Calcium in the structure of Structural Interaction of Natural and Synthetic Inhibitors With the Venom Metalloproteinase, Atrolysin C (Ht-D) (pdb 1htd)

The binding sites of Calcium atom in the structure of Structural Interaction of Natural and Synthetic Inhibitors With the Venom Metalloproteinase, Atrolysin C (Ht-D) (pdb code 1htd). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1htd structure was solved by D.ZHANG, I.BOTOS, F.-X.GOMIS-RUETH, R.DOLL, C.BLOOD, F.G.NJOROGE, J.W.FOX, W.BODE, E.F.MEYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.1 Space group P65 a (A) 97.320 b (A) 97.320 c (A) 87.760 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18 Rfree (%) n/a Calcium Binding Sites: Calcium binding site 1 out of 2 in 1htd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1htd. 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: Tyr7, A: Glu9, A: Asp93, A: Cys197, A: Ile198, A: Asn200, A: Hoh416, A: Hoh430, A: Hoh454, conact list: Atom Atom Distance (A) Ca O A:Tyr7 4.43 Ca N A:Glu9 4.93 Ca OE1 A:Glu9 2.33 Ca CB A:Glu9 4.48 Ca OE2 A:Glu9 4.45 Ca CD A:Glu9 3.44 Ca CG A:Glu9 4.01 Ca CB A:Asp93 4.37 Ca OD2 A:Asp93 2.48 Ca OD1 A:Asp93 2.42 Ca CG A:Asp93 2.85 Ca O A:Cys197 2.21 Ca CB A:Cys197 4.42 Ca SG A:Cys197 4.94 Ca C A:Cys197 3.39 Ca CA A:Cys197 4.14 Ca N A:Ile198 4.40 Ca CA A:Ile198 4.48 Ca O A:Asn200 4.57 Ca N A:Asn200 4.91 Ca CB A:Asn200 4.89 Ca ND2 A:Asn200 4.18 Ca OD1 A:Asn200 2.50 Ca CG A:Asn200 3.64 Ca O A:Hoh416 1.83 Ca O A:Hoh430 1.76 Ca O A:Hoh454 4.05 interactive model: Calcium binding site 2 out of 2 in 1htd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1htd. 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: Tyr7, B: Glu9, B: Asp93, B: Cys197, B: Ile198, B: Leu199, B: Asn200, B: Hoh321, B: Hoh332, B: Hoh333, B: Hoh349, B: Hoh357, conact list: Atom Atom Distance (A) Ca O B:Tyr7 4.35 Ca N B:Glu9 4.83 Ca OE1 B:Glu9 2.36 Ca CB B:Glu9 4.43 Ca OE2 B:Glu9 4.54 Ca CD B:Glu9 3.47 Ca CG B:Glu9 3.96 Ca CB B:Asp93 4.37 Ca OD2 B:Asp93 2.54 Ca OD1 B:Asp93 2.42 Ca CG B:Asp93 2.86 Ca O B:Cys197 2.25 Ca CB B:Cys197 4.37 Ca SG B:Cys197 4.93 Ca C B:Cys197 3.45 Ca CA B:Cys197 4.25 Ca N B:Ile198 4.42 Ca CA B:Ile198 4.46 Ca N B:Leu199 4.99 Ca O B:Asn200 4.56 Ca N B:Asn200 4.85 Ca CB B:Asn200 4.72 Ca ND2 B:Asn200 3.91 Ca OD1 B:Asn200 2.34 Ca CG B:Asn200 3.43 Ca O B:Hoh321 4.59 Ca O B:Hoh332 4.82 Ca O B:Hoh333 4.50 Ca O B:Hoh349 1.79 Ca O B:Hoh357 2.73 interactive model: