Cobalt in the structure of Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus (pdb 2z06)

The binding sites of Cobalt atom in the structure of Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus (pdb code 2z06). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2z06 structure was solved by M.KANAGAWA, S.KURAMITSU, S.YOKOYAMA, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.2-2.2 Space group P212121 a (A) 76.602 b (A) 110.928 c (A) 116.273 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.2 Rfree (%) 24.6 Cobalt Binding Sites: Cobalt binding site 1 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2z06. 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: Glu37, A: Asn65, A: His66, A: His145, A: His170, A: His172, A: Hoh317, A: Hoh364, conact list: Atom Atom Distance (A) Co OE1 A:Glu37 3.23 Co OE2 A:Glu37 2.77 Co CD A:Glu37 3.36 Co CG A:Glu37 4.82 Co N A:Asn65 4.77 Co CB A:Asn65 4.64 Co ND2 A:Asn65 2.54 Co OD1 A:Asn65 3.02 Co CG A:Asn65 3.15 Co ND1 A:His66 4.30 Co CE1 A:His66 4.62 Co NE2 A:His145 3.08 Co ND1 A:His145 3.74 Co CD2 A:His145 4.39 Co CE1 A:His145 2.55 Co CG A:His145 4.72 Co O A:His170 4.67 Co NE2 A:His170 4.65 Co CB A:His170 4.32 Co ND1 A:His170 2.72 Co CD2 A:His170 4.90 Co CE1 A:His170 3.40 Co CG A:His170 3.89 Co CA A:His170 4.37 Co NE2 A:His172 4.98 Co O A:Hoh317 3.03 Co O A:Hoh364 3.13 interactive model: Cobalt binding site 2 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2z06. 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: C: Glu37, C: Asn38, C: Asn65, C: His66, C: His145, C: His170, C: His172, C: Hoh339, C: Hoh387, conact list: Atom Atom Distance (A) Co OE1 C:Glu37 3.18 Co OE2 C:Glu37 2.80 Co CD C:Glu37 3.27 Co CG C:Glu37 4.60 Co ND2 C:Asn38 4.89 Co N C:Asn65 4.78 Co CB C:Asn65 4.55 Co ND2 C:Asn65 2.85 Co OD1 C:Asn65 2.49 Co CG C:Asn65 3.03 Co ND1 C:His66 4.46 Co CE1 C:His66 4.78 Co NE2 C:His145 2.92 Co ND1 C:His145 3.89 Co CD2 C:His145 4.25 Co CE1 C:His145 2.64 Co CG C:His145 4.72 Co O C:His170 4.56 Co NE2 C:His170 4.37 Co CB C:His170 4.15 Co ND1 C:His170 2.48 Co CD2 C:His170 4.63 Co C C:His170 4.93 Co CE1 C:His170 3.14 Co CG C:His170 3.65 Co CA C:His170 4.23 Co NE2 C:His172 4.77 Co O C:Hoh339 3.13 Co O C:Hoh387 2.85 interactive model: Cobalt binding site 3 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2z06. 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: His21, A: Ile25, A: Arg28, A: Tyr247, A: Hoh384, conact list: Atom Atom Distance (A) Co NE2 A:His21 4.45 Co CE1 A:His21 4.82 Co CG2 A:Ile25 4.31 Co CZ A:Arg28 3.96 Co NH2 A:Arg28 3.43 Co NH1 A:Arg28 3.58 Co CE2 A:Tyr247 3.95 Co CZ A:Tyr247 3.97 Co OH A:Tyr247 3.09 Co O A:Hoh384 3.77 interactive model: Cobalt binding site 4 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2z06. 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: Glu37, B: Asn65, B: His66, B: His145, B: His170, B: His172, B: Hoh335, B: Hoh369, B: Hoh415, conact list: Atom Atom Distance (A) Co OE1 B:Glu37 2.98 Co OE2 B:Glu37 2.55 Co CD B:Glu37 3.11 Co CG B:Glu37 4.59 Co N B:Asn65 4.82 Co CB B:Asn65 4.98 Co ND2 B:Asn65 3.94 Co OD1 B:Asn65 2.58 Co CG B:Asn65 3.61 Co ND1 B:His66 4.68 Co NE2 B:His145 2.91 Co ND1 B:His145 3.78 Co CD2 B:His145 4.23 Co CE1 B:His145 2.56 Co CG B:His145 4.65 Co O B:His170 4.55 Co NE2 B:His170 4.32 Co CB B:His170 4.15 Co ND1 B:His170 2.43 Co CD2 B:His170 4.61 Co C B:His170 4.87 Co CE1 B:His170 3.07 Co CG B:His170 3.63 Co CA B:His170 4.16 Co NE2 B:His172 4.86 Co CE1 B:His172 4.96 Co O B:Hoh335 3.07 Co O B:Hoh369 3.21 Co O B:Hoh415 4.84 interactive model: Cobalt binding site 5 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 2z06. 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: His157, A: Asp160, A: Pro182, A: Lys183, conact list: Atom Atom Distance (A) Co O A:His157 4.10 Co CB A:His157 4.44 Co ND1 A:His157 3.65 Co C A:His157 4.70 Co CE1 A:His157 4.61 Co CG A:His157 4.49 Co CA A:His157 4.48 Co CB A:Asp160 3.76 Co OD2 A:Asp160 2.86 Co OD1 A:Asp160 4.92 Co CG A:Asp160 3.72 Co CB A:Pro182 4.29 Co CD A:Pro182 4.32 Co CG A:Pro182 4.32 Co CE A:Lys183 4.22 Co CD A:Lys183 4.67 Co CG A:Lys183 4.63 interactive model: Cobalt binding site 6 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 2z06. 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: His21, B: Ile25, B: Arg28, B: Tyr247, B: Hoh358, conact list: Atom Atom Distance (A) Co NE2 B:His21 4.45 Co CE1 B:His21 4.84 Co CG2 B:Ile25 4.84 Co CZ B:Arg28 3.98 Co NH2 B:Arg28 3.44 Co NH1 B:Arg28 3.60 Co CE2 B:Tyr247 4.36 Co CZ B:Tyr247 4.17 Co OH B:Tyr247 3.13 Co O B:Hoh358 3.50 interactive model: Cobalt binding site 7 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 2z06. 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: His157, B: Asp160, B: Pro182, B: Lys183, B: Hoh405, conact list: Atom Atom Distance (A) Co O B:His157 4.25 Co CB B:His157 4.52 Co ND1 B:His157 3.87 Co C B:His157 4.83 Co CE1 B:His157 4.87 Co CG B:His157 4.66 Co CA B:His157 4.62 Co CB B:Asp160 3.94 Co OD2 B:Asp160 3.25 Co CG B:Asp160 4.05 Co CB B:Pro182 4.49 Co CD B:Pro182 4.48 Co CG B:Pro182 4.60 Co CE B:Lys183 4.96 Co CG B:Lys183 4.59 Co NZ B:Lys183 3.85 Co O B:Hoh405 3.67 interactive model: Cobalt binding site 8 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 2z06. 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: Thr169, B: His170, B: Thr171, B: His172, B: Val173, B: Asp190, B: Gly192, B: Met193, B: Hoh415, conact list: Atom Atom Distance (A) Co N B:Asp8 4.15 Co CB B:Asp8 3.46 Co OD2 B:Asp8 4.79 Co CG B:Asp8 4.55 Co CA B:Asp8 4.42 Co O B:Thr169 4.94 Co CB B:Thr169 3.98 Co CG2 B:Thr169 4.62 Co C B:Thr169 3.84 Co CA B:Thr169 3.79 Co O B:His170 4.45 Co N B:His170 3.11 Co C B:His170 3.93 Co CA B:His170 3.91 Co N B:Thr171 4.00 Co C B:Thr171 4.36 Co CA B:Thr171 4.73 Co NE2 B:His172 4.63 Co N B:His172 3.17 Co CB B:His172 4.49 Co CD2 B:His172 3.77 Co C B:His172 4.45 Co CG B:His172 4.33 Co CA B:His172 3.45 Co N B:Val173 4.96 Co OD2 B:Asp190 3.00 Co OD1 B:Asp190 4.19 Co CG B:Asp190 3.99 Co O B:Gly192 3.75 Co N B:Gly192 4.28 Co C B:Gly192 3.97 Co CA B:Gly192 4.43 Co N B:Met193 4.43 Co CA B:Met193 4.74 Co O B:Hoh415 3.27 interactive model: Cobalt binding site 9 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cobalt in the PDB 2z06. 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: C: His157, C: Asp160, C: Pro182, C: Lys183, C: Hoh370, D: Hoh337, conact list: Atom Atom Distance (A) Co O C:His157 4.40 Co CB C:His157 4.76 Co ND1 C:His157 4.04 Co CG C:His157 4.88 Co CA C:His157 4.91 Co CB C:Asp160 4.00 Co OD2 C:Asp160 2.99 Co CG C:Asp160 3.91 Co CB C:Pro182 4.15 Co CD C:Pro182 4.46 Co CG C:Pro182 4.30 Co CE C:Lys183 4.58 Co CG C:Lys183 4.72 Co NZ C:Lys183 3.55 Co O C:Hoh370 4.64 Co O D:Hoh337 4.30 interactive model: Cobalt binding site 10 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cobalt in the PDB 2z06. 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: C: Asp8, C: Thr169, C: His170, C: Thr171, C: His172, C: Val173, C: Asp190, C: Gly192, C: Met193, C: Hoh339, conact list: Atom Atom Distance (A) Co N C:Asp8 4.64 Co CB C:Asp8 4.13 Co OD2 C:Asp8 2.30 Co OD1 C:Asp8 2.42 Co CG C:Asp8 2.66 Co CB C:Thr169 4.12 Co CG2 C:Thr169 4.76 Co C C:Thr169 3.99 Co CA C:Thr169 3.97 Co O C:His170 4.71 Co N C:His170 3.22 Co C C:His170 3.98 Co CA C:His170 3.96 Co N C:Thr171 3.78 Co C C:Thr171 4.21 Co CA C:Thr171 4.53 Co NE2 C:His172 4.50 Co N C:His172 3.06 Co CB C:His172 4.49 Co CD2 C:His172 3.48 Co C C:His172 4.51 Co CG C:His172 4.30 Co CA C:His172 3.46 Co N C:Val173 4.78 Co OD2 C:Asp190 2.93 Co OD1 C:Asp190 4.04 Co CG C:Asp190 3.89 Co O C:Gly192 3.90 Co N C:Gly192 4.40 Co C C:Gly192 3.94 Co CA C:Gly192 4.41 Co N C:Met193 4.25 Co CB C:Met193 4.50 Co CA C:Met193 4.51 Co O C:Hoh339 5.00 interactive model: Cobalt binding site 11 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cobalt in the PDB 2z06. 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: D: His157, D: Asp160, D: Pro182, D: Lys183, conact list: Atom Atom Distance (A) Co O D:His157 3.93 Co CB D:His157 4.40 Co ND1 D:His157 3.67 Co C D:His157 4.61 Co CE1 D:His157 4.65 Co CG D:His157 4.48 Co CA D:His157 4.55 Co CB D:Asp160 3.97 Co OD2 D:Asp160 3.46 Co CG D:Asp160 4.17 Co CB D:Pro182 4.49 Co CD D:Pro182 4.59 Co CG D:Pro182 4.43 Co CE D:Lys183 4.17 Co CD D:Lys183 4.56 Co CG D:Lys183 4.81 Co NZ D:Lys183 4.44 interactive model: Cobalt binding site 12 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cobalt in the PDB 2z06. 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: D: His21, D: Ile25, D: Arg28, D: Tyr247, D: Trp249, conact list: Atom Atom Distance (A) Co NE2 D:His21 3.99 Co CE1 D:His21 4.52 Co CG2 D:Ile25 4.38 Co CZ D:Arg28 3.78 Co NH2 D:Arg28 3.55 Co NH1 D:Arg28 3.17 Co CE2 D:Tyr247 4.44 Co CZ D:Tyr247 4.12 Co OH D:Tyr247 2.95 Co CD1 D:Trp249 4.96 interactive model: Cobalt binding site 13 out of 13 in 2z06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cobalt in the PDB 2z06. 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: D: Asp8, D: Glu37, D: Asn65, D: His66, D: His145, D: His170, D: His172, D: Hoh302, D: Hoh373, conact list: Atom Atom Distance (A) Co OD2 D:Asp8 4.70 Co OE1 D:Glu37 2.80 Co OE2 D:Glu37 2.46 Co CD D:Glu37 2.99 Co CG D:Glu37 4.49 Co N D:Asn65 4.99 Co ND2 D:Asn65 3.79 Co OD1 D:Asn65 2.73 Co CG D:Asn65 3.63 Co ND1 D:His66 3.96 Co CE1 D:His66 4.01 Co NE2 D:His145 2.84 Co ND1 D:His145 3.85 Co CD2 D:His145 4.17 Co CE1 D:His145 2.60 Co CG D:His145 4.66 Co O D:His170 4.80 Co NE2 D:His170 4.26 Co CB D:His170 4.14 Co ND1 D:His170 2.39 Co CD2 D:His170 4.55 Co CE1 D:His170 3.02 Co CG D:His170 3.59 Co CA D:His170 4.21 Co NE2 D:His172 4.71 Co CE1 D:His172 4.82 Co O D:Hoh302 3.17 Co O D:Hoh373 2.92 interactive model: