Cobalt in the structure of Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine (pdb 3fo6)

The binding sites of Cobalt atom in the structure of Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine (pdb code 3fo6). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3fo6 structure was solved by S.D.GILBERT, F.E.REYES, R.T.BATEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.7-1.9 Space group C121 a (A) 133.180 b (A) 35.270 c (A) 42.120 alpha (°) 90.00 beta (°) 90.45 gamma (°) 90.00 Rfactor (%) 23.1 Rfree (%) 26.3 Cobalt Binding Sites: Cobalt binding site 1 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3fo6. 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: Hoh359, A: Hoh386, A: Hoh460, A: Hoh497, A: Hoh518, conact list: Atom Atom Distance (A) Co O3' A:A66 4.39 Co OP1 A:U67 4.06 Co P A:U67 4.91 Co N1 A:Nco101 1.95 Co N6 A:Nco101 1.97 Co CO A:Nco101 0.00 Co N3 A:Nco101 1.98 Co N2 A:Nco101 1.96 Co N5 A:Nco101 1.97 Co N4 A:Nco101 1.96 Co O A:Hoh359 3.99 Co O A:Hoh386 3.63 Co O A:Hoh460 4.18 Co O A:Hoh497 4.33 Co O A:Hoh518 4.32 interactive model: Cobalt binding site 2 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3fo6. 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: Hoh347, A: Hoh381, A: Hoh416, A: Hoh452, A: Hoh470, conact list: Atom Atom Distance (A) Co OP1 A:G38 4.01 Co OP1 A:G56 3.79 Co P A:G56 4.90 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:Hoh347 3.84 Co O A:Hoh381 4.17 Co O A:Hoh416 4.55 Co O A:Hoh452 3.91 Co O A:Hoh470 3.62 interactive model: Cobalt binding site 3 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 3fo6. 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: Hoh315, A: Hoh401, A: Hoh442, A: Hoh443, A: Hoh457, A: Hoh462, A: Hoh519, conact list: Atom Atom Distance (A) Co OP1 A:C39 4.92 Co OP2 A:C39 4.37 Co C6 A:G56 4.86 Co N7 A:G56 4.48 Co O6 A:G56 4.04 Co O6 A:G68 4.78 Co O4 A:U69 3.96 Co N1 A:Nco103 1.97 Co N6 A:Nco103 1.97 Co CO A:Nco103 0.00 Co N3 A:Nco103 1.96 Co N2 A:Nco103 1.96 Co N5 A:Nco103 1.97 Co N4 A:Nco103 1.96 Co O A:Hoh315 3.95 Co O A:Hoh401 4.22 Co O A:Hoh442 3.87 Co O A:Hoh443 4.59 Co O A:Hoh457 3.49 Co O A:Hoh462 4.02 Co O A:Hoh519 4.89 interactive model: Cobalt binding site 4 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 3fo6. 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: A66, A: Nco104, A: Hoh303, A: Hoh304, A: Hoh307, A: Hoh310, A: Hoh333, A: Hoh345, A: Hoh349, A: Hoh380, conact list: Atom Atom Distance (A) Co C6 A:G31 4.83 Co C5 A:G31 4.97 Co N7 A:G31 4.37 Co O6 A:G31 4.03 Co C6 A:G32 4.97 Co O6 A:G32 3.96 Co OP2 A:A66 3.94 Co N1 A:Nco104 1.97 Co N6 A:Nco104 1.96 Co CO A:Nco104 0.00 Co N3 A:Nco104 1.97 Co N2 A:Nco104 1.96 Co N5 A:Nco104 1.96 Co N4 A:Nco104 1.99 Co O A:Hoh303 3.94 Co O A:Hoh304 4.92 Co O A:Hoh307 4.19 Co O A:Hoh310 4.26 Co O A:Hoh333 4.29 Co O A:Hoh345 3.98 Co O A:Hoh349 4.24 Co O A:Hoh380 4.30 interactive model: Cobalt binding site 5 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 3fo6. 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: Hoh342, A: Hoh356, A: Hoh360, A: Hoh371, A: Hoh399, A: Hoh424, A: Hoh436, A: Hoh495, A: Hoh499, A: Hoh512, conact list: Atom Atom Distance (A) Co N7 A:G37 4.73 Co OP2 A:G37 4.18 Co N7 A:G38 4.46 Co O6 A:G38 4.32 Co N1 A:Nco105 1.96 Co N6 A:Nco105 1.97 Co CO A:Nco105 0.00 Co N3 A:Nco105 1.97 Co N2 A:Nco105 1.97 Co N5 A:Nco105 1.97 Co N4 A:Nco105 1.97 Co O A:Hoh342 4.11 Co O A:Hoh356 4.64 Co O A:Hoh360 3.56 Co O A:Hoh371 4.20 Co O A:Hoh399 4.26 Co O A:Hoh424 4.67 Co O A:Hoh436 4.83 Co O A:Hoh495 3.43 Co O A:Hoh499 3.52 Co O A:Hoh512 3.63 interactive model: Cobalt binding site 6 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 3fo6. 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: Hoh312, A: Hoh314, A: Hoh340, A: Hoh362, conact list: Atom Atom Distance (A) Co OP2 A:C41 4.16 Co OP2 A:G42 4.87 Co OP1 A:C53 4.80 Co OP1 A:C54 3.91 Co N1 A:Nco107 1.97 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 1.97 Co N4 A:Nco107 1.97 Co O A:Hoh312 4.24 Co O A:Hoh314 4.50 Co O A:Hoh340 4.09 Co O A:Hoh362 4.55 interactive model: Cobalt binding site 7 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 3fo6. 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: Nco108, A: Hoh379, A: Hoh420, conact list: Atom Atom Distance (A) Co N7 A:G46 4.62 Co O6 A:G46 4.23 Co C4 A:U47 4.95 Co O4 A:U47 4.00 Co N1 A:Nco108 1.96 Co N6 A:Nco108 1.96 Co CO A:Nco108 0.00 Co N3 A:Nco108 1.96 Co N2 A:Nco108 1.96 Co N5 A:Nco108 1.96 Co N4 A:Nco108 1.96 Co O A:Hoh379 4.96 Co O A:Hoh420 3.83 interactive model: Cobalt binding site 8 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 3fo6. 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: Hoh387, A: Hoh465, conact list: Atom Atom Distance (A) Co OP1 A:A24 3.85 Co OP2 A:C71 4.01 Co N1 A:Nco109 1.96 Co N6 A:Nco109 1.97 Co CO A:Nco109 0.00 Co N3 A:Nco109 1.96 Co N2 A:Nco109 1.96 Co N5 A:Nco109 1.97 Co N4 A:Nco109 1.97 Co O A:Hoh387 3.76 Co O A:Hoh465 4.33 interactive model: Cobalt binding site 9 out of 9 in 3fo6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cobalt in the PDB 3fo6. 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: A73, A: Nco112, conact list: Atom Atom Distance (A) Co OP1 A:G72 4.11 Co OP2 A:A73 4.88 Co N1 A:Nco112 1.97 Co N6 A:Nco112 1.97 Co CO A:Nco112 0.00 Co N3 A:Nco112 1.97 Co N2 A:Nco112 1.97 Co N5 A:Nco112 1.97 Co N4 A:Nco112 1.97 interactive model: