Zinc in the structure of Crystal Structure of Transcription Factor Dksa From E. Coli (pdb 1tjl)

The binding sites of Zinc atom in the structure of Crystal Structure of Transcription Factor Dksa From E. Coli (pdb code 1tjl). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1tjl structure was solved by A.PEREDERINA, V.SVETLOV, M.N.VASSYLYEVA, I.ARTSIMOVITCH, S.YOKOYAMA, D.G.VASSYLYEV, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.0-2.0 Space group P1211 a (A) 91.319 b (A) 96.593 c (A) 117.477 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.8 Rfree (%) 26.8 Zinc Binding Sites: Zinc binding site 1 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1tjl. 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: Cys114, A: Ser116, A: Cys117, A: Val119, A: Cys135, A: Cys138, conact list: Atom Atom Distance (A) Zn CB A:Cys114 3.35 Zn SG A:Cys114 2.33 Zn CA A:Cys114 4.78 Zn N A:Ser116 4.77 Zn CB A:Ser116 4.14 Zn C A:Ser116 4.52 Zn CA A:Ser116 4.72 Zn O A:Cys117 4.10 Zn N A:Cys117 3.49 Zn CB A:Cys117 3.37 Zn SG A:Cys117 2.34 Zn C A:Cys117 4.43 Zn CA A:Cys117 3.96 Zn CB A:Val119 4.78 Zn O A:Cys135 4.77 Zn N A:Cys135 4.00 Zn CB A:Cys135 3.48 Zn SG A:Cys135 2.39 Zn C A:Cys135 4.88 Zn CA A:Cys135 4.33 Zn N A:Cys138 4.16 Zn CB A:Cys138 3.15 Zn SG A:Cys138 2.28 Zn CA A:Cys138 4.24 interactive model: Zinc binding site 2 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 1tjl. 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: Cys114, B: Ser116, B: Cys117, B: Val119, B: Cys135, B: Cys138, conact list: Atom Atom Distance (A) Zn CB B:Cys114 3.24 Zn SG B:Cys114 2.34 Zn CA B:Cys114 4.68 Zn N B:Ser116 4.89 Zn CB B:Ser116 4.39 Zn OG B:Ser116 3.64 Zn C B:Ser116 4.66 Zn CA B:Ser116 4.90 Zn O B:Cys117 4.03 Zn N B:Cys117 3.58 Zn CB B:Cys117 3.33 Zn SG B:Cys117 2.34 Zn C B:Cys117 4.36 Zn CA B:Cys117 3.97 Zn CB B:Val119 4.61 Zn O B:Cys135 4.98 Zn N B:Cys135 4.08 Zn CB B:Cys135 3.52 Zn SG B:Cys135 2.38 Zn CA B:Cys135 4.40 Zn N B:Cys138 4.24 Zn CB B:Cys138 3.25 Zn SG B:Cys138 2.31 Zn CA B:Cys138 4.34 interactive model: Zinc binding site 3 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 1tjl. 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: Cys114, C: Ser116, C: Cys117, C: Val119, C: Cys135, C: Cys138, conact list: Atom Atom Distance (A) Zn CB C:Cys114 3.24 Zn SG C:Cys114 2.32 Zn CA C:Cys114 4.69 Zn CB C:Ser116 4.48 Zn C C:Ser116 4.87 Zn O C:Cys117 4.15 Zn N C:Cys117 3.79 Zn CB C:Cys117 3.46 Zn SG C:Cys117 2.35 Zn C C:Cys117 4.53 Zn CA C:Cys117 4.16 Zn CB C:Val119 4.64 Zn O C:Cys135 4.78 Zn N C:Cys135 3.95 Zn CB C:Cys135 3.35 Zn SG C:Cys135 2.34 Zn C C:Cys135 4.80 Zn CA C:Cys135 4.22 Zn N C:Cys138 4.17 Zn CB C:Cys138 3.33 Zn SG C:Cys138 2.33 Zn CA C:Cys138 4.36 interactive model: Zinc binding site 4 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 1tjl. 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: D: Cys114, D: Ser116, D: Cys117, D: Val119, D: Cys135, D: Cys138, D: Hoh218, D: Hoh221, conact list: Atom Atom Distance (A) Zn CB D:Cys114 3.25 Zn SG D:Cys114 2.33 Zn CA D:Cys114 4.69 Zn N D:Ser116 4.88 Zn CB D:Ser116 4.32 Zn OG D:Ser116 4.98 Zn C D:Ser116 4.66 Zn CA D:Ser116 4.88 Zn O D:Cys117 4.03 Zn N D:Cys117 3.59 Zn CB D:Cys117 3.36 Zn SG D:Cys117 2.32 Zn C D:Cys117 4.39 Zn CA D:Cys117 3.99 Zn CB D:Val119 4.66 Zn N D:Cys135 4.12 Zn CB D:Cys135 3.63 Zn SG D:Cys135 2.40 Zn CA D:Cys135 4.49 Zn N D:Cys138 4.23 Zn CB D:Cys138 3.19 Zn SG D:Cys138 2.29 Zn CA D:Cys138 4.29 Zn O D:Hoh218 4.80 Zn O D:Hoh221 4.10 interactive model: Zinc binding site 5 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 1tjl. 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: E: Cys114, E: Ser116, E: Cys117, E: Val119, E: Leu134, E: Cys135, E: Cys138, E: Hoh223, E: Hoh236, conact list: Atom Atom Distance (A) Zn CB E:Cys114 3.44 Zn SG E:Cys114 2.41 Zn CA E:Cys114 4.92 Zn CB E:Ser116 4.55 Zn O E:Cys117 4.56 Zn N E:Cys117 4.11 Zn CB E:Cys117 3.68 Zn SG E:Cys117 2.44 Zn C E:Cys117 4.92 Zn CA E:Cys117 4.47 Zn CB E:Val119 4.87 Zn C E:Leu134 4.96 Zn O E:Cys135 4.61 Zn N E:Cys135 3.83 Zn CB E:Cys135 3.34 Zn SG E:Cys135 2.36 Zn C E:Cys135 4.67 Zn CA E:Cys135 4.15 Zn N E:Cys138 3.91 Zn CB E:Cys138 3.08 Zn SG E:Cys138 2.26 Zn CA E:Cys138 4.09 Zn O E:Hoh223 4.40 Zn O E:Hoh236 4.47 interactive model: Zinc binding site 6 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 1tjl. 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: F: Cys114, F: Ser116, F: Cys117, F: Cys135, F: Cys138, conact list: Atom Atom Distance (A) Zn CB F:Cys114 3.53 Zn SG F:Cys114 2.41 Zn CA F:Cys114 4.96 Zn N F:Ser116 4.67 Zn CB F:Ser116 3.85 Zn OG F:Ser116 4.38 Zn C F:Ser116 4.48 Zn CA F:Ser116 4.57 Zn O F:Cys117 4.41 Zn N F:Cys117 3.55 Zn CB F:Cys117 3.56 Zn SG F:Cys117 2.38 Zn C F:Cys117 4.70 Zn CA F:Cys117 4.13 Zn O F:Cys135 4.81 Zn N F:Cys135 3.97 Zn CB F:Cys135 3.48 Zn SG F:Cys135 2.38 Zn C F:Cys135 4.91 Zn CA F:Cys135 4.33 Zn N F:Cys138 4.20 Zn CB F:Cys138 3.16 Zn SG F:Cys138 2.31 Zn CA F:Cys138 4.26 interactive model: Zinc binding site 7 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 1tjl. 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: G: Cys114, G: Ser116, G: Cys117, G: Val119, G: Cys135, G: Cys138, conact list: Atom Atom Distance (A) Zn CB G:Cys114 3.34 Zn SG G:Cys114 2.34 Zn CA G:Cys114 4.75 Zn N G:Ser116 4.73 Zn CB G:Ser116 4.09 Zn OG G:Ser116 4.86 Zn C G:Ser116 4.52 Zn CA G:Ser116 4.69 Zn O G:Cys117 4.13 Zn N G:Cys117 3.50 Zn CB G:Cys117 3.43 Zn SG G:Cys117 2.34 Zn C G:Cys117 4.46 Zn CA G:Cys117 4.00 Zn CB G:Val119 4.90 Zn O G:Cys135 4.97 Zn N G:Cys135 4.07 Zn CB G:Cys135 3.49 Zn SG G:Cys135 2.36 Zn CA G:Cys135 4.39 Zn N G:Cys138 4.27 Zn CB G:Cys138 3.31 Zn SG G:Cys138 2.35 Zn CA G:Cys138 4.39 interactive model: Zinc binding site 8 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 1tjl. 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: H: Cys114, H: Ser116, H: Cys117, H: Val119, H: Cys135, H: Cys138, conact list: Atom Atom Distance (A) Zn CB H:Cys114 3.25 Zn SG H:Cys114 2.33 Zn CA H:Cys114 4.71 Zn CB H:Ser116 4.55 Zn C H:Ser116 4.81 Zn O H:Cys117 4.00 Zn N H:Cys117 3.70 Zn CB H:Cys117 3.31 Zn SG H:Cys117 2.32 Zn C H:Cys117 4.36 Zn CA H:Cys117 4.01 Zn CB H:Val119 4.35 Zn CG2 H:Val119 4.91 Zn CG1 H:Val119 4.90 Zn O H:Cys135 4.88 Zn N H:Cys135 4.09 Zn CB H:Cys135 3.41 Zn SG H:Cys135 2.36 Zn C H:Cys135 4.89 Zn CA H:Cys135 4.32 Zn N H:Cys138 4.23 Zn CB H:Cys138 3.39 Zn SG H:Cys138 2.34 Zn CA H:Cys138 4.42 interactive model: Zinc binding site 9 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 1tjl. 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: Cys114, I: Ser116, I: Cys117, I: Val119, I: Cys135, I: Cys138, conact list: Atom Atom Distance (A) Zn CB I:Cys114 3.09 Zn SG I:Cys114 2.29 Zn C I:Cys114 4.98 Zn CA I:Cys114 4.52 Zn N I:Ser116 4.88 Zn CB I:Ser116 4.41 Zn OG I:Ser116 4.80 Zn C I:Ser116 4.72 Zn CA I:Ser116 4.94 Zn O I:Cys117 3.92 Zn N I:Cys117 3.63 Zn CB I:Cys117 3.37 Zn SG I:Cys117 2.33 Zn C I:Cys117 4.34 Zn CA I:Cys117 4.02 Zn CB I:Val119 4.52 Zn O I:Cys135 4.72 Zn N I:Cys135 3.88 Zn CB I:Cys135 3.32 Zn SG I:Cys135 2.34 Zn C I:Cys135 4.75 Zn CA I:Cys135 4.17 Zn N I:Cys138 4.18 Zn CB I:Cys138 3.31 Zn SG I:Cys138 2.34 Zn CA I:Cys138 4.35 interactive model: Zinc binding site 10 out of 10 in 1tjl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Zinc in the PDB 1tjl. 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: Cys114, J: Ser116, J: Cys117, J: Val119, J: Leu134, J: Cys135, J: Cys138, J: Hoh220, J: Hoh243, conact list: Atom Atom Distance (A) Zn CB J:Cys114 3.34 Zn SG J:Cys114 2.38 Zn CA J:Cys114 4.79 Zn CB J:Ser116 4.43 Zn C J:Ser116 4.97 Zn O J:Cys117 4.43 Zn N J:Cys117 3.95 Zn CB J:Cys117 3.67 Zn SG J:Cys117 2.42 Zn C J:Cys117 4.80 Zn CA J:Cys117 4.36 Zn CB J:Val119 4.96 Zn CG2 J:Val119 5.00 Zn C J:Leu134 4.94 Zn O J:Cys135 4.73 Zn N J:Cys135 3.86 Zn CB J:Cys135 3.41 Zn SG J:Cys135 2.39 Zn C J:Cys135 4.77 Zn CA J:Cys135 4.22 Zn N J:Cys138 4.10 Zn CB J:Cys138 3.20 Zn SG J:Cys138 2.29 Zn CA J:Cys138 4.26 Zn O J:Hoh220 4.56 Zn O J:Hoh243 4.49 interactive model: