Cobalt in the structure of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed With Ampcpp (pdb 2yye)

The binding sites of Cobalt atom in the structure of Crystal Structure of Selenophosphate Synthetase From Aquifex Aeolicus Complexed With Ampcpp (pdb code 2yye). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2yye structure was solved by Y.ITOH, S.SEKINE, E.MATSUMOTO, S.YOKOYAMA, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.5-2.1 Space group P3121 a (A) 80.536 b (A) 80.536 c (A) 160.641 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.3 Rfree (%) 22.5 Cobalt Binding Sites: Cobalt binding site 1 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2yye. 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: Asp44, A: Asp83, A: Thr218, A: Asp219, A: Thr221, A: Co703, A: Apc501, A: Hoh809, A: Hoh833, A: Hoh859, A: Hoh918, A: Hoh932, conact list: Atom Atom Distance (A) Co O A:Asp44 4.90 Co CB A:Asp44 3.70 Co OD2 A:Asp44 2.24 Co OD1 A:Asp44 4.33 Co CG A:Asp44 3.27 Co CA A:Asp44 4.17 Co CB A:Asp83 4.41 Co OD2 A:Asp83 2.05 Co OD1 A:Asp83 3.48 Co CG A:Asp83 3.10 Co CA A:Asp83 4.80 Co OG1 A:Thr218 4.48 Co O A:Asp219 4.17 Co N A:Asp219 4.38 Co CB A:Asp219 4.41 Co OD2 A:Asp219 3.26 Co C A:Asp219 4.81 Co OD1 A:Asp219 2.09 Co CG A:Asp219 3.02 Co CA A:Asp219 4.78 Co OG1 A:Thr221 4.15 Co CO A:Co703 3.66 Co PG A:Apc501 4.83 Co O3B A:Apc501 3.76 Co C3A A:Apc501 4.62 Co O2B A:Apc501 1.96 Co O1B A:Apc501 3.92 Co PB A:Apc501 3.23 Co O1G A:Apc501 4.61 Co O A:Hoh809 4.86 Co O A:Hoh833 3.98 Co O A:Hoh859 2.06 Co O A:Hoh918 2.22 Co O A:Hoh932 4.71 interactive model: Cobalt binding site 2 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2yye. 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: Asp60, A: Asn79, A: Asp83, A: Asp219, A: Thr221, A: Co702, A: Co704, A: Apc501, B: Co701, A: Hoh805, A: Hoh859, A: Hoh918, A: Hoh928, A: Hoh931, A: Hoh932, conact list: Atom Atom Distance (A) Co CB A:Asp60 4.34 Co OD2 A:Asp60 2.09 Co OD1 A:Asp60 3.46 Co CG A:Asp60 3.07 Co O A:Asn79 4.61 Co CB A:Asp83 4.45 Co OD2 A:Asp83 3.52 Co OD1 A:Asp83 2.10 Co CG A:Asp83 3.14 Co OD2 A:Asp219 4.31 Co OD1 A:Asp219 4.99 Co CB A:Thr221 4.86 Co CG2 A:Thr221 4.65 Co OG1 A:Thr221 4.27 Co CO A:Co702 3.66 Co CO A:Co704 3.80 Co PG A:Apc501 3.18 Co O3B A:Apc501 3.41 Co O2G A:Apc501 4.58 Co C3A A:Apc501 4.79 Co O2B A:Apc501 3.43 Co O3G A:Apc501 3.90 Co O1B A:Apc501 2.25 Co PB A:Apc501 3.07 Co O1G A:Apc501 2.18 Co CO B:Co701 3.76 Co O A:Hoh805 4.26 Co O A:Hoh859 2.26 Co O A:Hoh918 4.96 Co O A:Hoh928 4.13 Co O A:Hoh931 4.56 Co O A:Hoh932 2.23 interactive model: Cobalt binding site 3 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 2yye. 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: Asp44, A: Ala45, A: Thr58, A: Val59, A: Asp60, A: Asp83, B: Gly131, A: Co703, A: Apc501, B: Co701, A: Hoh804, A: Hoh805, A: Hoh806, A: Hoh860, A: Hoh931, conact list: Atom Atom Distance (A) Co O A:Asp44 2.80 Co C A:Asp44 3.91 Co CA A:Asp44 4.57 Co N A:Ala45 4.94 Co CB A:Thr58 3.79 Co CG2 A:Thr58 4.95 Co OG1 A:Thr58 2.59 Co C A:Thr58 4.84 Co CA A:Thr58 4.46 Co O A:Val59 3.87 Co N A:Val59 4.24 Co C A:Val59 4.70 Co OD2 A:Asp60 3.69 Co OD1 A:Asp60 4.64 Co CG A:Asp60 4.40 Co CB A:Asp83 3.87 Co OD2 A:Asp83 3.97 Co OD1 A:Asp83 2.90 Co CG A:Asp83 3.33 Co O B:Gly131 4.69 Co CO A:Co703 3.80 Co C3A A:Apc501 4.32 Co O2B A:Apc501 4.00 Co O1B A:Apc501 2.83 Co PB A:Apc501 3.78 Co O2' A:Apc501 4.90 Co O1A A:Apc501 4.83 Co CO B:Co701 4.21 Co O A:Hoh804 2.76 Co O A:Hoh805 3.80 Co O A:Hoh806 4.33 Co O A:Hoh860 2.75 Co O A:Hoh931 3.01 interactive model: Cobalt binding site 4 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 2yye. 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: Asp43, A: Asp44, A: Ala86, A: Met87, A: Ile155, A: Thr156, A: Gln157, A: Cys217, A: Thr218, conact list: Atom Atom Distance (A) Co OD2 A:Asp43 4.42 Co OD1 A:Asp43 2.79 Co CG A:Asp43 3.93 Co N A:Asp44 4.67 Co CB A:Asp44 4.16 Co OD1 A:Asp44 2.94 Co CG A:Asp44 3.92 Co O A:Ala86 2.79 Co C A:Ala86 3.67 Co CB A:Ala86 4.43 Co CA A:Ala86 4.66 Co N A:Met87 4.26 Co CB A:Met87 4.86 Co CE A:Met87 4.29 Co CG A:Met87 4.49 Co SD A:Met87 3.25 Co CA A:Met87 4.15 Co O A:Ile155 2.80 Co C A:Ile155 3.86 Co O A:Thr156 4.27 Co N A:Thr156 4.35 Co C A:Thr156 3.93 Co CA A:Thr156 3.93 Co NE2 A:Gln157 4.89 Co N A:Gln157 4.24 Co CG A:Gln157 4.26 Co CA A:Gln157 4.94 Co O A:Cys217 2.64 Co N A:Cys217 4.80 Co CB A:Cys217 4.66 Co C A:Cys217 3.62 Co CA A:Cys217 4.59 Co N A:Thr218 4.37 Co CA A:Thr218 4.36 interactive model: Cobalt binding site 5 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 2yye. 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: Gly131, A: His132, B: Val59, B: Asp60, B: Asp83, B: Co803, B: Co804, B: Apc601, A: Hoh929, B: Hoh935, B: Hoh944, B: Hoh991, conact list: Atom Atom Distance (A) Co O A:Gly131 4.47 Co NE2 A:His132 4.16 Co CB A:His132 3.82 Co ND1 A:His132 2.29 Co CD2 A:His132 4.35 Co CE1 A:His132 3.02 Co CG A:His132 3.36 Co CA A:His132 4.32 Co O B:Val59 3.93 Co CB B:Asp60 4.48 Co OD2 B:Asp60 3.56 Co OD1 B:Asp60 2.13 Co CG B:Asp60 3.17 Co CA B:Asp60 4.74 Co OD1 B:Asp83 5.00 Co CO B:Co803 3.79 Co CO B:Co804 4.22 Co PG B:Apc601 3.19 Co O3B B:Apc601 3.60 Co O2G B:Apc601 4.57 Co PA B:Apc601 3.33 Co C3A B:Apc601 3.82 Co O5' B:Apc601 4.52 Co O2B B:Apc601 4.81 Co O3G B:Apc601 2.12 Co O2A B:Apc601 4.16 Co O1B B:Apc601 2.47 Co PB B:Apc601 3.42 Co O1G B:Apc601 3.56 Co O1A B:Apc601 2.06 Co O A:Hoh929 4.02 Co O B:Hoh935 4.60 Co O B:Hoh944 4.10 Co O B:Hoh991 2.09 interactive model: Cobalt binding site 6 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 2yye. 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: Lys16, A: Val59, A: Asp60, B: Gly131, B: His132, A: Co703, A: Co704, A: Apc501, A: Hoh928, A: Hoh931, B: Hoh1048, conact list: Atom Atom Distance (A) Co NZ A:Lys16 4.06 Co O A:Val59 3.99 Co CB A:Asp60 4.53 Co OD2 A:Asp60 3.52 Co OD1 A:Asp60 2.20 Co CG A:Asp60 3.19 Co CA A:Asp60 4.83 Co O B:Gly131 4.42 Co NE2 B:His132 4.10 Co CB B:His132 3.86 Co ND1 B:His132 2.22 Co CD2 B:His132 4.31 Co CE1 B:His132 2.93 Co CG B:His132 3.34 Co CA B:His132 4.39 Co CO A:Co703 3.76 Co CO A:Co704 4.21 Co PG A:Apc501 3.19 Co O3B A:Apc501 3.66 Co O2G A:Apc501 4.54 Co PA A:Apc501 3.28 Co C3A A:Apc501 3.82 Co O5' A:Apc501 4.43 Co O2B A:Apc501 4.82 Co O3G A:Apc501 2.05 Co O2A A:Apc501 4.14 Co O1B A:Apc501 2.46 Co PB A:Apc501 3.43 Co O1G A:Apc501 3.52 Co O1A A:Apc501 1.98 Co O A:Hoh928 4.71 Co O A:Hoh931 2.18 Co O B:Hoh1048 4.10 interactive model: Cobalt binding site 7 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 2yye. 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: Asp44, B: Asp83, B: Thr218, B: Asp219, B: Thr221, B: Co803, B: Co804, B: Apc601, B: Hoh902, B: Hoh949, B: Hoh1027, B: Hoh1049, conact list: Atom Atom Distance (A) Co O B:Asp44 4.88 Co CB B:Asp44 3.78 Co OD2 B:Asp44 2.38 Co OD1 B:Asp44 4.43 Co CG B:Asp44 3.37 Co CA B:Asp44 4.25 Co CB B:Asp83 4.44 Co OD2 B:Asp83 2.06 Co OD1 B:Asp83 3.51 Co CG B:Asp83 3.12 Co CA B:Asp83 4.81 Co OG1 B:Thr218 4.52 Co O B:Asp219 4.20 Co N B:Asp219 4.36 Co CB B:Asp219 4.42 Co OD2 B:Asp219 3.28 Co C B:Asp219 4.79 Co OD1 B:Asp219 2.14 Co CG B:Asp219 3.04 Co CA B:Asp219 4.77 Co OG1 B:Thr221 4.09 Co CO B:Co803 3.57 Co CO B:Co804 4.99 Co PG B:Apc601 4.82 Co O3B B:Apc601 3.85 Co C3A B:Apc601 4.70 Co O2B B:Apc601 2.02 Co O1B B:Apc601 3.95 Co PB B:Apc601 3.30 Co O1G B:Apc601 4.54 Co O B:Hoh902 2.22 Co O B:Hoh949 3.86 Co O B:Hoh1027 4.68 Co O B:Hoh1049 2.08 interactive model: Cobalt binding site 8 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 2yye. 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: Asp60, B: Asn79, B: Asp83, B: Asp219, B: Thr221, A: Co801, B: Co802, B: Co804, B: Apc601, B: Hoh902, B: Hoh912, B: Hoh935, B: Hoh991, B: Hoh1027, B: Hoh1049, conact list: Atom Atom Distance (A) Co CB B:Asp60 4.34 Co OD2 B:Asp60 2.16 Co OD1 B:Asp60 3.35 Co CG B:Asp60 3.04 Co O B:Asn79 4.67 Co CB B:Asp83 4.54 Co OD2 B:Asp83 3.49 Co OD1 B:Asp83 2.25 Co CG B:Asp83 3.20 Co OD2 B:Asp219 4.36 Co CB B:Thr221 4.83 Co CG2 B:Thr221 4.53 Co OG1 B:Thr221 4.24 Co CO A:Co801 3.79 Co CO B:Co802 3.57 Co CO B:Co804 3.86 Co PG B:Apc601 3.13 Co O3B B:Apc601 3.38 Co O2G B:Apc601 4.50 Co C3A B:Apc601 4.79 Co O2B B:Apc601 3.38 Co O3G B:Apc601 3.91 Co O1B B:Apc601 2.30 Co PB B:Apc601 3.07 Co O1G B:Apc601 2.10 Co O B:Hoh902 4.81 Co O B:Hoh912 4.16 Co O B:Hoh935 4.11 Co O B:Hoh991 4.47 Co O B:Hoh1027 2.31 Co O B:Hoh1049 2.23 interactive model: Cobalt binding site 9 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cobalt in the PDB 2yye. 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: Gly131, B: Asp44, B: Ala45, B: Thr58, B: Val59, B: Asp60, B: Asp83, A: Co801, B: Co802, B: Co803, B: Apc601, B: Hoh903, B: Hoh908, B: Hoh912, B: Hoh917, B: Hoh991, conact list: Atom Atom Distance (A) Co O A:Gly131 4.73 Co O B:Asp44 2.81 Co C B:Asp44 3.89 Co CA B:Asp44 4.57 Co N B:Ala45 4.89 Co CB B:Thr58 3.82 Co CG2 B:Thr58 4.93 Co OG1 B:Thr58 2.54 Co C B:Thr58 4.85 Co CA B:Thr58 4.46 Co O B:Val59 3.76 Co N B:Val59 4.22 Co C B:Val59 4.64 Co OD2 B:Asp60 3.54 Co OD1 B:Asp60 4.52 Co CG B:Asp60 4.27 Co CB B:Asp83 3.83 Co OD2 B:Asp83 4.01 Co OD1 B:Asp83 2.68 Co CG B:Asp83 3.27 Co CO A:Co801 4.22 Co CO B:Co802 4.99 Co CO B:Co803 3.86 Co C3A B:Apc601 4.20 Co O2B B:Apc601 3.99 Co O1B B:Apc601 2.76 Co PB B:Apc601 3.71 Co O2' B:Apc601 4.86 Co O1A B:Apc601 4.85 Co O B:Hoh903 2.87 Co O B:Hoh908 4.42 Co O B:Hoh912 3.79 Co O B:Hoh917 2.66 Co O B:Hoh991 2.92 interactive model: Cobalt binding site 10 out of 10 in 2yye Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cobalt in the PDB 2yye. 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: Asp43, B: Asp44, B: Ala86, B: Met87, B: Ile155, B: Thr156, B: Gln157, B: Cys217, B: Thr218, conact list: Atom Atom Distance (A) Co OD2 B:Asp43 4.33 Co OD1 B:Asp43 2.78 Co CG B:Asp43 3.88 Co N B:Asp44 4.60 Co CB B:Asp44 4.13 Co OD1 B:Asp44 2.91 Co CG B:Asp44 3.89 Co O B:Ala86 2.83 Co C B:Ala86 3.73 Co CB B:Ala86 4.56 Co CA B:Ala86 4.76 Co N B:Met87 4.28 Co CB B:Met87 4.84 Co CE B:Met87 4.18 Co CG B:Met87 4.47 Co SD B:Met87 3.20 Co CA B:Met87 4.15 Co O B:Ile155 2.77 Co C B:Ile155 3.83 Co O B:Thr156 4.25 Co N B:Thr156 4.31 Co C B:Thr156 3.93 Co CA B:Thr156 3.88 Co NE2 B:Gln157 4.99 Co N B:Gln157 4.29 Co CG B:Gln157 4.41 Co O B:Cys217 2.67 Co N B:Cys217 4.81 Co CB B:Cys217 4.66 Co C B:Cys217 3.63 Co CA B:Cys217 4.60 Co N B:Thr218 4.33 Co CB B:Thr218 4.93 Co CA B:Thr218 4.27 interactive model: