Zinc in the structure of Rna Polymerase II Elongation Complex With Utp, Updated 11/2006 (pdb 2nvz)

The binding sites of Zinc atom in the structure of Rna Polymerase II Elongation Complex With Utp, Updated 11/2006 (pdb code 2nvz). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2nvz structure was solved by D.WANG, D.A.BUSHNELL, K.D.WESTOVER, C.D.KAPLAN, R.D.KORNBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-4.3 Space group C121 a (A) 169.647 b (A) 222.338 c (A) 194.316 alpha (°) 90.00 beta (°) 101.67 gamma (°) 90.00 Rfactor (%) 27 Rfree (%) 33.2 Zinc Binding Sites: Zinc binding site 1 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2nvz. 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 4.39 Zn C A:Cys107 5.00 Zn CB A:Met108 3.08 Zn CE A:Met108 4.25 Zn C A:Met108 4.92 Zn CG A:Met108 3.21 Zn SD A:Met108 2.96 Zn CA A:Met108 4.49 Zn N A:His109 4.87 Zn N A:Cys110 4.18 Zn CB A:Cys110 3.48 Zn SG A:Cys110 2.35 Zn C A:Cys110 4.76 Zn CA A:Cys110 4.29 Zn N A:Gly111 4.35 Zn SG A:Cys148 4.96 Zn CB A:Cys167 3.35 Zn SG A:Cys167 2.34 Zn CA A:Cys167 4.77 interactive model: Zinc binding site 2 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2nvz. 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: Gly59, A: Cys67, A: Gln68, A: Cys70, A: Cys77, A: Pro78, A: Gly79, A: His80, conact list: Atom Atom Distance (A) Zn N A:Gly59 4.98 Zn CA A:Gly59 4.73 Zn CB A:Cys67 3.50 Zn SG A:Cys67 2.35 Zn CA A:Cys67 4.88 Zn NE2 A:Gln68 4.76 Zn OE1 A:Gln68 3.75 Zn CD A:Gln68 4.66 Zn CB A:Cys70 3.24 Zn SG A:Cys70 2.34 Zn CA A:Cys70 4.72 Zn O A:Cys77 4.24 Zn CB A:Cys77 2.75 Zn SG A:Cys77 1.03 Zn C A:Cys77 4.01 Zn CA A:Cys77 3.79 Zn N A:Pro78 4.59 Zn CD A:Pro78 4.73 Zn N A:Gly79 4.59 Zn NE2 A:His80 2.37 Zn ND1 A:His80 3.82 Zn CD2 A:His80 3.69 Zn CE1 A:His80 2.54 Zn CG A:His80 4.40 interactive model: Zinc binding site 3 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2nvz. 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: Cys1166, B: Cys1182, B: Lys1183, B: Cys1185, conact list: Atom Atom Distance (A) Zn CD1 A:Ile30 4.41 Zn CB B:Cys1163 3.73 Zn SG B:Cys1163 3.22 Zn O B:Cys1166 4.06 Zn N B:Cys1166 4.70 Zn CB B:Cys1166 3.37 Zn SG B:Cys1166 2.33 Zn C B:Cys1166 4.71 Zn CA B:Cys1166 4.46 Zn O B:Cys1182 4.76 Zn CB B:Cys1182 3.53 Zn SG B:Cys1182 2.35 Zn C B:Cys1182 4.93 Zn CA B:Cys1182 4.80 Zn O B:Lys1183 4.75 Zn N B:Cys1185 4.47 Zn CB B:Cys1185 2.96 Zn SG B:Cys1185 2.52 Zn CA B:Cys1185 4.30 interactive model: Zinc binding site 4 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2nvz. 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: Cys95, conact list: Atom Atom Distance (A) Zn CB C:Cys86 3.36 Zn SG C:Cys86 2.35 Zn C C:Cys86 4.80 Zn CA C:Cys86 4.67 Zn N C:Phe87 4.77 Zn N C:Cys88 4.11 Zn CB C:Cys88 3.42 Zn SG C:Cys88 2.34 Zn C C:Cys88 4.88 Zn CA C:Cys88 4.30 Zn O C:Asp90 4.59 Zn C C:Asp90 4.97 Zn O C:His91 4.77 Zn N C:His91 4.72 Zn C C:His91 3.89 Zn CA C:His91 4.05 Zn N C:Cys92 3.33 Zn CB C:Cys92 3.34 Zn SG C:Cys92 2.34 Zn C C:Cys92 4.83 Zn CA C:Cys92 3.93 Zn N C:Cys95 4.79 Zn CB C:Cys95 3.33 Zn SG C:Cys95 2.34 Zn CA C:Cys95 4.63 interactive model: Zinc binding site 5 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2nvz. 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: Arg30, I: Cys32, I: Ser33, conact list: Atom Atom Distance (A) Zn CB I:Cys7 4.68 Zn SG I:Cys7 3.85 Zn CB I:Cys10 3.35 Zn SG I:Cys10 2.33 Zn CA I:Cys10 4.71 Zn CB I:Cys29 3.36 Zn SG I:Cys29 2.33 Zn CA I:Cys29 4.70 Zn N I:Arg30 4.28 Zn CB I:Arg30 4.92 Zn CD I:Arg30 4.32 Zn CG I:Arg30 3.63 Zn O I:Cys32 4.05 Zn N I:Cys32 4.42 Zn CB I:Cys32 3.46 Zn SG I:Cys32 2.34 Zn C I:Cys32 4.20 Zn CA I:Cys32 4.22 Zn N I:Ser33 4.94 interactive model: Zinc binding site 6 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2nvz. 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: Cys78, I: His79, I: Ser80, I: Cys103, I: Ser105, I: Cys106, I: His108, conact list: Atom Atom Distance (A) Zn O I:Cys75 4.83 Zn CB I:Cys75 3.34 Zn SG I:Cys75 2.34 Zn C I:Cys75 4.97 Zn CA I:Cys75 4.70 Zn O I:Cys78 2.78 Zn N I:Cys78 4.23 Zn CB I:Cys78 3.38 Zn SG I:Cys78 2.33 Zn C I:Cys78 3.52 Zn CA I:Cys78 3.90 Zn N I:His79 4.54 Zn O I:Ser80 4.75 Zn CB I:Ser80 3.27 Zn OG I:Ser80 2.97 Zn CA I:Ser80 4.71 Zn CB I:Cys103 3.26 Zn SG I:Cys103 2.32 Zn CA I:Cys103 4.51 Zn CB I:Ser105 4.66 Zn C I:Ser105 4.99 Zn N I:Cys106 4.63 Zn CB I:Cys106 3.49 Zn SG I:Cys106 2.34 Zn CA I:Cys106 4.71 Zn NE2 I:His108 4.61 Zn CD2 I:His108 4.28 interactive model: Zinc binding site 7 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 2nvz. 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: Phe8, J: Ser9, J: Cys10, J: Gly11, J: Cys45, J: Cys46, conact list: Atom Atom Distance (A) Zn O J:Cys7 3.63 Zn CB J:Cys7 3.46 Zn SG J:Cys7 2.15 Zn C J:Cys7 4.11 Zn CA J:Cys7 4.42 Zn N J:Phe8 4.91 Zn C J:Phe8 4.84 Zn O J:Ser9 4.70 Zn N J:Ser9 3.80 Zn CB J:Ser9 3.50 Zn OG J:Ser9 3.23 Zn C J:Ser9 3.55 Zn CA J:Ser9 3.74 Zn N J:Cys10 2.55 Zn CB J:Cys10 3.14 Zn SG J:Cys10 2.32 Zn C J:Cys10 4.17 Zn CA J:Cys10 3.32 Zn N J:Gly11 4.03 Zn O J:Cys45 3.47 Zn CB J:Cys45 3.45 Zn SG J:Cys45 2.35 Zn C J:Cys45 3.30 Zn CA J:Cys45 4.00 Zn N J:Cys46 3.32 Zn CB J:Cys46 3.30 Zn SG J:Cys46 2.35 Zn C J:Cys46 4.89 Zn CA J:Cys46 3.38 interactive model: Zinc binding site 8 out of 8 in 2nvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 2nvz. 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: Cys48, L: Lys49, L: Cys51, conact list: Atom Atom Distance (A) Zn CB L:Cys31 3.62 Zn SG L:Cys31 3.01 Zn O L:Glu33 4.32 Zn OE2 L:Glu33 4.85 Zn O L:Cys34 3.91 Zn CB L:Cys34 3.53 Zn SG L:Cys34 2.35 Zn C L:Cys34 4.64 Zn CA L:Cys34 4.60 Zn CB L:Cys48 2.97 Zn SG L:Cys48 1.91 Zn C L:Cys48 4.79 Zn CA L:Cys48 4.35 Zn N L:Lys49 4.76 Zn CB L:Cys51 3.41 Zn SG L:Cys51 2.34 Zn CA L:Cys51 4.74 interactive model: