Zinc in the structure of Mouse-Human SOD1 Chimera (pdb 3ltv)

The binding sites of Zinc atom in the structure of Mouse-Human SOD1 Chimera (pdb code 3ltv). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3ltv structure was solved by S.V.SEETHARAMAN, A.B.TAYLOR, P.J.HART, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.6-2.5 Space group P61 a (A) 127.480 b (A) 127.480 c (A) 102.494 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.5 Rfree (%) 26.5 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3ltv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3ltv. 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: His46, A: His63, A: His71, A: Gly72, A: His80, A: Asp83, A: Lys136, A: Hoh161, conact list: Atom Atom Distance (A) Zn ND1 A:His46 4.92 Zn NE2 A:His63 4.17 Zn CB A:His63 3.47 Zn ND1 A:His63 2.10 Zn CD2 A:His63 4.23 Zn CE1 A:His63 3.04 Zn CG A:His63 3.12 Zn NE2 A:His71 4.19 Zn N A:His71 4.91 Zn CB A:His71 3.55 Zn ND1 A:His71 2.13 Zn CD2 A:His71 4.28 Zn C A:His71 4.90 Zn CE1 A:His71 3.04 Zn CG A:His71 3.18 Zn CA A:His71 3.93 Zn O A:Gly72 4.99 Zn N A:Gly72 4.72 Zn NE2 A:His80 4.07 Zn N A:His80 4.75 Zn CB A:His80 3.61 Zn ND1 A:His80 2.05 Zn CD2 A:His80 4.22 Zn CE1 A:His80 2.89 Zn CG A:His80 3.17 Zn CA A:His80 4.81 Zn N A:Asp83 4.95 Zn CB A:Asp83 4.09 Zn OD2 A:Asp83 1.98 Zn OD1 A:Asp83 2.71 Zn CG A:Asp83 2.64 Zn CA A:Asp83 4.63 Zn O A:Lys136 3.74 Zn C A:Lys136 4.70 Zn O A:Hoh161 4.66 interactive model: Zinc binding site 2 out of 6 in 3ltv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3ltv. 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: His63, B: His71, B: Gly72, B: His80, B: Asp83, B: Lys136, B: Hoh166, conact list: Atom Atom Distance (A) Zn NE2 B:His63 4.30 Zn CB B:His63 3.36 Zn ND1 B:His63 2.20 Zn CD2 B:His63 4.28 Zn CE1 B:His63 3.21 Zn CG B:His63 3.13 Zn CA B:His63 4.89 Zn NE2 B:His71 4.14 Zn N B:His71 4.90 Zn CB B:His71 3.59 Zn ND1 B:His71 2.10 Zn CD2 B:His71 4.26 Zn C B:His71 4.96 Zn CE1 B:His71 2.98 Zn CG B:His71 3.18 Zn CA B:His71 3.95 Zn N B:Gly72 4.89 Zn NE2 B:His80 4.06 Zn N B:His80 4.62 Zn CB B:His80 3.47 Zn ND1 B:His80 2.12 Zn CD2 B:His80 4.13 Zn CE1 B:His80 2.99 Zn CG B:His80 3.08 Zn CA B:His80 4.67 Zn N B:Asp83 4.79 Zn CB B:Asp83 4.15 Zn OD2 B:Asp83 1.92 Zn OD1 B:Asp83 2.89 Zn CG B:Asp83 2.72 Zn CA B:Asp83 4.61 Zn O B:Lys136 3.93 Zn C B:Lys136 4.91 Zn O B:Hoh166 4.91 interactive model: Zinc binding site 3 out of 6 in 3ltv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3ltv. 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: His63, C: Lys70, C: His71, C: Gly72, C: His80, C: Asp83, C: Lys136, conact list: Atom Atom Distance (A) Zn NE2 C:His63 4.24 Zn CB C:His63 3.55 Zn ND1 C:His63 2.83 Zn CD2 C:His63 4.13 Zn CE1 C:His63 3.54 Zn CG C:His63 3.28 Zn O C:Lys70 4.80 Zn NE2 C:His71 4.45 Zn N C:His71 4.83 Zn CB C:His71 3.91 Zn ND1 C:His71 2.60 Zn CD2 C:His71 4.57 Zn C C:His71 4.95 Zn CE1 C:His71 3.36 Zn CG C:His71 3.55 Zn CA C:His71 3.99 Zn N C:Gly72 4.94 Zn O C:His80 4.84 Zn NE2 C:His80 3.78 Zn N C:His80 3.85 Zn CB C:His80 2.96 Zn ND1 C:His80 2.14 Zn CD2 C:His80 3.61 Zn C C:His80 4.88 Zn CE1 C:His80 3.02 Zn CG C:His80 2.64 Zn CA C:His80 4.01 Zn N C:Asp83 4.85 Zn CB C:Asp83 3.67 Zn OD2 C:Asp83 3.24 Zn OD1 C:Asp83 2.63 Zn CG C:Asp83 2.88 Zn CA C:Asp83 4.40 Zn O C:Lys136 3.94 interactive model: Zinc binding site 4 out of 6 in 3ltv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3ltv. 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: His63, D: His71, D: Gly72, D: His80, D: Asp83, D: Lys136, conact list: Atom Atom Distance (A) Zn NE2 D:His63 3.98 Zn CB D:His63 3.48 Zn ND1 D:His63 1.95 Zn CD2 D:His63 4.10 Zn CE1 D:His63 2.83 Zn CG D:His63 3.04 Zn NE2 D:His71 3.87 Zn CB D:His71 3.56 Zn ND1 D:His71 1.87 Zn CD2 D:His71 4.05 Zn C D:His71 4.83 Zn CE1 D:His71 2.68 Zn CG D:His71 3.04 Zn CA D:His71 3.95 Zn N D:Gly72 4.61 Zn NE2 D:His80 4.26 Zn N D:His80 4.79 Zn CB D:His80 3.75 Zn ND1 D:His80 2.68 Zn CD2 D:His80 4.29 Zn CE1 D:His80 3.38 Zn CG D:His80 3.39 Zn CA D:His80 4.88 Zn N D:Asp83 4.84 Zn CB D:Asp83 4.13 Zn OD2 D:Asp83 2.79 Zn OD1 D:Asp83 2.11 Zn CG D:Asp83 2.72 Zn CA D:Asp83 4.59 Zn O D:Lys136 3.93 Zn C D:Lys136 4.71 interactive model: Zinc binding site 5 out of 6 in 3ltv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3ltv. 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: His46, E: His63, E: His71, E: Gly72, E: His80, E: Asp83, E: Lys136, conact list: Atom Atom Distance (A) Zn ND1 E:His46 4.67 Zn NE2 E:His63 4.34 Zn CB E:His63 3.27 Zn ND1 E:His63 2.22 Zn CD2 E:His63 4.28 Zn CE1 E:His63 3.27 Zn CG E:His63 3.10 Zn CA E:His63 4.81 Zn NE2 E:His71 4.46 Zn N E:His71 4.84 Zn CB E:His71 3.67 Zn ND1 E:His71 2.39 Zn CD2 E:His71 4.52 Zn C E:His71 4.69 Zn CE1 E:His71 3.32 Zn CG E:His71 3.39 Zn CA E:His71 3.83 Zn O E:Gly72 4.90 Zn N E:Gly72 4.49 Zn NE2 E:His80 3.93 Zn N E:His80 4.53 Zn CB E:His80 3.54 Zn ND1 E:His80 1.93 Zn CD2 E:His80 4.09 Zn CE1 E:His80 2.76 Zn CG E:His80 3.06 Zn CA E:His80 4.66 Zn CB E:Asp83 4.22 Zn OD2 E:Asp83 2.30 Zn OD1 E:Asp83 2.50 Zn CG E:Asp83 2.72 Zn CA E:Asp83 4.91 Zn O E:Lys136 4.04 interactive model: Zinc binding site 6 out of 6 in 3ltv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3ltv. 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: His46, F: His63, F: His71, F: Gly72, F: His80, F: Asp83, F: Lys136, conact list: Atom Atom Distance (A) Zn ND1 F:His46 4.78 Zn NE2 F:His63 3.99 Zn CB F:His63 3.52 Zn ND1 F:His63 1.98 Zn CD2 F:His63 4.13 Zn CE1 F:His63 2.83 Zn CG F:His63 3.07 Zn NE2 F:His71 4.20 Zn N F:His71 4.82 Zn CB F:His71 3.43 Zn ND1 F:His71 2.12 Zn CD2 F:His71 4.24 Zn C F:His71 4.75 Zn CE1 F:His71 3.08 Zn CG F:His71 3.12 Zn CA F:His71 3.81 Zn N F:Gly72 4.57 Zn NE2 F:His80 4.11 Zn N F:His80 4.67 Zn CB F:His80 3.58 Zn ND1 F:His80 2.11 Zn CD2 F:His80 4.22 Zn CE1 F:His80 2.97 Zn CG F:His80 3.17 Zn CA F:His80 4.75 Zn N F:Asp83 4.97 Zn CB F:Asp83 4.15 Zn OD2 F:Asp83 2.02 Zn OD1 F:Asp83 2.85 Zn CG F:Asp83 2.74 Zn CA F:Asp83 4.68 Zn O F:Lys136 3.81 Zn C F:Lys136 4.78 interactive model: