Cobalt in the structure of Variant 5 Of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb 2pxf)

The binding sites of Cobalt atom in the structure of Variant 5 Of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 2pxf). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2pxf structure was solved by A.Y.KEEL, R.P.RAMBO, R.T.BATEY, J.S.KIEFT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.0 Space group C121 a (A) 132.320 b (A) 77.450 c (A) 32.690 alpha (°) 90.00 beta (°) 94.15 gamma (°) 90.00 Rfactor (%) 26.8 Rfree (%) 31.2 Cobalt Binding Sites: Cobalt binding site 1 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2pxf. 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: U137, B: G170, B: G171, B: Nco201, conact list: Atom Atom Distance (A) Co O4 B:U137 4.22 Co N7 B:G170 4.30 Co O6 B:G170 4.54 Co O6 B:G171 4.79 Co N1 B:Nco201 1.97 Co N6 B:Nco201 1.97 Co CO B:Nco201 0.00 Co N3 B:Nco201 1.97 Co N2 B:Nco201 1.96 Co N5 B:Nco201 1.97 Co N4 B:Nco201 1.97 interactive model: Cobalt binding site 2 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2pxf. 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: G144, B: G145, B: U146, B: C163, B: A164, B: Nco202, conact list: Atom Atom Distance (A) Co N7 B:G144 4.93 Co O6 B:G144 4.96 Co C6 B:G145 4.93 Co N7 B:G145 4.83 Co O6 B:G145 3.95 Co O4 B:U146 4.22 Co OP1 B:C163 3.94 Co P B:C163 4.62 Co OP2 B:C163 4.35 Co OP2 B:A164 4.56 Co N1 B:Nco202 1.97 Co N6 B:Nco202 1.96 Co CO B:Nco202 0.00 Co N3 B:Nco202 1.97 Co N2 B:Nco202 1.97 Co N5 B:Nco202 1.96 Co N4 B:Nco202 1.97 interactive model: Cobalt binding site 3 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2pxf. 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: A148, B: G149, B: G150, B: U151, B: Nco203, conact list: Atom Atom Distance (A) Co OP1 B:A148 3.92 Co P B:A148 4.86 Co OP2 B:A148 4.89 Co P B:G149 4.59 Co OP2 B:G149 3.26 Co C6 B:G150 4.93 Co C5 B:G150 4.94 Co N7 B:G150 4.19 Co O6 B:G150 4.18 Co O4 B:U151 4.91 Co N1 B:Nco203 1.96 Co N6 B:Nco203 1.97 Co CO B:Nco203 0.00 Co N3 B:Nco203 1.96 Co N2 B:Nco203 1.97 Co N5 B:Nco203 1.96 Co N4 B:Nco203 1.97 interactive model: Cobalt binding site 4 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2pxf. 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: G154, B: Nco204, conact list: Atom Atom Distance (A) Co N7 B:G154 4.40 Co O6 B:G154 4.45 Co N1 B:Nco204 1.97 Co N6 B:Nco204 1.97 Co CO B:Nco204 0.00 Co N3 B:Nco204 1.97 Co N2 B:Nco204 1.96 Co N5 B:Nco204 1.96 Co N4 B:Nco204 1.96 interactive model: Cobalt binding site 5 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 2pxf. 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: G158, B: Nco205, conact list: Atom Atom Distance (A) Co C8 B:G158 4.19 Co C6 B:G158 4.72 Co C5 B:G158 4.36 Co N7 B:G158 3.34 Co O6 B:G158 4.30 Co N1 B:Nco205 1.96 Co N6 B:Nco205 1.96 Co CO B:Nco205 0.00 Co N3 B:Nco205 1.96 Co N2 B:Nco205 1.96 Co N5 B:Nco205 1.97 Co N4 B:Nco205 1.96 interactive model: Cobalt binding site 6 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 2pxf. 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: U146, B: C147, B: A161, B: G162, B: Nco206, conact list: Atom Atom Distance (A) Co OP2 B:U146 4.89 Co OP2 B:C147 4.09 Co OP2 B:A161 4.24 Co C5 B:G162 5.00 Co N7 B:G162 4.21 Co O6 B:G162 4.25 Co N1 B:Nco206 1.96 Co N6 B:Nco206 1.96 Co CO B:Nco206 0.00 Co N3 B:Nco206 1.96 Co N2 B:Nco206 1.96 Co N5 B:Nco206 1.96 Co N4 B:Nco206 1.96 interactive model: Cobalt binding site 7 out of 7 in 2pxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 2pxf. 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: G131, B: G132, B: G133, B: U175, B: Nco207, conact list: Atom Atom Distance (A) Co C6 B:G131 4.76 Co C5 B:G131 4.83 Co N7 B:G131 4.58 Co O6 B:G131 4.40 Co C8 B:G132 4.80 Co C6 B:G132 4.82 Co C5 B:G132 4.68 Co N7 B:G132 3.86 Co O6 B:G132 4.23 Co N7 B:G133 4.47 Co O6 B:G133 4.34 Co O4 B:U175 4.62 Co N1 B:Nco207 1.96 Co N6 B:Nco207 1.96 Co CO B:Nco207 0.00 Co N3 B:Nco207 1.97 Co N2 B:Nco207 1.96 Co N5 B:Nco207 1.96 Co N4 B:Nco207 1.96 interactive model: