zinc atom in the structure of Crystal Structure of An Rna Polymerase II-Tfiib Complex (pdb code 3k7a). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3k7a structure was solved by X.LIU, D.A.BUSHNELL, D.WANG, G.CALERO, R.D.KORNBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.8 Space group I222 a (A) 204.150 b (A) 216.210 c (A) 420.980 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 26.3 Rfree (%) 31.3 Zinc Binding Sites: Zinc binding site 1 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3k7a. 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 4.66 Zn CB A:Cys107 3.98 Zn SG A:Cys107 3.19 Zn C A:Cys107 4.76 Zn O A:Met108 3.58 Zn C A:Met108 4.58 Zn CB A:His109 4.61 Zn C A:His109 4.89 Zn N A:Cys110 3.77 Zn CB A:Cys110 3.59 Zn SG A:Cys110 2.76 Zn C A:Cys110 4.81 Zn CA A:Cys110 4.19 Zn N A:Gly111 4.62 Zn CB A:Cys148 4.07 Zn SG A:Cys148 3.48 Zn O A:Cys167 3.75 Zn CB A:Cys167 3.76 Zn SG A:Cys167 2.27 Zn C A:Cys167 4.65 Zn CA A:Cys167 4.72 Zn ND2 A:Asn169 4.89 interactive model: Zinc binding site 2 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3k7a. 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: Cys70, A: Gln71, A: Glu76, A: Cys77, A: Pro78, A: His80, conact list: Atom Atom Distance (A) Zn O A:Cys67 4.26 Zn CB A:Cys67 4.01 Zn SG A:Cys67 2.52 Zn C A:Cys67 4.96 Zn CB A:Cys70 4.02 Zn SG A:Cys70 2.31 Zn O A:Gln71 4.77 Zn O A:Glu76 4.87 Zn O A:Cys77 4.81 Zn N A:Cys77 4.75 Zn CB A:Cys77 3.29 Zn SG A:Cys77 2.49 Zn C A:Cys77 4.02 Zn CA A:Cys77 3.46 Zn O A:Pro78 4.10 Zn N A:Pro78 4.20 Zn CD A:Pro78 4.08 Zn C A:Pro78 4.80 Zn CG A:Pro78 4.93 Zn NE2 A:His80 2.49 Zn ND1 A:His80 4.46 Zn CD2 A:His80 3.54 Zn CE1 A:His80 3.30 Zn CG A:His80 4.60 interactive model: Zinc binding site 3 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3k7a. 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, B: Asn1187, conact list: Atom Atom Distance (A) Zn CB B:Cys1163 3.11 Zn SG B:Cys1163 2.27 Zn CA B:Cys1163 4.57 Zn O B:Cys1166 4.28 Zn N B:Cys1166 4.18 Zn CB B:Cys1166 3.86 Zn SG B:Cys1166 2.35 Zn C B:Cys1166 4.91 Zn CA B:Cys1166 4.54 Zn O B:Cys1182 4.88 Zn CB B:Cys1182 3.71 Zn SG B:Cys1182 2.21 Zn CA B:Cys1182 4.98 Zn N B:Cys1185 4.48 Zn CB B:Cys1185 2.50 Zn SG B:Cys1185 2.24 Zn C B:Cys1185 4.96 Zn CA B:Cys1185 3.94 Zn ND2 B:Asn1187 4.44 interactive model: Zinc binding site 4 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3k7a. 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: Cys88, C: Asp90, C: His91, C: Cys92, C: Lys94, C: Cys95, conact list: Atom Atom Distance (A) Zn O C:Cys86 4.78 Zn CB C:Cys86 2.93 Zn SG C:Cys86 2.23 Zn C C:Cys86 4.56 Zn CA C:Cys86 4.30 Zn N C:Cys88 4.33 Zn CB C:Cys88 3.28 Zn SG C:Cys88 2.30 Zn CA C:Cys88 4.37 Zn O C:Asp90 4.67 Zn O C:His91 4.97 Zn N C:His91 4.98 Zn C C:His91 4.08 Zn CA C:His91 4.14 Zn N C:Cys92 3.58 Zn CB C:Cys92 3.53 Zn SG C:Cys92 2.27 Zn C C:Cys92 4.75 Zn CA C:Cys92 4.14 Zn N C:Lys94 4.76 Zn CB C:Lys94 4.45 Zn C C:Lys94 4.54 Zn CA C:Lys94 4.84 Zn N C:Cys95 4.03 Zn CB C:Cys95 3.25 Zn SG C:Cys95 2.31 Zn CA C:Cys95 4.25 interactive model: Zinc binding site 5 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3k7a. 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: Cys10, I: Cys29, I: Thr31, I: Cys32, conact list: Atom Atom Distance (A) Zn CB I:Cys7 4.82 Zn SG I:Cys7 3.82 Zn N I:Cys10 4.52 Zn CB I:Cys10 2.92 Zn SG I:Cys10 2.24 Zn CA I:Cys10 4.29 Zn CB I:Cys29 3.90 Zn SG I:Cys29 2.39 Zn O I:Thr31 4.47 Zn N I:Thr31 4.93 Zn CB I:Thr31 4.27 Zn CG2 I:Thr31 2.94 Zn OG1 I:Thr31 4.96 Zn C I:Thr31 4.02 Zn CA I:Thr31 4.59 Zn N I:Cys32 3.68 Zn CB I:Cys32 2.76 Zn SG I:Cys32 2.48 Zn CA I:Cys32 3.82 interactive model: Zinc binding site 6 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3k7a. 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: Cys106, I: His108, conact list: Atom Atom Distance (A) Zn O I:Cys75 4.32 Zn N I:Cys75 4.60 Zn CB I:Cys75 2.53 Zn SG I:Cys75 2.31 Zn C I:Cys75 4.34 Zn CA I:Cys75 3.90 Zn N I:Lys77 4.87 Zn CB I:Lys77 4.90 Zn C I:Lys77 4.47 Zn CA I:Lys77 4.99 Zn N I:Cys78 3.20 Zn CB I:Cys78 2.27 Zn SG I:Cys78 3.60 Zn C I:Cys78 4.14 Zn CA I:Cys78 3.24 Zn N I:His79 4.36 Zn N I:Ser80 4.77 Zn CB I:Ser80 4.72 Zn OG I:Ser80 4.41 Zn CB I:Cys103 3.02 Zn SG I:Cys103 2.26 Zn CA I:Cys103 4.50 Zn N I:Cys106 4.54 Zn CB I:Cys106 3.25 Zn SG I:Cys106 2.34 Zn CA I:Cys106 4.40 Zn CB I:His108 4.34 interactive model: Zinc binding site 7 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3k7a. 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: Arg43, J: Tyr44, J: Cys45, J: Cys46, J: Arg47, conact list: Atom Atom Distance (A) Zn CB J:Cys7 3.52 Zn SG J:Cys7 2.50 Zn CA J:Cys7 4.97 Zn N J:Ser9 4.83 Zn CB J:Ser9 4.40 Zn C J:Ser9 4.60 Zn CA J:Ser9 4.82 Zn N J:Cys10 3.49 Zn CB J:Cys10 3.24 Zn SG J:Cys10 2.36 Zn CA J:Cys10 3.94 Zn N J:Gly11 4.96 Zn O J:Arg43 4.71 Zn NE J:Arg43 4.90 Zn C J:Tyr44 5.00 Zn O J:Cys45 2.97 Zn N J:Cys45 4.06 Zn CB J:Cys45 2.92 Zn SG J:Cys45 2.32 Zn C J:Cys45 2.38 Zn CA J:Cys45 3.16 Zn O J:Cys46 4.90 Zn N J:Cys46 2.03 Zn CB J:Cys46 2.90 Zn SG J:Cys46 2.55 Zn C J:Cys46 4.02 Zn CA J:Cys46 2.53 Zn N J:Arg47 4.61 interactive model: Zinc binding site 8 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3k7a. 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: Ser35, L: Ser36, L: Cys48, L: Lys49, L: Cys51, conact list: Atom Atom Distance (A) Zn N L:Cys31 4.51 Zn CB L:Cys31 2.27 Zn SG L:Cys31 2.42 Zn C L:Cys31 4.64 Zn CA L:Cys31 3.78 Zn O L:Cys34 4.94 Zn N L:Cys34 4.18 Zn CB L:Cys34 3.94 Zn SG L:Cys34 2.52 Zn C L:Cys34 4.25 Zn CA L:Cys34 4.31 Zn N L:Ser35 4.00 Zn CA L:Ser35 4.71 Zn N L:Ser36 4.54 Zn OG L:Ser36 4.51 Zn CB L:Cys48 3.02 Zn SG L:Cys48 2.35 Zn CA L:Cys48 4.53 Zn N L:Lys49 4.78 Zn O L:Cys51 3.87 Zn CB L:Cys51 4.12 Zn SG L:Cys51 2.32 Zn C L:Cys51 4.82 Zn CA L:Cys51 4.96 interactive model: Zinc binding site 9 out of 9 in 3k7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 3k7a. 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: M: Cys24, M: Cys27, M: Cys45, M: Leu47, M: Cys48, M: Gly49, conact list: Atom Atom Distance (A) Zn C M:Cys24 4.78 Zn CA M:Cys24 4.15 Zn O M:Cys27 4.44 Zn N M:Cys27 4.23 Zn C M:Cys27 4.84 Zn CA M:Cys27 4.70 Zn CA M:Cys45 4.84 Zn O M:Leu47 4.42 Zn N M:Leu47 4.55 Zn C M:Leu47 3.50 Zn CA M:Leu47 4.05 Zn O M:Cys48 4.90 Zn N M:Cys48 2.44 Zn C M:Cys48 3.87 Zn CA M:Cys48 2.82 Zn N M:Gly49 3.97 interactive model: