Zinc in the structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 With Gmpcpp (pdb 2nvt)

The binding sites of Zinc atom in the structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 With Gmpcpp (pdb code 2nvt). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2nvt 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) 40.0-3.4 Space group C121 a (A) 170.872 b (A) 222.824 c (A) 195.802 alpha (°) 90.00 beta (°) 102.39 gamma (°) 90.00 Rfactor (%) 23 Rfree (%) 28.3 Zinc Binding Sites: Zinc binding site 1 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2nvt. 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: Cys110, A: Cys148, A: Gly166, A: Cys167, A: Gly168, A: Asn169, conact list: Atom Atom Distance (A) Zn CB A:Cys107 3.48 Zn SG A:Cys107 2.36 Zn CA A:Cys107 4.88 Zn O A:Met108 4.74 Zn N A:Cys110 4.59 Zn CB A:Cys110 3.54 Zn SG A:Cys110 2.38 Zn CA A:Cys110 4.63 Zn CB A:Cys148 3.60 Zn SG A:Cys148 2.37 Zn C A:Gly166 4.71 Zn O A:Cys167 3.35 Zn N A:Cys167 3.65 Zn CB A:Cys167 3.67 Zn SG A:Cys167 2.38 Zn C A:Cys167 3.85 Zn CA A:Cys167 3.85 Zn N A:Gly168 4.97 Zn ND2 A:Asn169 4.94 interactive model: Zinc binding site 2 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2nvt. 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: Glu72, A: Cys77, A: His80, conact list: Atom Atom Distance (A) Zn O A:Cys67 3.71 Zn CB A:Cys67 3.37 Zn SG A:Cys67 2.33 Zn C A:Cys67 4.36 Zn CA A:Cys67 4.44 Zn NE2 A:Gln68 3.11 Zn OE1 A:Gln68 4.70 Zn CD A:Gln68 4.12 Zn CB A:Cys70 3.33 Zn SG A:Cys70 2.32 Zn C A:Cys70 4.95 Zn CA A:Cys70 4.65 Zn CB A:Glu72 4.96 Zn CB A:Cys77 3.34 Zn SG A:Cys77 2.34 Zn CA A:Cys77 4.13 Zn NE2 A:His80 2.46 Zn ND1 A:His80 4.60 Zn CD2 A:His80 3.07 Zn CE1 A:His80 3.65 Zn CG A:His80 4.36 interactive model: Zinc binding site 3 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2nvt. 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: Gly1167, B: Thr1170, B: Cys1182, B: Cys1185, conact list: Atom Atom Distance (A) Zn CD1 A:Ile30 4.84 Zn CB B:Cys1163 3.38 Zn SG B:Cys1163 2.35 Zn CA B:Cys1163 4.74 Zn CB B:Ile1165 4.65 Zn N B:Cys1166 3.92 Zn CB B:Cys1166 3.48 Zn SG B:Cys1166 2.34 Zn CA B:Cys1166 4.26 Zn N B:Gly1167 4.90 Zn OG1 B:Thr1170 4.86 Zn O B:Cys1182 4.60 Zn CB B:Cys1182 3.61 Zn SG B:Cys1182 2.38 Zn CA B:Cys1182 4.93 Zn N B:Cys1185 4.66 Zn CB B:Cys1185 3.53 Zn SG B:Cys1185 2.37 Zn CA B:Cys1185 4.60 interactive model: Zinc binding site 4 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2nvt. 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: Asp93, C: Lys94, C: Cys95, conact list: Atom Atom Distance (A) Zn CB C:Cys86 3.50 Zn SG C:Cys86 2.33 Zn CA C:Cys86 4.87 Zn O C:Cys88 4.79 Zn N C:Cys88 4.69 Zn CB C:Cys88 3.43 Zn SG C:Cys88 2.32 Zn CA C:Cys88 4.60 Zn O C:Asp90 4.90 Zn O C:His91 4.66 Zn N C:His91 4.91 Zn CB C:His91 4.91 Zn C C:His91 3.71 Zn CA C:His91 3.96 Zn O C:Cys92 4.20 Zn N C:Cys92 2.94 Zn CB C:Cys92 3.47 Zn SG C:Cys92 2.36 Zn C C:Cys92 4.12 Zn CA C:Cys92 3.65 Zn N C:Asp93 4.97 Zn N C:Lys94 4.74 Zn CB C:Lys94 4.67 Zn C C:Lys94 4.66 Zn CA C:Lys94 4.93 Zn N C:Cys95 3.82 Zn CB C:Cys95 3.31 Zn SG C:Cys95 2.34 Zn C C:Cys95 4.97 Zn CA C:Cys95 4.15 interactive model: Zinc binding site 5 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2nvt. 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: Asp9, I: Cys10, I: Cys29, I: Thr31, I: Cys32, I: Ser33, I: Tyr34, conact list: Atom Atom Distance (A) Zn CB I:Cys7 3.20 Zn SG I:Cys7 2.32 Zn CA I:Cys7 4.59 Zn C I:Asp9 4.83 Zn N I:Cys10 3.89 Zn CB I:Cys10 3.06 Zn SG I:Cys10 2.31 Zn CA I:Cys10 4.05 Zn CB I:Cys29 3.42 Zn SG I:Cys29 2.34 Zn CA I:Cys29 4.81 Zn N I:Thr31 4.48 Zn CB I:Thr31 3.80 Zn OG1 I:Thr31 3.81 Zn C I:Thr31 4.32 Zn CA I:Thr31 4.47 Zn N I:Cys32 3.29 Zn CB I:Cys32 3.48 Zn SG I:Cys32 2.36 Zn C I:Cys32 4.52 Zn CA I:Cys32 3.90 Zn N I:Ser33 4.87 Zn N I:Tyr34 4.79 Zn CB I:Tyr34 4.15 interactive model: Zinc binding site 6 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2nvt. 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: His108, conact list: Atom Atom Distance (A) Zn O I:Cys75 4.74 Zn CB I:Cys75 3.34 Zn SG I:Cys75 2.35 Zn C I:Cys75 4.93 Zn CA I:Cys75 4.68 Zn CG I:Lys77 4.51 Zn O I:Cys78 3.01 Zn N I:Cys78 4.09 Zn CB I:Cys78 3.40 Zn SG I:Cys78 2.35 Zn C I:Cys78 3.82 Zn CA I:Cys78 3.96 Zn O I:Ser80 4.93 Zn CB I:Cys103 3.41 Zn SG I:Cys103 2.34 Zn CA I:Cys103 4.83 Zn CB I:Ser105 4.50 Zn C I:Ser105 4.53 Zn CA I:Ser105 4.95 Zn N I:Cys106 4.15 Zn CB I:Cys106 3.33 Zn SG I:Cys106 2.35 Zn CA I:Cys106 4.35 Zn CB I:His108 4.50 interactive model: Zinc binding site 7 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 2nvt. 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: Arg43, J: Cys45, J: Cys46, conact list: Atom Atom Distance (A) Zn CB J:Cys7 3.46 Zn SG J:Cys7 2.39 Zn CA J:Cys7 4.87 Zn CB J:Ser9 4.71 Zn OG J:Ser9 3.89 Zn C J:Ser9 4.68 Zn N J:Cys10 3.66 Zn CB J:Cys10 3.31 Zn SG J:Cys10 2.34 Zn CA J:Cys10 4.07 Zn O J:Arg43 4.34 Zn CB J:Arg43 4.91 Zn CD J:Arg43 4.25 Zn CG J:Arg43 3.84 Zn O J:Cys45 3.85 Zn N J:Cys45 4.46 Zn CB J:Cys45 3.43 Zn SG J:Cys45 2.35 Zn C J:Cys45 3.29 Zn CA J:Cys45 3.92 Zn N J:Cys46 2.80 Zn CB J:Cys46 3.30 Zn SG J:Cys46 2.30 Zn C J:Cys46 4.82 Zn CA J:Cys46 3.32 interactive model: Zinc binding site 8 out of 8 in 2nvt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 2nvt. 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: Asp50, L: Cys51, L: Gly52, L: His53, conact list: Atom Atom Distance (A) Zn CB L:Cys31 3.34 Zn SG L:Cys31 2.34 Zn CA L:Cys31 4.74 Zn N L:Cys34 4.72 Zn CB L:Cys34 3.48 Zn SG L:Cys34 2.35 Zn CA L:Cys34 4.62 Zn CB L:Ser36 4.74 Zn CB L:Cys48 3.37 Zn SG L:Cys48 2.33 Zn CA L:Cys48 4.76 Zn N L:Lys49 4.58 Zn N L:Asp50 4.80 Zn C L:Asp50 4.86 Zn N L:Cys51 4.02 Zn CB L:Cys51 3.47 Zn SG L:Cys51 2.35 Zn C L:Cys51 4.51 Zn CA L:Cys51 4.15 Zn N L:Gly52 4.13 Zn N L:His53 4.96 interactive model: