Zinc in the structure of Human Cytochrome P450 2D6 With Two Thioridazines Bound in Active Site (pdb 3tbg)

The binding sites of Zinc atom in the structure of Human Cytochrome P450 2D6 With Two Thioridazines Bound in Active Site (pdb code 3tbg). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3tbg structure was solved by A.WANG, C.D.STOUT, E.F.JOHNSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.9-2.1 Space group P212121 a (A) 57.190 b (A) 191.960 c (A) 249.480 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.2 Rfree (%) 24.7 Zinc Binding Sites: Zinc binding site 1 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3tbg. 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: Cys191, A: Gly192, A: His258, A: Arg269, A: Asp270, A: Glu273, A: Hoh581, A: Hoh586, conact list: Atom Atom Distance (A) Zn O A:Cys191 3.57 Zn C A:Cys191 4.16 Zn CA A:Cys191 4.99 Zn N A:Gly192 4.62 Zn CA A:Gly192 4.54 Zn NE2 A:His258 1.97 Zn ND1 A:His258 3.95 Zn CD2 A:His258 3.08 Zn CE1 A:His258 2.79 Zn CG A:His258 4.12 Zn CB A:Arg269 4.59 Zn CZ A:Arg269 4.85 Zn NE A:Arg269 4.37 Zn NH2 A:Arg269 4.40 Zn N A:Asp270 4.83 Zn CB A:Asp270 4.34 Zn OD2 A:Asp270 2.03 Zn OD1 A:Asp270 3.19 Zn CG A:Asp270 2.95 Zn OE1 A:Glu273 3.82 Zn CB A:Glu273 4.56 Zn OE2 A:Glu273 1.88 Zn CD A:Glu273 2.80 Zn CG A:Glu273 3.30 Zn O A:Hoh581 4.21 Zn O A:Hoh586 4.10 interactive model: Zinc binding site 2 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3tbg. 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: Asp422, A: Gln424, A: His426, C: Asp422, C: Gln424, C: His426, A: Hoh564, conact list: Atom Atom Distance (A) Zn CB A:Asp422 4.30 Zn OD2 A:Asp422 2.18 Zn OD1 A:Asp422 3.38 Zn CG A:Asp422 3.05 Zn CB A:Gln424 4.01 Zn CG A:Gln424 4.69 Zn NE2 A:His426 3.81 Zn N A:His426 4.85 Zn CB A:His426 3.46 Zn ND1 A:His426 1.84 Zn CD2 A:His426 3.96 Zn CE1 A:His426 2.67 Zn CG A:His426 2.94 Zn CA A:His426 4.75 Zn CB C:Asp422 4.24 Zn OD2 C:Asp422 3.39 Zn OD1 C:Asp422 1.97 Zn CG C:Asp422 2.98 Zn CB C:Gln424 3.94 Zn CG C:Gln424 4.49 Zn NE2 C:His426 3.92 Zn N C:His426 4.79 Zn CB C:His426 3.36 Zn ND1 C:His426 1.94 Zn CD2 C:His426 3.99 Zn CE1 C:His426 2.84 Zn CG C:His426 2.94 Zn CA C:His426 4.68 Zn O A:Hoh564 4.20 interactive model: Zinc binding site 3 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3tbg. 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: Gln341, A: Gln462, A: His463, A: Arg497, conact list: Atom Atom Distance (A) Zn O A:Gln341 4.64 Zn O A:Gln462 4.74 Zn O A:His463 4.09 Zn NE2 A:His463 4.77 Zn N A:His463 4.96 Zn CB A:His463 3.81 Zn ND1 A:His463 2.74 Zn CD2 A:His463 4.79 Zn C A:His463 4.48 Zn CE1 A:His463 3.67 Zn CG A:His463 3.65 Zn CA A:His463 3.86 Zn O A:Arg497 4.26 Zn N A:Arg497 4.82 interactive model: Zinc binding site 4 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3tbg. 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: Cys191, B: Gly192, B: His258, B: Arg269, B: Asp270, B: Glu273, conact list: Atom Atom Distance (A) Zn O B:Cys191 3.53 Zn C B:Cys191 4.16 Zn N B:Gly192 4.63 Zn CA B:Gly192 4.51 Zn NE2 B:His258 1.90 Zn ND1 B:His258 3.90 Zn CD2 B:His258 2.96 Zn CE1 B:His258 2.77 Zn CG B:His258 4.02 Zn CD B:Arg269 4.33 Zn CZ B:Arg269 4.75 Zn CG B:Arg269 3.99 Zn NE B:Arg269 3.92 Zn NH2 B:Arg269 4.90 Zn N B:Asp270 4.94 Zn CB B:Asp270 4.30 Zn OD2 B:Asp270 1.96 Zn OD1 B:Asp270 3.31 Zn CG B:Asp270 2.96 Zn OE1 B:Glu273 3.85 Zn CB B:Glu273 4.62 Zn OE2 B:Glu273 1.87 Zn CD B:Glu273 2.83 Zn CG B:Glu273 3.38 interactive model: Zinc binding site 5 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3tbg. 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: Cys191, C: Gly192, C: His258, C: Arg269, C: Asp270, C: Glu273, C: Hoh529, conact list: Atom Atom Distance (A) Zn O C:Cys191 3.58 Zn C C:Cys191 4.15 Zn CA C:Cys191 4.95 Zn N C:Gly192 4.62 Zn CA C:Gly192 4.55 Zn NE2 C:His258 1.91 Zn ND1 C:His258 3.91 Zn CD2 C:His258 3.02 Zn CE1 C:His258 2.75 Zn CG C:His258 4.06 Zn CD C:Arg269 4.49 Zn CZ C:Arg269 4.80 Zn CG C:Arg269 4.06 Zn NE C:Arg269 4.03 Zn NH2 C:Arg269 4.91 Zn N C:Asp270 4.99 Zn CB C:Asp270 4.32 Zn OD2 C:Asp270 2.01 Zn OD1 C:Asp270 3.17 Zn CG C:Asp270 2.93 Zn OE1 C:Glu273 3.78 Zn CB C:Glu273 4.58 Zn OE2 C:Glu273 1.83 Zn CD C:Glu273 2.78 Zn CG C:Glu273 3.35 Zn O C:Hoh529 4.15 interactive model: Zinc binding site 6 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3tbg. 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: Gln341, C: Gln462, C: His463, C: Arg497, conact list: Atom Atom Distance (A) Zn O C:Gln341 4.47 Zn NE2 C:Gln341 3.38 Zn CD C:Gln341 4.20 Zn CG C:Gln341 4.17 Zn O C:Gln462 4.68 Zn O C:His463 4.30 Zn NE2 C:His463 4.39 Zn N C:His463 4.93 Zn CB C:His463 3.75 Zn ND1 C:His463 2.36 Zn CD2 C:His463 4.50 Zn C C:His463 4.61 Zn CE1 C:His463 3.23 Zn CG C:His463 3.41 Zn CA C:His463 3.89 Zn O C:Arg497 4.50 Zn N C:Arg497 4.87 interactive model: Zinc binding site 7 out of 7 in 3tbg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3tbg. 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: Cys191, D: Gly192, D: His258, D: Arg269, D: Asp270, D: Glu273, conact list: Atom Atom Distance (A) Zn O D:Cys191 3.59 Zn C D:Cys191 4.16 Zn CA D:Cys191 5.00 Zn N D:Gly192 4.62 Zn CA D:Gly192 4.52 Zn NE2 D:His258 1.97 Zn ND1 D:His258 4.03 Zn CD2 D:His258 3.04 Zn CE1 D:His258 2.88 Zn CG D:His258 4.14 Zn CD D:Arg269 4.56 Zn CZ D:Arg269 4.58 Zn CG D:Arg269 4.24 Zn NE D:Arg269 3.96 Zn NH2 D:Arg269 4.57 Zn N D:Asp270 4.95 Zn CB D:Asp270 4.25 Zn OD2 D:Asp270 1.93 Zn OD1 D:Asp270 3.25 Zn CG D:Asp270 2.91 Zn OE1 D:Glu273 1.91 Zn CB D:Glu273 4.64 Zn OE2 D:Glu273 3.87 Zn CD D:Glu273 2.83 Zn CG D:Glu273 3.32 interactive model: