Cadmium in the structure of The Structural Identification Of the Interaction Site and Functional State of Rbp For Its Membrane Receptor (pdb 2nnd)

The binding sites of Cadmium atom in the structure of The Structural Identification Of the Interaction Site and Functional State of Rbp For Its Membrane Receptor (pdb code 2nnd). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2nnd structure was solved by C.REDONDO, R.J.BINGHAM, M.VOUROPOULOU, S.W.HOMANS, J.B.FINDLAY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.3-1.6 Space group P43212 a (A) 53.636 b (A) 53.636 c (A) 137.347 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19 Rfree (%) 22.7 Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 2nnd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2nnd. 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: Gln140, A: Glu143, A: Hoh381, A: Hoh419, A: Hoh446, A: Hoh485, A: Hoh563, A: Hoh567, A: Hoh594, conact list: Atom Atom Distance (A) Cd NE2 A:Gln140 4.17 Cd OE1 A:Gln140 4.51 Cd CD A:Gln140 4.80 Cd OE1 A:Glu143 2.26 Cd OE2 A:Glu143 2.48 Cd CD A:Glu143 2.69 Cd CG A:Glu143 4.21 Cd O A:Hoh381 2.42 Cd O A:Hoh419 4.52 Cd O A:Hoh446 4.29 Cd O A:Hoh485 4.94 Cd O A:Hoh563 4.14 Cd O A:Hoh567 3.93 Cd O A:Hoh594 2.36 interactive model: Cadmium binding site 2 out of 4 in 2nnd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2nnd. 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: Glu13, A: Hoh410, A: Hoh431, A: Hoh433, A: Hoh448, A: Hoh552, conact list: Atom Atom Distance (A) Cd OE1 A:Glu13 2.27 Cd OE2 A:Glu13 2.62 Cd CD A:Glu13 2.78 Cd CG A:Glu13 4.30 Cd O A:Hoh410 5.00 Cd O A:Hoh431 2.42 Cd O A:Hoh433 2.30 Cd O A:Hoh448 2.16 Cd O A:Hoh552 4.52 interactive model: Cadmium binding site 3 out of 4 in 2nnd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2nnd. 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: Thr95, A: His108, A: His145, A: Cd373, A: Hoh400, A: Hoh430, A: Hoh487, A: Hoh534, A: Hoh547, A: Hoh554, conact list: Atom Atom Distance (A) Cd CB A:Thr95 4.90 Cd CG2 A:Thr95 4.90 Cd OG1 A:Thr95 3.70 Cd O A:His108 4.73 Cd NE2 A:His108 4.12 Cd CB A:His108 3.86 Cd ND1 A:His108 2.51 Cd CD2 A:His108 4.25 Cd CE1 A:His108 3.14 Cd CG A:His108 3.37 Cd CE1 A:His145 4.46 Cd CD A:Cd373 3.63 Cd O A:Hoh400 4.39 Cd O A:Hoh430 2.30 Cd O A:Hoh487 2.32 Cd O A:Hoh534 4.33 Cd O A:Hoh547 2.57 Cd O A:Hoh554 3.67 interactive model: Cadmium binding site 4 out of 4 in 2nnd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2nnd. 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: His145, A: Cd202, A: Hoh383, A: Hoh480, A: Hoh505, A: Hoh523, A: Hoh547, A: Hoh554, conact list: Atom Atom Distance (A) Cd NE2 A:His145 2.97 Cd ND1 A:His145 3.63 Cd CD2 A:His145 4.29 Cd CE1 A:His145 2.43 Cd CG A:His145 4.61 Cd CD A:Cd202 3.63 Cd O A:Hoh383 3.81 Cd O A:Hoh480 2.44 Cd O A:Hoh505 4.39 Cd O A:Hoh523 4.62 Cd O A:Hoh547 2.49 Cd O A:Hoh554 3.86 interactive model: