Cadmium in the structure of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed With CD2+, Pep and E4P (pdb 1rzm)

The binding sites of Cadmium atom in the structure of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed With CD2+, Pep and E4P (pdb code 1rzm). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1rzm structure was solved by I.A.SHUMILIN, R.BAUERLE, J.WU, R.W.WOODARD, R.H.KRETSINGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.2 Space group C2221 a (A) 71.581 b (A) 144.215 c (A) 141.057 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.9 Rfree (%) 25.1 Cadmium Binding Sites: Cadmium binding site 1 out of 3 in 1rzm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1rzm. 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: Cys102, A: Arg126, A: Lys131, A: His272, A: Glu298, A: Asp309, A: Gln312, A: Pep8002, A: E4p8003, A: Hoh8055, conact list: Atom Atom Distance (A) Cd CB A:Cys102 3.56 Cd SG A:Cys102 2.69 Cd C A:Cys102 4.88 Cd CA A:Cys102 4.16 Cd NH2 A:Arg126 4.42 Cd CE A:Lys131 5.00 Cd NZ A:Lys131 4.21 Cd NE2 A:His272 2.35 Cd ND1 A:His272 4.32 Cd CD2 A:His272 3.34 Cd CE1 A:His272 3.20 Cd CG A:His272 4.42 Cd OE1 A:Glu298 3.04 Cd OE2 A:Glu298 2.47 Cd CD A:Glu298 3.08 Cd CG A:Glu298 4.52 Cd CB A:Asp309 3.77 Cd OD2 A:Asp309 2.36 Cd OD1 A:Asp309 4.48 Cd CG A:Asp309 3.39 Cd NE2 A:Gln312 4.04 Cd C1 A:Pep8002 4.30 Cd O1 A:Pep8002 3.89 Cd C3 A:Pep8002 4.73 Cd O2' A:Pep8002 4.95 Cd C2 A:Pep8002 4.54 Cd O2 A:E4p8003 3.72 Cd C2 A:E4p8003 4.93 Cd O A:Hoh8055 3.42 interactive model: Cadmium binding site 2 out of 3 in 1rzm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1rzm. 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: B: Cys102, B: Arg126, B: Lys131, B: His272, B: Glu298, B: Asp309, B: Gln312, B: Pep9002, B: E4p9003, conact list: Atom Atom Distance (A) Cd O B:Cys102 4.83 Cd CB B:Cys102 3.50 Cd SG B:Cys102 2.74 Cd C B:Cys102 4.79 Cd CA B:Cys102 4.11 Cd NH2 B:Arg126 4.46 Cd NZ B:Lys131 4.57 Cd NE2 B:His272 2.35 Cd ND1 B:His272 4.33 Cd CD2 B:His272 3.30 Cd CE1 B:His272 3.23 Cd CG B:His272 4.39 Cd OE1 B:Glu298 3.00 Cd OE2 B:Glu298 2.45 Cd CD B:Glu298 3.08 Cd CG B:Glu298 4.55 Cd CB B:Asp309 3.77 Cd OD2 B:Asp309 2.46 Cd OD1 B:Asp309 4.61 Cd CG B:Asp309 3.47 Cd NE2 B:Gln312 3.91 Cd CD B:Gln312 4.97 Cd C1 B:Pep9002 4.47 Cd O1 B:Pep9002 4.36 Cd C3 B:Pep9002 4.96 Cd O2' B:Pep9002 4.90 Cd C2 B:Pep9002 4.69 Cd O2 B:E4p9003 4.89 Cd C1 B:E4p9003 3.20 Cd O1 B:E4p9003 2.91 Cd C3 B:E4p9003 4.87 Cd C2 B:E4p9003 4.51 interactive model: Cadmium binding site 3 out of 3 in 1rzm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1rzm. 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: B: His115, B: Glu119, B: Hoh9063, conact list: Atom Atom Distance (A) Cd NE2 B:His115 2.25 Cd ND1 B:His115 4.27 Cd CD2 B:His115 3.26 Cd CE1 B:His115 3.14 Cd CG B:His115 4.36 Cd OE1 B:Glu119 2.87 Cd OE2 B:Glu119 2.39 Cd CD B:Glu119 2.97 Cd CG B:Glu119 4.46 Cd O B:Hoh9063 4.59 interactive model: