Gold in the structure of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea (pdb 3k3g)

The binding sites of Gold atom in the structure of Crystal Structure of the Urea Transporter From Desulfovibrio Vulgaris Bound to 1,3-Dimethylurea (pdb code 3k3g). This binding sites where shown with 5.0 Angstroms radius around Gold atom. The 3k3g structure was solved by E.J.LEVIN, M.ZHOU, NEW YORK CONSORTIUM ON MEMBRANE PROTEIN STRUCTURE(NYCOMPS), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 27.5-2.4 Space group P63 a (A) 110.106 b (A) 110.106 c (A) 84.872 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.6 Rfree (%) 21.4 Gold Binding Sites: Gold binding site 1 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gln24, A: Phe27, A: Ile255, A: Ala322, A: Mmu348, A: Hoh365, conact list: Atom Atom Distance (A) Au NE2 A:Gln24 3.85 Au OE1 A:Gln24 3.38 Au CD A:Gln24 4.03 Au O A:Phe27 3.97 Au CB A:Phe27 4.67 Au CD1 A:Phe27 4.88 Au C A:Phe27 4.59 Au CA A:Phe27 4.67 Au CG2 A:Ile255 4.95 Au O A:Ala322 4.10 Au CAA A:Mmu348 4.55 Au O A:Hoh365 4.90 interactive model: Gold binding site 2 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys15, A: Cys19, A: Thr31, A: Leu35, A: Au340, A: Au341, A: Au342, conact list: Atom Atom Distance (A) Au O A:Cys15 4.45 Au CB A:Cys19 3.20 Au SG A:Cys19 2.69 Au CA A:Cys19 4.68 Au O A:Thr31 3.93 Au CB A:Thr31 4.58 Au CG2 A:Thr31 3.14 Au C A:Thr31 4.61 Au CA A:Thr31 4.96 Au N A:Leu35 4.89 Au CB A:Leu35 3.87 Au CD1 A:Leu35 3.45 Au CD2 A:Leu35 4.42 Au CG A:Leu35 4.09 Au CA A:Leu35 4.64 Au AU A:Au340 2.96 Au AU A:Au341 3.59 Au AU A:Au342 4.63 interactive model: Gold binding site 3 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys15, A: Asp16, A: Val18, A: Cys19, A: Au339, A: Au341, A: Au342, conact list: Atom Atom Distance (A) Au O A:Cys15 2.15 Au CB A:Cys15 3.85 Au SG A:Cys15 2.87 Au C A:Cys15 3.13 Au CA A:Cys15 3.81 Au N A:Asp16 4.13 Au CA A:Asp16 4.53 Au CB A:Val18 4.87 Au C A:Val18 4.94 Au N A:Cys19 3.96 Au CB A:Cys19 3.43 Au SG A:Cys19 2.41 Au CA A:Cys19 4.26 Au AU A:Au339 2.96 Au AU A:Au341 3.24 Au AU A:Au342 3.36 interactive model: Gold binding site 4 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile12, A: Cys15, A: Asp16, A: Thr31, A: Au339, A: Au340, A: Au342, conact list: Atom Atom Distance (A) Au O A:Ile12 4.18 Au CD1 A:Ile12 4.09 Au CG1 A:Ile12 4.76 Au O A:Cys15 3.56 Au CB A:Cys15 3.53 Au SG A:Cys15 3.34 Au C A:Cys15 3.54 Au CA A:Cys15 4.20 Au N A:Asp16 3.63 Au CB A:Asp16 4.27 Au OD1 A:Asp16 4.91 Au CA A:Asp16 3.87 Au CG2 A:Thr31 4.51 Au AU A:Au339 3.59 Au AU A:Au340 3.24 Au AU A:Au342 3.08 interactive model: Gold binding site 5 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ile12, A: Cys15, A: Au339, A: Au340, A: Au341, conact list: Atom Atom Distance (A) Au CD1 A:Ile12 4.32 Au O A:Cys15 4.57 Au CB A:Cys15 3.35 Au SG A:Cys15 1.89 Au C A:Cys15 4.71 Au CA A:Cys15 4.51 Au AU A:Au339 4.63 Au AU A:Au340 3.36 Au AU A:Au341 3.08 interactive model: Gold binding site 6 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Thr47, A: Val50, A: Cys51, A: Leu100, A: Au344, conact list: Atom Atom Distance (A) Au O A:Thr47 3.29 Au CG2 A:Thr47 4.30 Au C A:Thr47 4.31 Au CA A:Thr47 4.62 Au O A:Val50 4.70 Au CB A:Val50 3.67 Au CG2 A:Val50 4.95 Au C A:Val50 4.03 Au CG1 A:Val50 3.30 Au CA A:Val50 4.42 Au N A:Cys51 3.54 Au CB A:Cys51 3.72 Au SG A:Cys51 2.79 Au CA A:Cys51 3.92 Au CD1 A:Leu100 3.73 Au CG A:Leu100 4.50 Au AU A:Au344 3.02 interactive model: Gold binding site 7 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Thr47, A: Cys51, A: Pro90, A: Met99, A: Leu100, A: Au343, conact list: Atom Atom Distance (A) Au O A:Thr47 4.05 Au CG2 A:Thr47 3.70 Au C A:Thr47 4.82 Au CB A:Cys51 3.68 Au SG A:Cys51 2.36 Au CA A:Cys51 4.85 Au CB A:Pro90 3.93 Au CD A:Pro90 4.70 Au CG A:Pro90 3.71 Au CB A:Met99 4.88 Au CG A:Met99 3.79 Au SD A:Met99 4.90 Au CD1 A:Leu100 3.84 Au AU A:Au343 3.02 interactive model: Gold binding site 8 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys224, A: Au346, conact list: Atom Atom Distance (A) Au CB A:Cys224 3.08 Au SG A:Cys224 2.59 Au CA A:Cys224 4.63 Au AU A:Au346 3.08 interactive model: Gold binding site 9 out of 9 in 3k3g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Gold in the PDB 3k3g. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe177, A: Cys224, A: Leu227, A: Ile228, A: Au345, conact list: Atom Atom Distance (A) Au CZ A:Phe177 4.80 Au CE1 A:Phe177 4.69 Au O A:Cys224 4.02 Au N A:Cys224 4.92 Au CB A:Cys224 2.85 Au SG A:Cys224 1.73 Au C A:Cys224 4.28 Au CA A:Cys224 3.65 Au CB A:Leu227 4.41 Au CD1 A:Leu227 4.48 Au CD1 A:Ile228 4.91 Au CG1 A:Ile228 4.60 Au AU A:Au345 3.08 interactive model: