Cobalt in the structure of Guanine Riboswitch A21U, U75A Mutant Bound to Hypoxanthine (pdb 2ees)

The binding sites of Cobalt atom in the structure of Guanine Riboswitch A21U, U75A Mutant Bound to Hypoxanthine (pdb code 2ees). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2ees 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) 19.9-1.8 Space group C121 a (A) 132.540 b (A) 35.960 c (A) 41.470 alpha (°) 90.00 beta (°) 91.31 gamma (°) 90.00 Rfactor (%) 20.7 Rfree (%) 24.1 Cobalt Binding Sites: Cobalt binding site 1 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2ees. 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: Hoh137, A: Hoh165, A: Hoh182, A: Hoh199, A: Hoh307, A: Hoh348, conact list: Atom Atom Distance (A) Co O3' A:A66 4.46 Co OP1 A:U67 4.02 Co P A:U67 4.91 Co N1 A:Nco101 1.93 Co N6 A:Nco101 2.02 Co CO A:Nco101 0.00 Co N3 A:Nco101 2.00 Co N2 A:Nco101 1.95 Co N5 A:Nco101 2.00 Co N4 A:Nco101 2.02 Co O A:Hoh137 3.94 Co O A:Hoh165 3.77 Co O A:Hoh182 4.05 Co O A:Hoh199 4.33 Co O A:Hoh307 3.91 Co O A:Hoh348 4.14 interactive model: Cobalt binding site 2 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2ees. 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: C39, A: G56, A: Nco102, A: Hoh164, A: Hoh211, A: Hoh241, A: Hoh365, conact list: Atom Atom Distance (A) Co OP1 A:G38 3.95 Co P A:G38 4.94 Co OP2 A:G38 4.90 Co C5' A:C39 4.98 Co OP1 A:G56 3.87 Co N1 A:Nco102 2.01 Co N6 A:Nco102 1.99 Co CO A:Nco102 0.00 Co N3 A:Nco102 1.97 Co N2 A:Nco102 1.99 Co N5 A:Nco102 2.00 Co N4 A:Nco102 1.98 Co O A:Hoh164 3.79 Co O A:Hoh211 3.76 Co O A:Hoh241 3.42 Co O A:Hoh365 4.21 interactive model: Cobalt binding site 3 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2ees. 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: Hoh197, A: Hoh218, A: Hoh239, A: Hoh260, A: Hoh289, A: Hoh301, conact list: Atom Atom Distance (A) Co OP1 A:C39 4.77 Co OP2 A:C39 4.69 Co C6 A:G56 4.98 Co N7 A:G56 4.51 Co O6 A:G56 4.12 Co O6 A:G68 4.55 Co O4 A:U69 3.86 Co N1 A:Nco103 1.99 Co N6 A:Nco103 2.02 Co CO A:Nco103 0.00 Co N3 A:Nco103 1.97 Co N2 A:Nco103 1.99 Co N5 A:Nco103 1.99 Co N4 A:Nco103 1.98 Co O A:Hoh197 4.09 Co O A:Hoh218 4.20 Co O A:Hoh239 4.02 Co O A:Hoh260 4.35 Co O A:Hoh289 3.68 Co O A:Hoh301 4.13 interactive model: Cobalt binding site 4 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2ees. 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: U30, A: G31, A: G32, A: A65, A: A66, A: Nco104, A: Hoh114, A: Hoh117, A: Hoh123, A: Hoh125, A: Hoh133, A: Hoh135, A: Hoh180, conact list: Atom Atom Distance (A) Co O4 A:U30 4.98 Co C6 A:G31 4.90 Co N7 A:G31 4.40 Co O6 A:G31 4.10 Co C6 A:G32 4.97 Co O6 A:G32 3.95 Co O2' A:A65 4.99 Co OP2 A:A66 3.88 Co N1 A:Nco104 2.00 Co N6 A:Nco104 2.02 Co CO A:Nco104 0.00 Co N3 A:Nco104 2.02 Co N2 A:Nco104 2.01 Co N5 A:Nco104 1.96 Co N4 A:Nco104 2.04 Co O A:Hoh114 4.89 Co O A:Hoh117 4.29 Co O A:Hoh123 3.91 Co O A:Hoh125 4.27 Co O A:Hoh133 4.24 Co O A:Hoh135 4.06 Co O A:Hoh180 4.34 interactive model: Cobalt binding site 5 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 2ees. 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: G57, A: Nco105, A: Hoh186, A: Hoh188, A: Hoh203, A: Hoh259, A: Hoh261, A: Hoh268, A: Hoh349, conact list: Atom Atom Distance (A) Co N7 A:G37 4.75 Co OP2 A:G37 4.10 Co N7 A:G38 4.15 Co O6 A:G38 4.40 Co OP2 A:G57 4.87 Co N1 A:Nco105 1.99 Co N6 A:Nco105 1.97 Co CO A:Nco105 0.00 Co N3 A:Nco105 1.97 Co N2 A:Nco105 1.98 Co N5 A:Nco105 1.97 Co N4 A:Nco105 1.98 Co O A:Hoh186 4.22 Co O A:Hoh188 4.39 Co O A:Hoh203 4.30 Co O A:Hoh259 3.36 Co O A:Hoh261 4.32 Co O A:Hoh268 3.62 Co O A:Hoh349 4.06 interactive model: Cobalt binding site 6 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 2ees. 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: G27, A: Nco106, A: Hoh189, A: Hoh215, A: Hoh314, conact list: Atom Atom Distance (A) Co O3' A:C26 4.85 Co OP1 A:G27 4.26 Co N1 A:Nco106 1.98 Co N6 A:Nco106 2.00 Co CO A:Nco106 0.00 Co N3 A:Nco106 1.98 Co N2 A:Nco106 1.98 Co N5 A:Nco106 1.98 Co N4 A:Nco106 2.00 Co O A:Hoh189 4.53 Co O A:Hoh215 3.86 Co O A:Hoh314 4.96 interactive model: Cobalt binding site 7 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 2ees. 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: G42, A: C53, A: C54, A: Nco107, A: Hoh113, A: Hoh127, A: Hoh156, A: Hoh177, conact list: Atom Atom Distance (A) Co OP2 A:C41 3.88 Co OP2 A:G42 4.97 Co OP1 A:C53 4.45 Co OP1 A:C54 3.90 Co P A:C54 4.90 Co C5' A:C54 4.62 Co O5' A:C54 4.86 Co N1 A:Nco107 1.98 Co N6 A:Nco107 1.99 Co CO A:Nco107 0.00 Co N3 A:Nco107 1.99 Co N2 A:Nco107 2.00 Co N5 A:Nco107 1.98 Co N4 A:Nco107 1.97 Co O A:Hoh113 4.32 Co O A:Hoh127 4.12 Co O A:Hoh156 4.08 Co O A:Hoh177 4.44 interactive model: Cobalt binding site 8 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 2ees. 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: Nco108, A: Hoh232, A: Hoh257, A: Hoh286, conact list: Atom Atom Distance (A) Co O6 A:G46 4.87 Co O4 A:U47 4.03 Co OP1 A:C50 4.69 Co P A:C50 4.97 Co OP2 A:C50 4.49 Co N1 A:Nco108 1.97 Co N6 A:Nco108 1.96 Co CO A:Nco108 0.00 Co N3 A:Nco108 2.00 Co N2 A:Nco108 1.99 Co N5 A:Nco108 1.96 Co N4 A:Nco108 1.97 Co O A:Hoh232 4.00 Co O A:Hoh257 4.15 Co O A:Hoh286 4.14 interactive model: Cobalt binding site 9 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cobalt in the PDB 2ees. 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: Hoh194, A: Hoh195, A: Hoh240, A: Hoh323, conact list: Atom Atom Distance (A) Co OP1 A:A24 4.37 Co OP2 A:C71 3.97 Co N1 A:Nco109 1.98 Co N6 A:Nco109 2.00 Co CO A:Nco109 0.00 Co N3 A:Nco109 1.99 Co N2 A:Nco109 2.00 Co N5 A:Nco109 2.00 Co N4 A:Nco109 1.98 Co O A:Hoh194 4.06 Co O A:Hoh195 4.72 Co O A:Hoh240 4.07 Co O A:Hoh323 4.28 interactive model: Cobalt binding site 10 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cobalt in the PDB 2ees. 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: U21, A: U22, A: Nco110, conact list: Atom Atom Distance (A) Co OP1 A:U21 3.73 Co OP2 A:U22 4.61 Co N1 A:Nco110 1.97 Co N6 A:Nco110 1.97 Co CO A:Nco110 0.00 Co N3 A:Nco110 1.97 Co N2 A:Nco110 1.97 Co N5 A:Nco110 1.97 Co N4 A:Nco110 1.97 interactive model: Cobalt binding site 11 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cobalt in the PDB 2ees. 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: Hoh160, A: Hoh181, A: Hoh184, A: Hoh227, A: Hoh367, conact list: Atom Atom Distance (A) Co OP2 A:G32 4.13 Co OP2 A:A33 4.07 Co N1 A:Nco111 2.00 Co N6 A:Nco111 1.98 Co CO A:Nco111 0.00 Co N3 A:Nco111 2.00 Co N2 A:Nco111 1.98 Co N5 A:Nco111 1.99 Co N4 A:Nco111 1.98 Co O A:Hoh160 4.69 Co O A:Hoh181 3.90 Co O A:Hoh184 4.31 Co O A:Hoh227 4.50 Co O A:Hoh367 4.72 interactive model: Cobalt binding site 12 out of 12 in 2ees Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cobalt in the PDB 2ees. 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: Hoh249, conact list: Atom Atom Distance (A) Co OP1 A:G72 4.10 Co N1 A:Nco112 1.98 Co N6 A:Nco112 1.98 Co CO A:Nco112 0.00 Co N3 A:Nco112 1.98 Co N2 A:Nco112 1.97 Co N5 A:Nco112 1.98 Co N4 A:Nco112 1.98 Co O A:Hoh249 3.18 interactive model: