Cadmium in the structure of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) (pdb 1a5z)

The binding sites of Cadmium atom in the structure of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) (pdb code 1a5z). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1a5z structure was solved by G.AUERBACH, R.OSTENDORP, L.PRADE, I.KORNDOERFER, T.DAMS, R.HUBER, R.JAENICKE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.1 Space group I4122 a (A) 105.480 b (A) 105.480 c (A) 187.700 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 28.6 Cadmium Binding Sites: Cadmium binding site 1 out of 3 in 1a5z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1a5z. 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: Arg234, A: Glu238, A: Glu241, A: Arg242, A: Hoh368, A: Hoh570, A: Hoh588, conact list: Atom Atom Distance (A) Cd NH1 A:Arg234 4.29 Cd OE1 A:Glu238 2.99 Cd OE2 A:Glu238 2.08 Cd CD A:Glu238 2.88 Cd CG A:Glu238 4.32 Cd OE1 A:Glu241 2.81 Cd OE2 A:Glu241 2.61 Cd CD A:Glu241 3.07 Cd CG A:Glu241 4.58 Cd NH2 A:Arg242 4.81 Cd NH1 A:Arg242 4.25 Cd O A:Hoh368 3.48 Cd O A:Hoh570 4.78 Cd O A:Hoh588 4.25 interactive model: Cadmium binding site 2 out of 3 in 1a5z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1a5z. 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: Glu259, A: Phe263, A: Glu265, A: Arg267, A: Hoh374, A: Hoh549, conact list: Atom Atom Distance (A) Cd OE1 A:Glu259 4.60 Cd OE2 A:Glu259 2.86 Cd CD A:Glu259 3.64 Cd CG A:Glu259 3.96 Cd CD2 A:Phe263 4.84 Cd OE1 A:Glu265 3.00 Cd OE2 A:Glu265 2.33 Cd CD A:Glu265 3.01 Cd CG A:Glu265 4.47 Cd CD A:Arg267 4.98 Cd NH1 A:Arg267 4.46 Cd O A:Hoh374 4.30 Cd O A:Hoh549 3.26 interactive model: Cadmium binding site 3 out of 3 in 1a5z Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1a5z. 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: Asp168, A: His195, A: Glu199, A: Thr232, A: Oxm355, A: Hoh360, A: Hoh363, A: Hoh366, A: Hoh584, A: Hoh620, A: Hoh678, conact list: Atom Atom Distance (A) Cd N A:Asp168 4.96 Cd CB A:Asp168 4.28 Cd OD2 A:Asp168 2.60 Cd OD1 A:Asp168 2.18 Cd CG A:Asp168 2.75 Cd CA A:Asp168 4.97 Cd NE2 A:His195 3.45 Cd ND1 A:His195 3.40 Cd CD2 A:His195 4.60 Cd CE1 A:His195 2.51 Cd CG A:His195 4.59 Cd OE1 A:Glu199 4.79 Cd O A:Thr232 4.46 Cd O2 A:Oxm355 4.94 Cd O3 A:Oxm355 3.55 Cd C2 A:Oxm355 4.67 Cd O A:Hoh360 4.05 Cd O A:Hoh363 4.35 Cd O A:Hoh366 4.60 Cd O A:Hoh584 4.24 Cd O A:Hoh620 2.66 Cd O A:Hoh678 3.79 interactive model: