Cadmium in the structure of The Crystal Structure E. Coli Spy (pdb 3oeo)

The binding sites of Cadmium atom in the structure of The Crystal Structure E. Coli Spy (pdb code 3oeo). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3oeo structure was solved by E.KWON, D.Y.KIM, C.A.GROSS, J.D.GROSS, K.K.KIM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.7 Space group P32 a (A) 69.195 b (A) 69.195 c (A) 126.347 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 25.2 Rfree (%) 30 Cadmium Binding Sites: Cadmium binding site 1 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3oeo. 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: Asp59, A: Lys62, A: Hoh164, A: Hoh167, A: Hoh168, A: Hoh180, conact list: Atom Atom Distance (A) Cd CB A:Asp59 4.61 Cd OD2 A:Asp59 2.79 Cd OD1 A:Asp59 2.65 Cd CG A:Asp59 3.09 Cd NZ A:Lys62 4.95 Cd O A:Hoh164 4.04 Cd O A:Hoh167 2.12 Cd O A:Hoh168 3.46 Cd O A:Hoh180 2.14 interactive model: Cadmium binding site 2 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3oeo. 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: Gln123, A: Hoh181, C: Hoh179, conact list: Atom Atom Distance (A) Cd NE2 A:Gln123 4.72 Cd OE1 A:Gln123 4.54 Cd O A:Hoh181 2.56 Cd O C:Hoh179 2.14 interactive model: Cadmium binding site 3 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3oeo. 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: Arg85, A: Asp89, C: Cd19, C: Cd20, C: Hoh183, C: Hoh185, conact list: Atom Atom Distance (A) Cd CD A:Arg85 4.54 Cd CG A:Arg85 4.28 Cd CB A:Asp89 4.40 Cd OD2 A:Asp89 3.65 Cd OD1 A:Asp89 2.49 Cd CG A:Asp89 3.27 Cd CA A:Asp89 4.69 Cd CD C:Cd19 3.64 Cd CD C:Cd20 4.01 Cd O C:Hoh183 2.65 Cd O C:Hoh185 2.44 interactive model: Cadmium binding site 4 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3oeo. 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: Glu143, C: Arg85, C: His88, C: Asp89, A: Cd23, C: Cd21, A: Hoh188, C: Hoh186, C: Hoh187, conact list: Atom Atom Distance (A) Cd OE1 A:Glu143 3.17 Cd OE2 A:Glu143 3.62 Cd CD A:Glu143 3.79 Cd CB C:Arg85 4.58 Cd CD C:Arg85 4.56 Cd CG C:Arg85 4.22 Cd NE2 C:His88 3.76 Cd CE1 C:His88 4.08 Cd OD2 C:Asp89 4.92 Cd OD1 C:Asp89 4.56 Cd CD A:Cd23 3.17 Cd CD C:Cd21 3.02 Cd O A:Hoh188 3.64 Cd O C:Hoh186 3.69 Cd O C:Hoh187 2.66 interactive model: Cadmium binding site 5 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3oeo. 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: Glu143, A: Cd22, C: Cd21, A: Hoh188, C: Hoh186, C: Hoh187, conact list: Atom Atom Distance (A) Cd OE1 A:Glu143 4.12 Cd OE2 A:Glu143 3.75 Cd CD A:Glu143 4.30 Cd CD A:Cd22 3.17 Cd CD C:Cd21 3.15 Cd O A:Hoh188 2.19 Cd O C:Hoh186 2.81 Cd O C:Hoh187 4.22 interactive model: Cadmium binding site 6 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 3oeo. 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: Glu82, A: Lys107, A: Hoh178, A: Hoh182, conact list: Atom Atom Distance (A) Cd OE1 A:Glu82 2.56 Cd OE2 A:Glu82 2.62 Cd CD A:Glu82 2.70 Cd CG A:Glu82 3.86 Cd NZ A:Lys107 4.82 Cd O A:Hoh178 4.80 Cd O A:Hoh182 2.68 interactive model: Cadmium binding site 7 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 3oeo. 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: Asp59, B: Lys62, B: Hoh165, B: Hoh166, B: Hoh178, conact list: Atom Atom Distance (A) Cd CB B:Asp59 4.68 Cd OD2 B:Asp59 2.80 Cd OD1 B:Asp59 3.02 Cd CG B:Asp59 3.24 Cd NZ B:Lys62 4.85 Cd O B:Hoh165 3.37 Cd O B:Hoh166 4.66 Cd O B:Hoh178 2.05 interactive model: Cadmium binding site 8 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 3oeo. 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: Asp97, B: Val99, B: Lys100, C: Cd162, B: Hoh3, B: Hoh179, C: Hoh163, C: Hoh189, conact list: Atom Atom Distance (A) Cd CB B:Asp97 4.09 Cd OD2 B:Asp97 2.02 Cd OD1 B:Asp97 3.53 Cd CG B:Asp97 2.98 Cd CB B:Val99 4.88 Cd CG1 B:Val99 3.44 Cd CE B:Lys100 4.85 Cd CD B:Lys100 4.72 Cd NZ B:Lys100 4.89 Cd CD C:Cd162 4.81 Cd O B:Hoh3 3.16 Cd O B:Hoh179 2.50 Cd O C:Hoh163 4.66 Cd O C:Hoh189 4.46 interactive model: Cadmium binding site 9 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 3oeo. 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: His119, B: Hoh173, B: Hoh180, D: Hoh177, conact list: Atom Atom Distance (A) Cd ND1 B:His119 4.65 Cd O B:Hoh173 4.40 Cd O B:Hoh180 4.45 Cd O D:Hoh177 4.54 interactive model: Cadmium binding site 10 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 3oeo. 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: Glu82, B: Hoh181, conact list: Atom Atom Distance (A) Cd OE1 B:Glu82 2.56 Cd OE2 B:Glu82 4.05 Cd CD B:Glu82 3.64 Cd CG B:Glu82 4.90 Cd O B:Hoh181 2.83 interactive model: Cadmium binding site 11 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 3oeo. 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: Glu109, B: Glu109, B: Lys113, C: Glu109, C: Lys113, D: Glu109, B: Hoh182, C: Hoh167, conact list: Atom Atom Distance (A) Cd OE1 A:Glu109 2.28 Cd CB A:Glu109 4.82 Cd OE2 A:Glu109 3.86 Cd CD A:Glu109 3.40 Cd CG A:Glu109 4.68 Cd OE1 B:Glu109 2.94 Cd OE2 B:Glu109 2.02 Cd CD B:Glu109 2.81 Cd CG B:Glu109 4.26 Cd NZ B:Lys113 4.23 Cd OE1 C:Glu109 2.00 Cd OE2 C:Glu109 2.97 Cd CD C:Glu109 2.82 Cd CG C:Glu109 4.26 Cd CE C:Lys113 4.23 Cd NZ C:Lys113 4.17 Cd OE1 D:Glu109 2.38 Cd CB D:Glu109 4.98 Cd OE2 D:Glu109 2.89 Cd CD D:Glu109 2.97 Cd CG D:Glu109 4.43 Cd O B:Hoh182 2.82 Cd O C:Hoh167 2.86 interactive model: Cadmium binding site 12 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 3oeo. 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: C: Asp59, C: Hoh172, C: Hoh175, C: Hoh180, conact list: Atom Atom Distance (A) Cd CB C:Asp59 4.16 Cd OD2 C:Asp59 2.55 Cd OD1 C:Asp59 2.11 Cd CG C:Asp59 2.65 Cd CA C:Asp59 4.82 Cd O C:Hoh172 3.09 Cd O C:Hoh175 1.93 Cd O C:Hoh180 2.70 interactive model: Cadmium binding site 13 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cadmium in the PDB 3oeo. 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: C: His119, C: Gln123, C: Hoh171, C: Hoh181, conact list: Atom Atom Distance (A) Cd NE2 C:His119 2.16 Cd ND1 C:His119 4.23 Cd CD2 C:His119 2.76 Cd CE1 C:His119 3.32 Cd CG C:His119 4.00 Cd OE1 C:Gln123 3.85 Cd CD C:Gln123 4.76 Cd O C:Hoh171 4.90 Cd O C:Hoh181 2.75 interactive model: Cadmium binding site 14 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Cadmium in the PDB 3oeo. 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: C: Glu82, C: Lys107, C: Hoh182, conact list: Atom Atom Distance (A) Cd OE1 C:Glu82 3.67 Cd CB C:Glu82 4.47 Cd OE2 C:Glu82 3.80 Cd CD C:Glu82 3.77 Cd CG C:Glu82 4.61 Cd NZ C:Lys107 3.87 Cd O C:Hoh182 1.96 interactive model: Cadmium binding site 15 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Cadmium in the PDB 3oeo. 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: Arg85, A: His88, A: Asp89, C: Glu143, A: Cd18, C: Cd20, C: Hoh183, C: Hoh184, C: Hoh185, conact list: Atom Atom Distance (A) Cd CB A:Arg85 4.42 Cd CD A:Arg85 4.03 Cd CG A:Arg85 3.32 Cd NE A:Arg85 4.61 Cd CA A:Arg85 4.77 Cd ND1 A:His88 4.44 Cd OD1 A:Asp89 4.38 Cd OE1 C:Glu143 4.07 Cd OE2 C:Glu143 2.35 Cd CD C:Glu143 3.15 Cd CG C:Glu143 3.62 Cd CD A:Cd18 3.64 Cd CD C:Cd20 3.06 Cd O C:Hoh183 2.22 Cd O C:Hoh184 2.42 Cd O C:Hoh185 3.92 interactive model: Cadmium binding site 16 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Cadmium in the PDB 3oeo. 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: His88, C: Asn139, C: Glu143, A: Cd18, C: Cd19, C: Hoh183, C: Hoh184, C: Hoh185, conact list: Atom Atom Distance (A) Cd ND1 A:His88 4.92 Cd ND2 C:Asn139 4.97 Cd OE1 C:Glu143 4.91 Cd CB C:Glu143 4.54 Cd OE2 C:Glu143 4.21 Cd CD C:Glu143 4.08 Cd CG C:Glu143 3.47 Cd CD A:Cd18 4.01 Cd CD C:Cd19 3.06 Cd O C:Hoh183 3.09 Cd O C:Hoh184 4.56 Cd O C:Hoh185 2.39 interactive model: Cadmium binding site 17 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Cadmium in the PDB 3oeo. 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: C: Arg85, C: His88, C: Asp89, A: Cd22, A: Cd23, A: Hoh188, C: Hoh178, C: Hoh186, C: Hoh187, conact list: Atom Atom Distance (A) Cd O C:Arg85 4.65 Cd NE2 C:His88 4.61 Cd CE1 C:His88 4.26 Cd CB C:Asp89 4.36 Cd OD2 C:Asp89 2.83 Cd OD1 C:Asp89 2.21 Cd CG C:Asp89 2.87 Cd CD A:Cd22 3.02 Cd CD A:Cd23 3.15 Cd O A:Hoh188 4.04 Cd O C:Hoh178 4.73 Cd O C:Hoh186 2.41 Cd O C:Hoh187 3.09 interactive model: Cadmium binding site 18 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Cadmium in the PDB 3oeo. 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: Lys100, C: Asp97, C: Lys100, B: Cd8, B: Hoh3, C: Hoh163, C: Hoh189, conact list: Atom Atom Distance (A) Cd CE B:Lys100 4.93 Cd CB C:Asp97 4.39 Cd OD2 C:Asp97 2.16 Cd OD1 C:Asp97 3.02 Cd CG C:Asp97 2.94 Cd N C:Lys100 4.53 Cd CB C:Lys100 4.17 Cd CG C:Lys100 4.94 Cd CA C:Lys100 4.81 Cd CD B:Cd8 4.81 Cd O B:Hoh3 4.14 Cd O C:Hoh163 2.60 Cd O C:Hoh189 2.94 interactive model: Cadmium binding site 19 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Cadmium in the PDB 3oeo. 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: D: Asp59, D: Hoh20, D: Hoh166, D: Hoh173, D: Hoh184, conact list: Atom Atom Distance (A) Cd CB D:Asp59 4.16 Cd OD2 D:Asp59 2.08 Cd OD1 D:Asp59 3.41 Cd CG D:Asp59 2.98 Cd O D:Hoh20 2.25 Cd O D:Hoh166 3.55 Cd O D:Hoh173 4.12 Cd O D:Hoh184 2.17 interactive model: Cadmium binding site 20 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Cadmium in the PDB 3oeo. 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: D: His119, D: Gln123, D: Hoh164, D: Hoh180, conact list: Atom Atom Distance (A) Cd NE2 D:His119 2.17 Cd ND1 D:His119 3.80 Cd CD2 D:His119 3.44 Cd CE1 D:His119 2.56 Cd CG D:His119 4.25 Cd NE2 D:Gln123 3.84 Cd CD D:Gln123 4.96 Cd O D:Hoh164 3.24 Cd O D:Hoh180 2.54 interactive model: Cadmium binding site 21 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 21 of Cadmium in the PDB 3oeo. 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: D: Glu82, D: Hoh181, conact list: Atom Atom Distance (A) Cd OE1 D:Glu82 2.70 Cd CB D:Glu82 3.76 Cd OE2 D:Glu82 4.78 Cd CD D:Glu82 3.77 Cd CG D:Glu82 4.30 Cd O D:Hoh181 3.48 interactive model: Cadmium binding site 22 out of 22 in 3oeo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 22 of Cadmium in the PDB 3oeo. 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: C: Glu110, D: Glu110, D: Hoh179, D: Hoh182, conact list: Atom Atom Distance (A) Cd CB C:Glu110 4.78 Cd OE2 C:Glu110 4.43 Cd CD C:Glu110 4.32 Cd CG C:Glu110 3.64 Cd OE1 D:Glu110 2.01 Cd CB D:Glu110 4.95 Cd OE2 D:Glu110 2.74 Cd CD D:Glu110 2.64 Cd CG D:Glu110 4.01 Cd O D:Hoh179 3.50 Cd O D:Hoh182 2.75 interactive model: