Cadmium in the structure of Structure of Recombinant Mouse L Chain Ferritin At 1.2 A Resolution (pdb 1lb3)

The binding sites of Cadmium atom in the structure of Structure of Recombinant Mouse L Chain Ferritin At 1.2 A Resolution (pdb code 1lb3). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1lb3 structure was solved by T.GRANIER, B.LANGLOIS D'ESTAINTOT, B.GALLOIS, J-M.CHEVALIER, G.PRECIGOUX, P.SANTAMBROGIO, P.AROSIO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 14.0-1.2 Space group F432 a (A) 180.590 b (A) 180.590 c (A) 180.590 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.2 Rfree (%) 16 Cadmium Binding Sites: Cadmium binding site 1 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1lb3. 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: Asp84, A: Hoh270, conact list: Atom Atom Distance (A) Cd CB A:Asp84 4.24 Cd OD2 A:Asp84 2.25 Cd OD1 A:Asp84 2.53 Cd CG A:Asp84 2.77 Cd O A:Hoh270 4.41 interactive model: Cadmium binding site 2 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1lb3. 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: Glu60, A: Glu61, A: Glu64, A: Cd722, A: Hoh243, A: Hoh441, A: Hoh505, A: Hoh506, A: Hoh507, conact list: Atom Atom Distance (A) Cd OE1 A:Glu60 4.38 Cd CB A:Glu60 4.83 Cd CB A:Glu60 4.82 Cd OE2 A:Glu60 2.24 Cd CD A:Glu60 3.26 Cd CG A:Glu60 3.58 Cd OE1 A:Glu61 4.69 Cd OE1 A:Glu64 2.73 Cd OE2 A:Glu64 2.18 Cd CD A:Glu64 2.79 Cd CG A:Glu64 4.25 Cd CD A:Cd722 1.84 Cd O A:Hoh243 4.03 Cd O A:Hoh441 4.64 Cd O A:Hoh505 2.34 Cd O A:Hoh506 2.48 Cd O A:Hoh507 4.66 interactive model: Cadmium binding site 3 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1lb3. 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: Glu60, A: Glu61, A: Glu64, A: Cd718, A: Hoh243, A: Hoh249, A: Hoh441, A: Hoh505, A: Hoh506, conact list: Atom Atom Distance (A) Cd OE2 A:Glu60 3.98 Cd CD A:Glu60 4.87 Cd CG A:Glu60 4.91 Cd OE1 A:Glu61 3.31 Cd OE2 A:Glu61 4.73 Cd CD A:Glu61 4.30 Cd OE1 A:Glu64 2.27 Cd OE2 A:Glu64 3.23 Cd CD A:Glu64 3.12 Cd CG A:Glu64 4.56 Cd CD A:Cd718 1.84 Cd O A:Hoh243 4.33 Cd O A:Hoh249 3.74 Cd O A:Hoh441 3.14 Cd O A:Hoh505 2.63 Cd O A:Hoh506 2.19 interactive model: Cadmium binding site 4 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1lb3. 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: Glu57, A: Glu60, A: Hoh243, A: Hoh439, A: Hoh505, A: Hoh507, conact list: Atom Atom Distance (A) Cd OE1 A:Glu57 2.14 Cd CB A:Glu57 4.81 Cd OE2 A:Glu57 2.32 Cd CD A:Glu57 2.53 Cd CG A:Glu57 4.84 Cd CG A:Glu57 4.05 Cd OE1 A:Glu60 2.65 Cd CB A:Glu60 4.89 Cd CB A:Glu60 4.97 Cd OE2 A:Glu60 3.57 Cd CD A:Glu60 3.38 Cd CG A:Glu60 4.68 Cd CG A:Glu60 4.54 Cd O A:Hoh243 4.09 Cd O A:Hoh439 4.12 Cd O A:Hoh505 4.76 Cd O A:Hoh507 2.00 interactive model: Cadmium binding site 5 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1lb3. 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: Asp131, A: Glu134, A: Ser135, A: Hoh488, A: Hoh508, A: Hoh509, A: Hoh510, A: Hoh511, A: Hoh512, conact list: Atom Atom Distance (A) Cd O A:Asp131 4.99 Cd CB A:Asp131 4.81 Cd CB A:Asp131 4.60 Cd OD2 A:Asp131 4.81 Cd OD2 A:Asp131 3.43 Cd OD1 A:Asp131 2.69 Cd OD1 A:Asp131 2.32 Cd CG A:Asp131 3.93 Cd CG A:Asp131 3.21 Cd OE1 A:Glu134 4.84 Cd OE2 A:Glu134 3.90 Cd CD A:Glu134 4.36 Cd CG A:Glu134 4.33 Cd OG A:Ser135 3.65 Cd O A:Hoh488 4.64 Cd O A:Hoh508 2.40 Cd O A:Hoh509 2.15 Cd O A:Hoh510 2.05 Cd O A:Hoh511 2.08 Cd O A:Hoh512 2.23 interactive model: Cadmium binding site 6 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 1lb3. 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: Glu134, A: Hoh452, A: Hoh509, A: Hoh510, A: Hoh513, A: Hoh514, A: Hoh515, A: Hoh519, A: Hoh520, conact list: Atom Atom Distance (A) Cd OE1 A:Glu134 4.39 Cd OE1 A:Glu134 4.11 Cd OE2 A:Glu134 3.54 Cd OE2 A:Glu134 4.73 Cd CD A:Glu134 4.41 Cd CD A:Glu134 4.85 Cd O A:Hoh452 4.43 Cd O A:Hoh509 4.25 Cd O A:Hoh510 4.67 Cd O A:Hoh513 2.11 Cd O A:Hoh514 2.47 Cd O A:Hoh515 2.40 Cd O A:Hoh519 4.93 Cd O A:Hoh520 4.50 interactive model: Cadmium binding site 7 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 1lb3. 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: Ser135, A: His136, A: Hoh255, A: Hoh409, A: Hoh516, A: Hoh517, A: Hoh518, conact list: Atom Atom Distance (A) Cd CB A:Ser135 4.80 Cd NE2 A:His136 2.35 Cd ND1 A:His136 4.46 Cd CD2 A:His136 3.35 Cd CE1 A:His136 3.30 Cd CG A:His136 4.49 Cd O A:Hoh255 4.31 Cd O A:Hoh409 2.91 Cd O A:Hoh516 2.37 Cd O A:Hoh517 2.46 Cd O A:Hoh518 2.36 interactive model: Cadmium binding site 8 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 1lb3. 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: His118, A: Ser122, A: Cys130, A: Glu134, A: Hoh435, A: Hoh436, A: Hoh452, A: Hoh513, A: Hoh514, A: Hoh519, A: Hoh520, A: Hoh521, conact list: Atom Atom Distance (A) Cd NE2 A:His118 3.09 Cd NE2 A:His118 2.47 Cd ND1 A:His118 3.81 Cd ND1 A:His118 4.23 Cd CD2 A:His118 4.38 Cd CD2 A:His118 3.68 Cd CE1 A:His118 2.64 Cd CE1 A:His118 3.00 Cd CG A:His118 4.72 Cd CG A:His118 4.57 Cd CB A:Ser122 4.98 Cd CB A:Ser122 4.97 Cd OG A:Ser122 3.84 Cd CB A:Cys130 3.63 Cd SG A:Cys130 3.75 Cd CA A:Cys130 4.81 Cd OE2 A:Glu134 3.21 Cd CD A:Glu134 4.44 Cd O A:Hoh435 1.92 Cd O A:Hoh436 4.86 Cd O A:Hoh452 2.67 Cd O A:Hoh513 4.31 Cd O A:Hoh514 4.21 Cd O A:Hoh519 2.17 Cd O A:Hoh520 2.56 Cd O A:Hoh521 2.19 interactive model: Cadmium binding site 9 out of 9 in 1lb3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 1lb3. 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: His53, A: Glu57, A: Hoh420, A: Hoh522, A: Hoh523, A: Hoh524, conact list: Atom Atom Distance (A) Cd NE2 A:His53 2.19 Cd ND1 A:His53 4.29 Cd CD2 A:His53 3.10 Cd CE1 A:His53 3.16 Cd CG A:His53 4.27 Cd OE1 A:Glu57 4.15 Cd OE1 A:Glu57 4.82 Cd OE2 A:Glu57 2.05 Cd OE2 A:Glu57 4.61 Cd CD A:Glu57 3.24 Cd CD A:Glu57 4.20 Cd CG A:Glu57 3.96 Cd CG A:Glu57 3.94 Cd O A:Hoh420 4.96 Cd O A:Hoh522 2.36 Cd O A:Hoh523 2.13 Cd O A:Hoh524 2.29 interactive model: