Cobalt in the structure of Glycerophosphodiesterase From Enterobacter Aerogenes (pdb 2dxl)

The binding sites of Cobalt atom in the structure of Glycerophosphodiesterase From Enterobacter Aerogenes (pdb code 2dxl). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2dxl structure was solved by C.J.JACKSON, P.D.CARR, D.L.OLLIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.0 Space group P213 a (A) 164.462 b (A) 164.462 c (A) 164.462 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.8 Rfree (%) 19.4 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 2dxl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2dxl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp8, A: His10, A: Asp50, A: His81, A: His156, A: His195, A: His197, A: Co1002, conact list: Atom Atom Distance (A) Co CB A:Asp8 3.88 Co OD2 A:Asp8 3.96 Co OD1 A:Asp8 2.01 Co CG A:Asp8 3.09 Co CA A:Asp8 4.71 Co NE2 A:His10 2.29 Co ND1 A:His10 4.31 Co CD2 A:His10 3.38 Co CE1 A:His10 3.13 Co CG A:His10 4.46 Co CB A:Asp50 3.94 Co OD2 A:Asp50 2.41 Co OD1 A:Asp50 4.58 Co CG A:Asp50 3.51 Co ND1 A:His81 4.44 Co CE1 A:His81 4.64 Co NE2 A:His156 4.70 Co CE1 A:His156 4.47 Co O A:His195 4.26 Co C A:His195 4.84 Co CA A:His195 4.68 Co NE2 A:His197 2.17 Co ND1 A:His197 4.26 Co CD2 A:His197 3.15 Co CE1 A:His197 3.15 Co CG A:His197 4.30 Co CO A:Co1002 3.63 interactive model: Cobalt binding site 2 out of 4 in 2dxl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2dxl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp8, A: Asp50, A: Asn80, A: His81, A: His156, A: His195, A: Co1001, conact list: Atom Atom Distance (A) Co OD1 A:Asp8 4.20 Co CB A:Asp50 4.61 Co OD2 A:Asp50 2.42 Co OD1 A:Asp50 3.17 Co CG A:Asp50 3.16 Co N A:Asn80 4.44 Co CB A:Asn80 4.55 Co ND2 A:Asn80 3.84 Co OD1 A:Asn80 2.15 Co CG A:Asn80 3.29 Co CA A:Asn80 5.00 Co N A:His81 4.99 Co ND1 A:His81 4.02 Co CE1 A:His81 4.54 Co NE2 A:His156 2.24 Co ND1 A:His156 4.29 Co CD2 A:His156 3.31 Co CE1 A:His156 3.12 Co CG A:His156 4.41 Co O A:His195 4.44 Co NE2 A:His195 4.22 Co N A:His195 4.56 Co CB A:His195 4.04 Co ND1 A:His195 2.35 Co CD2 A:His195 4.48 Co C A:His195 4.65 Co CE1 A:His195 3.01 Co CG A:His195 3.51 Co CA A:His195 3.78 Co CO A:Co1001 3.63 interactive model: Cobalt binding site 3 out of 4 in 2dxl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2dxl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp8, B: His10, B: Asp50, B: His81, B: His156, B: His195, B: His197, B: Co1004, conact list: Atom Atom Distance (A) Co CB B:Asp8 3.67 Co OD2 B:Asp8 4.13 Co OD1 B:Asp8 2.20 Co CG B:Asp8 3.14 Co CA B:Asp8 4.59 Co NE2 B:His10 2.25 Co ND1 B:His10 4.25 Co CD2 B:His10 3.38 Co CE1 B:His10 3.05 Co CG B:His10 4.44 Co N B:Asp50 4.91 Co CB B:Asp50 3.61 Co OD2 B:Asp50 2.65 Co OD1 B:Asp50 4.71 Co CG B:Asp50 3.52 Co CA B:Asp50 4.89 Co ND1 B:His81 4.57 Co CE1 B:His81 4.78 Co NE2 B:His156 4.64 Co CE1 B:His156 4.38 Co O B:His195 4.24 Co N B:His195 4.83 Co C B:His195 4.70 Co CA B:His195 4.47 Co NE2 B:His197 2.13 Co ND1 B:His197 4.25 Co CD2 B:His197 3.06 Co CE1 B:His197 3.16 Co CG B:His197 4.24 Co CO B:Co1004 3.49 interactive model: Cobalt binding site 4 out of 4 in 2dxl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2dxl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp8, B: Asp50, B: Asn80, B: His81, B: His156, B: His195, B: Co1003, conact list: Atom Atom Distance (A) Co OD1 B:Asp8 4.03 Co CB B:Asp50 4.43 Co OD2 B:Asp50 2.08 Co OD1 B:Asp50 3.51 Co CG B:Asp50 3.13 Co N B:Asn80 4.61 Co CB B:Asn80 4.39 Co ND2 B:Asn80 3.25 Co OD1 B:Asn80 2.03 Co CG B:Asn80 2.96 Co ND1 B:His81 4.12 Co CE1 B:His81 4.60 Co NE2 B:His156 2.31 Co ND1 B:His156 4.32 Co CD2 B:His156 3.40 Co CE1 B:His156 3.14 Co CG B:His156 4.48 Co O B:His195 4.16 Co NE2 B:His195 4.34 Co N B:His195 4.44 Co CB B:His195 3.73 Co ND1 B:His195 2.34 Co CD2 B:His195 4.45 Co C B:His195 4.36 Co CE1 B:His195 3.20 Co CG B:His195 3.37 Co CA B:His195 3.53 Co CO B:Co1003 3.49 interactive model: