Cobalt in the structure of Recombinant Thiocyanate Hydrolase, Fully-Matured Form (pdb 2dxc)

The binding sites of Cobalt atom in the structure of Recombinant Thiocyanate Hydrolase, Fully-Matured Form (pdb code 2dxc). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2dxc structure was solved by T.ARAKAWA, Y.KAWANO, Y.KATAYAMA, M.YOHDA, M.ODAKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.9-1.9 Space group P212121 a (A) 114.874 b (A) 170.531 c (A) 175.152 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.1 Rfree (%) 19.3 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 2dxc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2dxc. 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: Arg55, C: Cys128, C: Leu130, C: Csd131, C: Ser132, C: Cso133, C: Ser181, C: Tla3001, conact list: Atom Atom Distance (A) Co NH2 A:Arg55 4.94 Co O C:Cys128 4.81 Co CB C:Cys128 3.43 Co SG C:Cys128 2.38 Co CA C:Cys128 4.84 Co C C:Leu130 4.78 Co O C:Csd131 4.15 Co N C:Csd131 3.75 Co CB C:Csd131 3.14 Co SG C:Csd131 2.23 Co OD2 C:Csd131 3.15 Co C C:Csd131 3.06 Co OD1 C:Csd131 3.11 Co CA C:Csd131 3.32 Co O C:Ser132 3.92 Co N C:Ser132 2.12 Co CB C:Ser132 4.12 Co OG C:Ser132 4.11 Co C C:Ser132 2.78 Co CA C:Ser132 2.94 Co O C:Cso133 4.66 Co N C:Cso133 1.93 Co CB C:Cso133 3.13 Co SG C:Cso133 2.45 Co OD C:Cso133 2.88 Co C C:Cso133 4.25 Co CA C:Cso133 2.92 Co O C:Ser181 4.95 Co O41 C:Tla3001 4.67 Co O2 C:Tla3001 2.40 Co C4 C:Tla3001 4.78 Co C1 C:Tla3001 4.64 Co O11 C:Tla3001 4.32 Co C3 C:Tla3001 4.71 Co O3 C:Tla3001 4.83 Co C2 C:Tla3001 3.87 interactive model: Cobalt binding site 2 out of 4 in 2dxc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2dxc. 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: Arg55, F: Cys128, F: Leu130, F: Csd131, F: Ser132, F: Cso133, F: Ser181, E: Tla3002, conact list: Atom Atom Distance (A) Co NH2 D:Arg55 4.95 Co O F:Cys128 4.82 Co CB F:Cys128 3.40 Co SG F:Cys128 2.45 Co CA F:Cys128 4.81 Co C F:Leu130 4.77 Co O F:Csd131 4.22 Co N F:Csd131 3.76 Co CB F:Csd131 3.19 Co SG F:Csd131 2.31 Co OD2 F:Csd131 3.35 Co C F:Csd131 3.10 Co OD1 F:Csd131 3.04 Co CA F:Csd131 3.33 Co O F:Ser132 3.95 Co N F:Ser132 2.16 Co CB F:Ser132 4.14 Co OG F:Ser132 4.11 Co C F:Ser132 2.81 Co CA F:Ser132 2.99 Co O F:Cso133 4.67 Co N F:Cso133 1.94 Co CB F:Cso133 3.07 Co SG F:Cso133 2.43 Co OD F:Cso133 2.77 Co C F:Cso133 4.24 Co CA F:Cso133 2.89 Co O F:Ser181 4.89 Co O41 E:Tla3002 4.78 Co O2 E:Tla3002 3.03 Co C1 E:Tla3002 4.89 Co O11 E:Tla3002 4.58 Co C3 E:Tla3002 4.94 Co O3 E:Tla3002 4.58 Co C2 E:Tla3002 4.40 interactive model: Cobalt binding site 3 out of 4 in 2dxc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2dxc. 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: G: Arg55, H: Arg91, I: Cys128, I: Leu130, I: Csd131, I: Ser132, I: Cso133, I: Ser181, I: Tla3003, I: Hoh3159, conact list: Atom Atom Distance (A) Co NH2 G:Arg55 4.97 Co NE H:Arg91 4.97 Co O I:Cys128 4.79 Co CB I:Cys128 3.42 Co SG I:Cys128 2.40 Co CA I:Cys128 4.82 Co C I:Leu130 4.79 Co O I:Csd131 4.16 Co N I:Csd131 3.77 Co CB I:Csd131 3.17 Co SG I:Csd131 2.24 Co OD2 I:Csd131 3.17 Co C I:Csd131 3.07 Co OD1 I:Csd131 3.07 Co CA I:Csd131 3.36 Co O I:Ser132 3.94 Co N I:Ser132 2.13 Co CB I:Ser132 4.12 Co OG I:Ser132 4.12 Co C I:Ser132 2.78 Co CA I:Ser132 2.93 Co O I:Cso133 4.67 Co N I:Cso133 1.94 Co CB I:Cso133 3.14 Co SG I:Cso133 2.48 Co OD I:Cso133 2.81 Co C I:Cso133 4.28 Co CA I:Cso133 2.94 Co O I:Ser181 4.95 Co O41 I:Tla3003 4.88 Co O2 I:Tla3003 2.51 Co C4 I:Tla3003 4.84 Co C1 I:Tla3003 4.67 Co O11 I:Tla3003 4.26 Co C3 I:Tla3003 4.85 Co C2 I:Tla3003 3.83 Co O I:Hoh3159 4.99 interactive model: Cobalt binding site 4 out of 4 in 2dxc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2dxc. 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: J: Arg55, K: Arg91, L: Cys128, L: Leu130, L: Csd131, L: Ser132, L: Cso133, L: Ser181, L: Tla3004, conact list: Atom Atom Distance (A) Co NH2 J:Arg55 4.93 Co NE K:Arg91 4.91 Co O L:Cys128 4.89 Co CB L:Cys128 3.48 Co SG L:Cys128 2.44 Co CA L:Cys128 4.89 Co C L:Leu130 4.79 Co O L:Csd131 4.22 Co N L:Csd131 3.78 Co CB L:Csd131 3.14 Co SG L:Csd131 2.21 Co OD2 L:Csd131 2.98 Co C L:Csd131 3.13 Co OD1 L:Csd131 3.18 Co CA L:Csd131 3.36 Co O L:Ser132 3.93 Co N L:Ser132 2.20 Co CB L:Ser132 4.18 Co OG L:Ser132 4.14 Co C L:Ser132 2.81 Co CA L:Ser132 3.01 Co O L:Cso133 4.68 Co N L:Cso133 1.94 Co CB L:Cso133 3.06 Co SG L:Cso133 2.42 Co OD L:Cso133 2.90 Co C L:Cso133 4.25 Co CA L:Cso133 2.89 Co O L:Ser181 4.99 Co O41 L:Tla3004 4.63 Co O2 L:Tla3004 2.50 Co C4 L:Tla3004 4.73 Co C1 L:Tla3004 4.80 Co O11 L:Tla3004 4.48 Co C3 L:Tla3004 4.79 Co C2 L:Tla3004 3.92 interactive model: