Calcium in the structure of Pseudomonas Fluorescens Phox in Complex With Vanadate, A Transition State Analogue (pdb 3zwu)

The binding sites of Calcium atom in the structure of Pseudomonas Fluorescens Phox in Complex With Vanadate, A Transition State Analogue (pdb code 3zwu). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 3zwu structure was solved by S.C.YONG, P.ROVERSI, J.E.D.LILLINGTON, O.B.ZELDIN, E.F.GARMAN, S.M.LEA, B.C.BERKS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.4-1.4 Space group P212121 a (A) 68.790 b (A) 71.470 c (A) 227.830 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.8 Rfree (%) 17.13 Calcium Binding Sites: Calcium binding site 1 out of 6 in 3zwu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 3zwu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp69, A: Cys179, A: Glu273, A: Glu387, A: Trp388, A: Asp479, A: Asp494, A: Glu532, A: Thr534, A: Vo4700, A: Ca1592, A: Ca1593, A: Feo1594, A: Hoh2195, A: Hoh2196, A: Hoh2244, A: Hoh2815, A: Hoh2816, conact list: Atom Atom Distance (A) Ca OD2 A:Asp69 4.81 Ca OD1 A:Asp69 4.76 Ca SG A:Cys179 3.98 Ca OE1 A:Glu273 3.90 Ca OE2 A:Glu273 2.33 Ca CD A:Glu273 3.45 Ca CG A:Glu273 4.69 Ca OE1 A:Glu387 4.24 Ca CB A:Glu387 4.94 Ca OE2 A:Glu387 2.86 Ca CD A:Glu387 3.73 Ca CG A:Glu387 4.73 Ca CD1 A:Trp388 4.49 Ca NE1 A:Trp388 4.00 Ca CB A:Asp479 4.30 Ca OD2 A:Asp479 2.40 Ca OD1 A:Asp479 2.51 Ca CG A:Asp479 2.79 Ca OD2 A:Asp494 4.71 Ca OE2 A:Glu532 4.19 Ca OG1 A:Thr534 4.68 Ca O2 A:Vo4700 2.63 Ca O4 A:Vo4700 4.32 Ca O3 A:Vo4700 4.37 Ca V A:Vo4700 3.68 Ca CA A:Ca1592 3.62 Ca CA A:Ca1593 4.85 Ca O A:Feo1594 2.35 Ca FE1 A:Feo1594 3.63 Ca FE2 A:Feo1594 3.59 Ca O A:Hoh2195 2.55 Ca O A:Hoh2196 2.72 Ca O A:Hoh2244 4.72 Ca O A:Hoh2815 2.44 Ca O A:Hoh2816 4.73 interactive model: Calcium binding site 2 out of 6 in 3zwu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 3zwu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp292, A: Arg385, A: Glu387, A: Thr403, A: Asp479, A: Asp494, A: Glu532, A: Vo4700, A: Ca1591, A: Ca1593, A: Feo1594, A: Hoh2720, A: Hoh2721, A: Hoh2722, A: Hoh2815, A: Hoh2832, conact list: Atom Atom Distance (A) Ca OD2 A:Asp292 4.50 Ca CZ A:Arg385 4.73 Ca NH2 A:Arg385 3.82 Ca OE1 A:Glu387 2.52 Ca OE2 A:Glu387 2.56 Ca CD A:Glu387 2.88 Ca CG A:Glu387 4.38 Ca CB A:Thr403 4.88 Ca CG2 A:Thr403 4.57 Ca OG1 A:Thr403 4.48 Ca CB A:Asp479 4.01 Ca OD2 A:Asp479 2.31 Ca OD1 A:Asp479 4.15 Ca CG A:Asp479 3.30 Ca O A:Asp494 4.40 Ca CB A:Asp494 3.71 Ca OD2 A:Asp494 2.39 Ca OD1 A:Asp494 4.52 Ca CG A:Asp494 3.39 Ca OE2 A:Glu532 4.56 Ca O1 A:Vo4700 3.84 Ca O2 A:Vo4700 2.37 Ca O4 A:Vo4700 3.35 Ca V A:Vo4700 3.37 Ca CA A:Ca1591 3.62 Ca CA A:Ca1593 3.95 Ca O A:Feo1594 4.04 Ca FE2 A:Feo1594 4.11 Ca O A:Hoh2720 4.77 Ca O A:Hoh2721 2.45 Ca O A:Hoh2722 2.35 Ca O A:Hoh2815 4.66 Ca O A:Hoh2832 4.97 interactive model: Calcium binding site 3 out of 6 in 3zwu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 3zwu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu90, A: Tyr91, A: Asp479, A: Asp494, A: Glu532, A: Gln550, A: His551, A: Vo4700, A: Ca1591, A: Ca1592, A: Feo1594, A: Hoh2196, A: Hoh2244, A: Hoh2245, A: Hoh2252, A: Hoh2721, A: Hoh2815, A: Hoh2832, A: Hoh2877, A: Hoh2910, conact list: Atom Atom Distance (A) Ca OE1 A:Glu90 4.94 Ca OH A:Tyr91 4.97 Ca OD2 A:Asp479 4.63 Ca CB A:Asp494 4.37 Ca OD2 A:Asp494 2.48 Ca OD1 A:Asp494 3.39 Ca CG A:Asp494 3.15 Ca OE1 A:Glu532 2.26 Ca CB A:Glu532 4.99 Ca OE2 A:Glu532 2.75 Ca CD A:Glu532 2.84 Ca CG A:Glu532 4.33 Ca OE1 A:Gln550 4.30 Ca NE2 A:His551 4.54 Ca O1 A:Vo4700 2.39 Ca O2 A:Vo4700 2.50 Ca O4 A:Vo4700 4.53 Ca O3 A:Vo4700 3.76 Ca V A:Vo4700 3.09 Ca CA A:Ca1591 4.85 Ca CA A:Ca1592 3.95 Ca O A:Feo1594 4.86 Ca O A:Hoh2196 4.21 Ca O A:Hoh2244 2.43 Ca O A:Hoh2245 4.06 Ca O A:Hoh2252 2.65 Ca O A:Hoh2721 3.81 Ca O A:Hoh2815 4.70 Ca O A:Hoh2832 2.50 Ca O A:Hoh2877 4.51 Ca O A:Hoh2910 4.39 interactive model: Calcium binding site 4 out of 6 in 3zwu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 3zwu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp69, B: Cys179, B: Glu273, B: Glu387, B: Trp388, B: Asp479, B: Asp494, B: Glu532, B: Thr534, B: Vo4700, B: Ca1592, B: Ca1593, B: Feo1594, B: Hoh2179, B: Hoh2180, B: Hoh2213, B: Hoh2706, B: Hoh2707, conact list: Atom Atom Distance (A) Ca OD2 B:Asp69 4.82 Ca OD1 B:Asp69 4.76 Ca SG B:Cys179 3.99 Ca OE1 B:Glu273 3.90 Ca OE2 B:Glu273 2.33 Ca CD B:Glu273 3.44 Ca CG B:Glu273 4.69 Ca OE1 B:Glu387 4.24 Ca CB B:Glu387 4.95 Ca OE2 B:Glu387 2.86 Ca CD B:Glu387 3.73 Ca CG B:Glu387 4.73 Ca CD1 B:Trp388 4.49 Ca NE1 B:Trp388 4.00 Ca CB B:Asp479 4.30 Ca OD2 B:Asp479 2.40 Ca OD1 B:Asp479 2.51 Ca CG B:Asp479 2.79 Ca OD2 B:Asp494 4.71 Ca OE2 B:Glu532 4.18 Ca OG1 B:Thr534 4.68 Ca O2 B:Vo4700 2.62 Ca O4 B:Vo4700 4.31 Ca O3 B:Vo4700 4.38 Ca V B:Vo4700 3.67 Ca CA B:Ca1592 3.62 Ca CA B:Ca1593 4.84 Ca O B:Feo1594 2.40 Ca FE1 B:Feo1594 3.64 Ca FE2 B:Feo1594 3.59 Ca O B:Hoh2179 2.48 Ca O B:Hoh2180 2.72 Ca O B:Hoh2213 4.71 Ca O B:Hoh2706 2.46 Ca O B:Hoh2707 4.73 interactive model: Calcium binding site 5 out of 6 in 3zwu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 3zwu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp292, B: Arg385, B: Glu387, B: Thr403, B: Asp479, B: Asp494, B: Glu532, B: Vo4700, B: Ca1591, B: Ca1593, B: Feo1594, B: Hoh2620, B: Hoh2621, B: Hoh2706, B: Hoh2723, B: Hoh2724, conact list: Atom Atom Distance (A) Ca OD2 B:Asp292 4.51 Ca CZ B:Arg385 4.74 Ca NH2 B:Arg385 3.83 Ca OE1 B:Glu387 2.52 Ca OE2 B:Glu387 2.56 Ca CD B:Glu387 2.88 Ca CG B:Glu387 4.39 Ca CB B:Thr403 4.88 Ca CG2 B:Thr403 4.57 Ca OG1 B:Thr403 4.48 Ca CB B:Asp479 4.00 Ca OD2 B:Asp479 2.30 Ca OD1 B:Asp479 4.14 Ca CG B:Asp479 3.29 Ca O B:Asp494 4.40 Ca CB B:Asp494 3.69 Ca OD2 B:Asp494 2.38 Ca OD1 B:Asp494 4.51 Ca CG B:Asp494 3.38 Ca CA B:Asp494 5.00 Ca OE2 B:Glu532 4.56 Ca O1 B:Vo4700 3.85 Ca O2 B:Vo4700 2.37 Ca O4 B:Vo4700 3.36 Ca V B:Vo4700 3.38 Ca CA B:Ca1591 3.62 Ca CA B:Ca1593 3.95 Ca O B:Feo1594 4.14 Ca FE2 B:Feo1594 4.12 Ca O B:Hoh2620 2.42 Ca O B:Hoh2621 2.32 Ca O B:Hoh2706 4.65 Ca O B:Hoh2723 4.52 Ca O B:Hoh2724 4.92 interactive model: Calcium binding site 6 out of 6 in 3zwu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 3zwu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu90, B: Tyr91, B: Asp479, B: Asp494, B: Glu532, B: Gln550, B: His551, B: Vo4700, B: Ca1591, B: Ca1592, B: Feo1594, B: Hoh2180, B: Hoh2212, B: Hoh2213, B: Hoh2217, B: Hoh2620, B: Hoh2706, B: Hoh2723, B: Hoh2724, B: Hoh2764, B: Hoh2798, conact list: Atom Atom Distance (A) Ca OE1 B:Glu90 4.94 Ca OH B:Tyr91 4.98 Ca OD2 B:Asp479 4.62 Ca CB B:Asp494 4.37 Ca OD2 B:Asp494 2.48 Ca OD1 B:Asp494 3.39 Ca CG B:Asp494 3.14 Ca OE1 B:Glu532 2.24 Ca CB B:Glu532 4.97 Ca OE2 B:Glu532 2.73 Ca CD B:Glu532 2.82 Ca CG B:Glu532 4.31 Ca OE1 B:Gln550 4.30 Ca NE2 B:His551 4.54 Ca O1 B:Vo4700 2.40 Ca O2 B:Vo4700 2.49 Ca O4 B:Vo4700 4.52 Ca O3 B:Vo4700 3.75 Ca V B:Vo4700 3.08 Ca CA B:Ca1591 4.84 Ca CA B:Ca1592 3.95 Ca O B:Feo1594 4.92 Ca O B:Hoh2180 4.25 Ca O B:Hoh2212 4.16 Ca O B:Hoh2213 2.48 Ca O B:Hoh2217 2.55 Ca O B:Hoh2620 3.71 Ca O B:Hoh2706 4.68 Ca O B:Hoh2723 4.71 Ca O B:Hoh2724 2.41 Ca O B:Hoh2764 4.47 Ca O B:Hoh2798 4.42 interactive model: