Cadmium in the structure of Human Gelsolin Domain 2 With A CD2+ Bound (pdb 1kcq)

The binding sites of Cadmium atom in the structure of Human Gelsolin Domain 2 With A CD2+ Bound (pdb code 1kcq). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1kcq structure was solved by S.L.KAZMIRSKI, R.L.ISAACSON, C.AN, A.BUCKLE, C.M.JOHNSON, V.DAGGETT, A.R.FERSHT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.2-1.6 Space group C121 a (A) 96.968 b (A) 26.525 c (A) 50.294 alpha (°) 90.00 beta (°) 121.19 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 23.3 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 1kcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1kcq. 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: Glu258, A: Asp259, A: Hoh267, A: Hoh268, A: Hoh273, A: Hoh318, A: Hoh358, conact list: Atom Atom Distance (A) Cd OE1 A:Glu258 2.79 Cd OE2 A:Glu258 1.95 Cd CD A:Glu258 2.77 Cd CG A:Glu258 4.21 Cd CA A:Glu258 4.94 Cd N A:Asp259 4.57 Cd OD1 A:Asp259 4.31 Cd O A:Hoh267 4.93 Cd O A:Hoh268 4.15 Cd O A:Hoh273 2.47 Cd O A:Hoh318 4.77 Cd O A:Hoh358 2.55 interactive model: Cadmium binding site 2 out of 5 in 1kcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1kcq. 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: Lys166, A: Gly167, A: Gly186, A: Asp187, A: Asn204, A: Ser205, A: Asn206, A: Glu209, A: Thr257, A: Asp259, A: Hoh267, A: Hoh268, A: Hoh358, conact list: Atom Atom Distance (A) Cd CG A:Lys166 4.69 Cd NZ A:Lys166 4.21 Cd O A:Gly167 4.89 Cd N A:Gly167 4.79 Cd O A:Gly186 2.21 Cd C A:Gly186 3.24 Cd CA A:Gly186 4.30 Cd N A:Asp187 3.86 Cd CB A:Asp187 4.21 Cd OD2 A:Asp187 4.51 Cd OD1 A:Asp187 2.38 Cd CG A:Asp187 3.55 Cd CA A:Asp187 3.80 Cd O A:Asn204 4.84 Cd CA A:Ser205 4.68 Cd N A:Asn206 4.75 Cd ND2 A:Asn206 3.98 Cd CG A:Asn206 4.96 Cd OE1 A:Glu209 2.68 Cd OE2 A:Glu209 2.31 Cd CD A:Glu209 2.79 Cd CG A:Glu209 4.29 Cd O A:Thr257 4.77 Cd CB A:Asp259 4.48 Cd OD2 A:Asp259 2.80 Cd OD1 A:Asp259 2.45 Cd CG A:Asp259 2.96 Cd O A:Hoh267 2.37 Cd O A:Hoh268 2.48 Cd O A:Hoh358 4.83 interactive model: Cadmium binding site 3 out of 5 in 1kcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1kcq. 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: Arg161, A: Glu175, A: Hoh266, A: Hoh270, conact list: Atom Atom Distance (A) Cd CB A:Arg161 4.96 Cd CD A:Arg161 3.72 Cd CG A:Arg161 4.17 Cd NH1 A:Arg161 4.72 Cd OE1 A:Glu175 2.48 Cd CB A:Glu175 4.80 Cd OE2 A:Glu175 2.36 Cd CD A:Glu175 2.71 Cd CG A:Glu175 4.21 Cd O A:Hoh266 4.93 Cd O A:Hoh270 2.32 interactive model: Cadmium binding site 4 out of 5 in 1kcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1kcq. 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: His232, A: Cd265, A: Hoh282, A: Hoh331, A: Hoh352, A: Hoh355, A: Hoh360, A: Hoh374, conact list: Atom Atom Distance (A) Cd NE2 A:His232 4.31 Cd CB A:His232 3.81 Cd ND1 A:His232 2.33 Cd CD2 A:His232 4.47 Cd CE1 A:His232 3.12 Cd CG A:His232 3.43 Cd CA A:His232 4.44 Cd CD A:Cd265 0.00 Cd CD A:Cd265 1.50 Cd O A:Hoh282 4.45 Cd O A:Hoh331 4.08 Cd O A:Hoh352 4.96 Cd O A:Hoh355 2.59 Cd O A:Hoh360 2.38 Cd O A:Hoh374 2.80 interactive model: Cadmium binding site 5 out of 5 in 1kcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1kcq. 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: Arg230, A: Val231, A: His232, A: Val233, A: Cd265, A: Hoh331, A: Hoh352, A: Hoh355, A: Hoh360, A: Hoh374, conact list: Atom Atom Distance (A) Cd CD A:Arg230 4.96 Cd O A:Val231 4.21 Cd C A:Val231 4.89 Cd NE2 A:His232 4.57 Cd N A:His232 4.79 Cd CB A:His232 3.81 Cd ND1 A:His232 2.59 Cd CD2 A:His232 4.65 Cd C A:His232 4.92 Cd CE1 A:His232 3.45 Cd CG A:His232 3.56 Cd CA A:His232 3.89 Cd N A:Val233 4.98 Cd CD A:Cd265 1.50 Cd CD A:Cd265 0.00 Cd O A:Hoh331 4.55 Cd O A:Hoh352 3.79 Cd O A:Hoh355 2.43 Cd O A:Hoh360 3.76 Cd O A:Hoh374 2.39 interactive model: