Cadmium in the structure of Extracellular Domain of Mycobacterium Tuberculosis Pknd (pdb 1rwl)

The binding sites of Cadmium atom in the structure of Extracellular Domain of Mycobacterium Tuberculosis Pknd (pdb code 1rwl). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1rwl structure was solved by M.C.GOOD, A.E.GREENSTEIN, T.A.YOUNG, H.L.NG, T.ALBER, TBSTRUCTURAL GENOMICS CONSORTIUM (TBSGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.9 Space group P1211 a (A) 43.940 b (A) 94.580 c (A) 71.770 alpha (°) 90.00 beta (°) 98.10 gamma (°) 90.00 Rfactor (%) 21.4 Rfree (%) 26.2 Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 1rwl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1rwl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu42, A: Gln70, A: Leu237, A: Arg252, A: Hoh518, conact list: Atom Atom Distance (A) Cd OE1 A:Glu42 2.51 Cd OE2 A:Glu42 2.28 Cd CD A:Glu42 2.69 Cd CG A:Glu42 4.17 Cd NE2 A:Gln70 4.33 Cd OE1 A:Gln70 4.16 Cd CD A:Gln70 4.68 Cd CD1 A:Leu237 4.69 Cd NH1 A:Arg252 4.72 Cd O A:Hoh518 4.87 interactive model: Cadmium binding site 2 out of 4 in 1rwl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1rwl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp151, A: Asp169, A: Hoh524, A: Hoh540, conact list: Atom Atom Distance (A) Cd CB A:Asp151 3.66 Cd OD2 A:Asp151 2.20 Cd OD1 A:Asp151 4.37 Cd CG A:Asp151 3.25 Cd CB A:Asp169 4.28 Cd OD2 A:Asp169 2.38 Cd OD1 A:Asp169 2.48 Cd CG A:Asp169 2.80 Cd O A:Hoh524 4.43 Cd O A:Hoh540 2.68 interactive model: Cadmium binding site 3 out of 4 in 1rwl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1rwl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr109, conact list: Atom Atom Distance (A) Cd CD1 A:Tyr109 4.76 Cd CZ A:Tyr109 4.12 Cd CE1 A:Tyr109 3.71 Cd OH A:Tyr109 3.73 interactive model: Cadmium binding site 4 out of 4 in 1rwl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1rwl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Pro103, A: Phe104, A: Asp105, A: Lys139, A: Hoh528, conact list: Atom Atom Distance (A) Cd O A:Pro103 3.91 Cd CB A:Pro103 4.70 Cd C A:Pro103 4.67 Cd O A:Phe104 4.86 Cd C A:Phe104 4.93 Cd N A:Asp105 4.89 Cd CB A:Asp105 4.19 Cd OD2 A:Asp105 2.22 Cd OD1 A:Asp105 2.52 Cd CG A:Asp105 2.72 Cd CA A:Asp105 4.90 Cd O A:Lys139 3.95 Cd O A:Hoh528 2.92 interactive model: