Cobalt in the structure of Guanine Riboswitch A21G, U75C Mutant Bound to Hypoxanthine (pdb 2eet)

The binding sites of Cobalt atom in the structure of Guanine Riboswitch A21G, U75C Mutant Bound to Hypoxanthine (pdb code 2eet). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2eet structure was solved by S.D.GILBERT, A.L.EDWARDS, R.T.BATEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-1.9 Space group C121 a (A) 133.790 b (A) 35.280 c (A) 41.660 alpha (°) 90.00 beta (°) 90.66 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 25.1 Cobalt Binding Sites: Cobalt binding site 1 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2eet. 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: A66, A: U67, A: Nco101, A: Hoh138, A: Hoh140, A: Hoh192, A: Hoh204, A: Hoh209, A: Hoh253, A: Hoh311, conact list: Atom Atom Distance (A) Co O3' A:A66 4.43 Co OP1 A:U67 4.09 Co P A:U67 4.94 Co N1 A:Nco101 1.95 Co N6 A:Nco101 1.97 Co CO A:Nco101 0.00 Co N3 A:Nco101 1.97 Co N2 A:Nco101 1.96 Co N5 A:Nco101 1.97 Co N4 A:Nco101 1.97 Co O A:Hoh138 4.03 Co O A:Hoh140 3.76 Co O A:Hoh192 3.96 Co O A:Hoh204 4.13 Co O A:Hoh209 3.68 Co O A:Hoh253 4.04 Co O A:Hoh311 4.34 interactive model: Cobalt binding site 2 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2eet. 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: G38, A: G56, A: Nco102, A: Hoh158, A: Hoh176, A: Hoh200, A: Hoh267, conact list: Atom Atom Distance (A) Co OP1 A:G38 3.89 Co P A:G38 4.93 Co OP2 A:G38 4.96 Co OP1 A:G56 3.94 Co P A:G56 4.98 Co N1 A:Nco102 1.97 Co N6 A:Nco102 1.97 Co CO A:Nco102 0.00 Co N3 A:Nco102 1.96 Co N2 A:Nco102 1.96 Co N5 A:Nco102 1.97 Co N4 A:Nco102 1.96 Co O A:Hoh158 3.83 Co O A:Hoh176 3.95 Co O A:Hoh200 4.83 Co O A:Hoh267 4.15 interactive model: Cobalt binding site 3 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2eet. 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: C39, A: G56, A: G68, A: U69, A: Nco103, A: Hoh145, A: Hoh195, A: Hoh214, A: Hoh256, A: Hoh346, conact list: Atom Atom Distance (A) Co OP1 A:C39 4.85 Co OP2 A:C39 4.36 Co C6 A:G56 4.84 Co C5 A:G56 4.99 Co N7 A:G56 4.37 Co O6 A:G56 4.04 Co O6 A:G68 4.70 Co O4 A:U69 3.97 Co N1 A:Nco103 1.96 Co N6 A:Nco103 1.96 Co CO A:Nco103 0.00 Co N3 A:Nco103 1.95 Co N2 A:Nco103 1.96 Co N5 A:Nco103 1.96 Co N4 A:Nco103 1.94 Co O A:Hoh145 4.23 Co O A:Hoh195 3.87 Co O A:Hoh214 4.09 Co O A:Hoh256 4.02 Co O A:Hoh346 3.75 interactive model: Cobalt binding site 4 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2eet. 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: G31, A: G32, A: A65, A: A66, A: Nco104, A: Hoh113, A: Hoh115, A: Hoh123, A: Hoh124, A: Hoh129, A: Hoh137, A: Hoh147, A: Hoh148, A: Hoh181, conact list: Atom Atom Distance (A) Co C6 A:G31 4.93 Co N7 A:G31 4.42 Co O6 A:G31 4.15 Co C6 A:G32 4.93 Co O6 A:G32 3.86 Co O2' A:A65 4.99 Co OP2 A:A66 3.78 Co N1 A:Nco104 1.96 Co N6 A:Nco104 1.96 Co CO A:Nco104 0.00 Co N3 A:Nco104 1.96 Co N2 A:Nco104 1.96 Co N5 A:Nco104 1.96 Co N4 A:Nco104 1.98 Co O A:Hoh113 3.93 Co O A:Hoh115 4.26 Co O A:Hoh123 4.90 Co O A:Hoh124 4.11 Co O A:Hoh129 4.21 Co O A:Hoh137 4.24 Co O A:Hoh147 4.34 Co O A:Hoh148 3.91 Co O A:Hoh181 4.97 interactive model: Cobalt binding site 5 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 2eet. 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: G37, A: G38, A: Nco105, A: Hoh135, A: Hoh161, A: Hoh171, A: Hoh223, A: Hoh249, A: Hoh260, A: Hoh354, conact list: Atom Atom Distance (A) Co N7 A:G37 4.52 Co OP2 A:G37 3.85 Co N7 A:G38 4.51 Co O6 A:G38 4.31 Co N1 A:Nco105 1.96 Co N6 A:Nco105 1.96 Co CO A:Nco105 0.00 Co N3 A:Nco105 1.96 Co N2 A:Nco105 1.97 Co N5 A:Nco105 1.96 Co N4 A:Nco105 1.97 Co O A:Hoh135 4.12 Co O A:Hoh161 3.98 Co O A:Hoh171 3.57 Co O A:Hoh223 4.25 Co O A:Hoh249 4.13 Co O A:Hoh260 4.10 Co O A:Hoh354 4.88 interactive model: Cobalt binding site 6 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 2eet. 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: C26, A: G68, A: U69, A: Nco106, A: Hoh159, A: Hoh160, A: Hoh235, A: Hoh301, A: Hoh304, conact list: Atom Atom Distance (A) Co OP1 A:C26 4.98 Co O3' A:G68 4.59 Co OP1 A:U69 3.18 Co P A:U69 4.17 Co OP2 A:U69 4.44 Co N1 A:Nco106 1.96 Co N6 A:Nco106 1.97 Co CO A:Nco106 0.00 Co N3 A:Nco106 1.97 Co N2 A:Nco106 1.97 Co N5 A:Nco106 1.97 Co N4 A:Nco106 1.98 Co O A:Hoh159 3.50 Co O A:Hoh160 4.26 Co O A:Hoh235 3.99 Co O A:Hoh301 4.32 Co O A:Hoh304 4.00 interactive model: Cobalt binding site 7 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 2eet. 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: C41, A: C53, A: C54, A: Nco107, A: Hoh117, A: Hoh166, A: Hoh187, conact list: Atom Atom Distance (A) Co OP1 A:C41 4.94 Co P A:C41 4.81 Co OP2 A:C41 3.74 Co OP1 A:C53 4.08 Co P A:C53 4.86 Co OP2 A:C53 4.93 Co OP1 A:C54 3.92 Co C5' A:C54 4.87 Co N1 A:Nco107 1.96 Co N6 A:Nco107 1.96 Co CO A:Nco107 0.00 Co N3 A:Nco107 1.97 Co N2 A:Nco107 1.97 Co N5 A:Nco107 1.96 Co N4 A:Nco107 1.96 Co O A:Hoh117 4.43 Co O A:Hoh166 4.88 Co O A:Hoh187 4.58 interactive model: Cobalt binding site 8 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 2eet. 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: G46, A: U47, A: C50, A: U51, A: Nco108, A: Hoh220, A: Hoh331, conact list: Atom Atom Distance (A) Co O6 A:G46 4.93 Co C4 A:U47 4.65 Co O4 A:U47 3.65 Co OP1 A:C50 4.51 Co P A:C50 4.80 Co OP2 A:C50 4.29 Co OP2 A:U51 3.98 Co N1 A:Nco108 1.97 Co N6 A:Nco108 1.96 Co CO A:Nco108 0.00 Co N3 A:Nco108 1.97 Co N2 A:Nco108 1.96 Co N5 A:Nco108 1.97 Co N4 A:Nco108 1.96 Co O A:Hoh220 3.85 Co O A:Hoh331 4.12 interactive model: Cobalt binding site 9 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cobalt in the PDB 2eet. 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: A24, A: C71, A: Nco109, A: Hoh232, A: Hoh319, A: Hoh340, conact list: Atom Atom Distance (A) Co OP1 A:A24 4.39 Co OP2 A:C71 4.15 Co N1 A:Nco109 1.97 Co N6 A:Nco109 1.97 Co CO A:Nco109 0.00 Co N3 A:Nco109 1.97 Co N2 A:Nco109 1.97 Co N5 A:Nco109 1.97 Co N4 A:Nco109 1.97 Co O A:Hoh232 3.92 Co O A:Hoh319 4.15 Co O A:Hoh340 3.97 interactive model: Cobalt binding site 10 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cobalt in the PDB 2eet. 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: G21, A: Nco110, A: Hoh248, conact list: Atom Atom Distance (A) Co OP2 A:G21 4.02 Co N1 A:Nco110 1.96 Co N6 A:Nco110 1.96 Co CO A:Nco110 0.00 Co N3 A:Nco110 1.96 Co N2 A:Nco110 1.96 Co N5 A:Nco110 1.97 Co N4 A:Nco110 1.96 Co O A:Hoh248 4.37 interactive model: Cobalt binding site 11 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cobalt in the PDB 2eet. 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: G32, A: A33, A: Nco111, A: Hoh165, A: Hoh181, A: Hoh203, A: Hoh206, conact list: Atom Atom Distance (A) Co OP2 A:G32 4.15 Co OP2 A:A33 3.89 Co N1 A:Nco111 1.97 Co N6 A:Nco111 1.97 Co CO A:Nco111 0.00 Co N3 A:Nco111 1.97 Co N2 A:Nco111 1.97 Co N5 A:Nco111 1.97 Co N4 A:Nco111 1.97 Co O A:Hoh165 4.08 Co O A:Hoh181 4.82 Co O A:Hoh203 4.74 Co O A:Hoh206 4.17 interactive model: Cobalt binding site 12 out of 12 in 2eet Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cobalt in the PDB 2eet. 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: G72, A: Nco112, A: Hoh212, A: Hoh272, conact list: Atom Atom Distance (A) Co OP1 A:G72 4.15 Co N1 A:Nco112 1.96 Co N6 A:Nco112 1.96 Co CO A:Nco112 0.00 Co N3 A:Nco112 1.96 Co N2 A:Nco112 1.96 Co N5 A:Nco112 1.96 Co N4 A:Nco112 1.96 Co O A:Hoh212 3.56 Co O A:Hoh272 3.82 interactive model: