Calcium in the structure of Crystal Structure of A Putative Yden-Like Hydrolase (ECA3091) From Pectobacterium Atrosepticum SCRI1043 At 1.66 A Resolution (pdb 3bdv)

The binding sites of Calcium atom in the structure of Crystal Structure of A Putative Yden-Like Hydrolase (ECA3091) From Pectobacterium Atrosepticum SCRI1043 At 1.66 A Resolution (pdb code 3bdv). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 3bdv structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.6-1.7 Space group P212121 a (A) 35.655 b (A) 93.302 c (A) 104.095 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 21.3 Calcium Binding Sites: Calcium binding site 1 out of 3 in 3bdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 3bdv. 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: Gln45, A: Arg46, A: Ile47, A: Arg48, A: Glu67, A: Hoh235, A: Hoh239, A: Hoh268, A: Hoh342, conact list: Atom Atom Distance (A) Ca OE1 A:Gln45 4.31 Ca OE1 A:Gln45 4.92 Ca O A:Arg46 2.44 Ca N A:Arg46 4.08 Ca C A:Arg46 3.58 Ca CA A:Arg46 4.45 Ca N A:Ile47 4.45 Ca C A:Ile47 4.73 Ca CA A:Ile47 4.41 Ca N A:Arg48 4.73 Ca CD A:Arg48 4.99 Ca CG A:Arg48 4.22 Ca NE A:Arg48 4.52 Ca OE1 A:Glu67 2.53 Ca OE2 A:Glu67 2.56 Ca CD A:Glu67 2.91 Ca CG A:Glu67 4.41 Ca O A:Hoh235 4.78 Ca O A:Hoh239 2.37 Ca O A:Hoh268 2.44 Ca O A:Hoh342 2.27 interactive model: Calcium binding site 2 out of 3 in 3bdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 3bdv. 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: Glu113, A: Asp115, A: Edo194, A: Hoh265, A: Hoh285, A: Hoh293, A: Hoh313, A: Hoh367, conact list: Atom Atom Distance (A) Ca OE1 A:Glu113 4.73 Ca OD2 A:Asp115 4.52 Ca OD1 A:Asp115 4.62 Ca O1 A:Edo194 2.52 Ca O2 A:Edo194 2.51 Ca C2 A:Edo194 3.43 Ca C1 A:Edo194 3.47 Ca O A:Hoh265 2.39 Ca O A:Hoh285 2.34 Ca O A:Hoh293 3.89 Ca O A:Hoh313 2.32 Ca O A:Hoh367 4.62 Ca O A:Hoh367 2.88 interactive model: Calcium binding site 3 out of 3 in 3bdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 3bdv. 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: Ile185, A: Leu186, A: Ile187, B: Asp151, A: Edo195, A: Hoh242, B: Hoh248, conact list: Atom Atom Distance (A) Ca O A:Ile185 2.37 Ca CB A:Ile185 4.64 Ca C A:Ile185 3.50 Ca CA A:Ile185 4.26 Ca N A:Leu186 4.46 Ca C A:Leu186 4.91 Ca CA A:Leu186 4.55 Ca O A:Ile187 4.57 Ca CB B:Asp151 4.80 Ca OD2 B:Asp151 2.47 Ca OD1 B:Asp151 3.57 Ca CG B:Asp151 3.38 Ca O1 A:Edo195 2.41 Ca O2 A:Edo195 2.24 Ca C2 A:Edo195 3.13 Ca C1 A:Edo195 3.09 Ca O A:Hoh242 2.39 Ca O B:Hoh248 2.46 interactive model: