Calcium in the structure of A Carboxylic Acid Based Inhibitor in Complex With MMP3 (pdb 1hy7)

The binding sites of Calcium atom in the structure of A Carboxylic Acid Based Inhibitor in Complex With MMP3 (pdb code 1hy7). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1hy7 structure was solved by M.G.NATCHUS, R.G.BOOKLAND, M.J.LAUFERSWEILER, S.PIKUL, N.G.ALMSTEAD, B.DE, M.J.JANUSZ, L.C.HSIEH, F.GU, M.E.POKROSS, V.S.PATEL, S.M.GARVER, S.X.PENG, T.M.BRANCH, S.L.KING, T.R.BAKER, D.J.FOLTZ, G.E.MIELING, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 63.2-1.5 Space group P212121 a (A) 37.918 b (A) 78.059 c (A) 105.801 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.8 Rfree (%) 22 Calcium Binding Sites: Calcium binding site 1 out of 6 in 1hy7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1hy7. 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: Asp158, A: Gly159, A: Pro160, A: Gly161, A: Asn162, A: Val163, A: Leu164, A: Asp181, A: Glu184, A: Hoh335, conact list: Atom Atom Distance (A) Ca O A:Asp158 4.70 Ca N A:Asp158 4.36 Ca CB A:Asp158 4.70 Ca OD2 A:Asp158 4.06 Ca C A:Asp158 4.29 Ca OD1 A:Asp158 2.35 Ca CG A:Asp158 3.52 Ca CA A:Asp158 4.66 Ca O A:Gly159 2.28 Ca N A:Gly159 4.12 Ca C A:Gly159 3.50 Ca CA A:Gly159 4.39 Ca O A:Pro160 4.49 Ca N A:Pro160 4.42 Ca C A:Pro160 4.05 Ca CA A:Pro160 4.43 Ca O A:Gly161 2.42 Ca N A:Gly161 3.82 Ca C A:Gly161 3.53 Ca CA A:Gly161 4.22 Ca N A:Asn162 4.57 Ca C A:Asn162 4.46 Ca CA A:Asn162 4.90 Ca O A:Val163 2.27 Ca N A:Val163 3.97 Ca CB A:Val163 4.60 Ca C A:Val163 3.46 Ca CA A:Val163 4.23 Ca N A:Leu164 4.47 Ca CA A:Leu164 4.62 Ca CB A:Asp181 4.06 Ca OD2 A:Asp181 2.30 Ca OD1 A:Asp181 4.28 Ca CG A:Asp181 3.37 Ca OE1 A:Glu184 4.23 Ca OE2 A:Glu184 2.28 Ca CD A:Glu184 3.51 Ca CG A:Glu184 4.53 Ca O A:Hoh335 4.62 interactive model: Calcium binding site 2 out of 6 in 1hy7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1hy7. 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: Thr105, A: Asp107, A: Asp182, A: Asp183, A: Glu184, A: Gln185, A: Trp186, A: Hoh326, A: Hoh341, A: Hoh365, A: Hoh371, A: Hoh386, A: Hoh458, B: Hoh73, B: Hoh186, conact list: Atom Atom Distance (A) Ca OG1 A:Thr105 4.12 Ca CB A:Asp107 4.42 Ca OD2 A:Asp107 2.45 Ca OD1 A:Asp107 2.57 Ca CG A:Asp107 2.92 Ca O A:Asp182 2.39 Ca CB A:Asp182 4.02 Ca OD2 A:Asp182 4.41 Ca C A:Asp182 3.34 Ca OD1 A:Asp182 2.42 Ca CG A:Asp182 3.46 Ca CA A:Asp182 3.79 Ca N A:Asp183 4.45 Ca C A:Asp183 4.61 Ca CA A:Asp183 4.73 Ca O A:Glu184 2.40 Ca N A:Glu184 4.40 Ca C A:Glu184 3.60 Ca CA A:Glu184 4.68 Ca N A:Gln185 4.36 Ca OE1 A:Gln185 4.73 Ca CA A:Gln185 4.29 Ca N A:Trp186 4.74 Ca CD1 A:Trp186 4.33 Ca NE1 A:Trp186 4.85 Ca O A:Hoh326 2.37 Ca O A:Hoh341 2.37 Ca O A:Hoh365 4.62 Ca O A:Hoh371 4.36 Ca O A:Hoh386 4.92 Ca O A:Hoh458 4.46 Ca O B:Hoh73 4.65 Ca O B:Hoh186 4.36 interactive model: Calcium binding site 3 out of 6 in 1hy7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1hy7. 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: Trp92, A: Ala140, A: Asp141, A: Ile142, A: Met143, A: Gly171, A: Pro172, A: Gly173, A: Ile174, A: Asn175, A: Gly176, A: Asp177, A: Hoh306, A: Hoh307, A: Hoh317, A: Hoh330, A: Hoh338, conact list: Atom Atom Distance (A) Ca CH2 A:Trp92 4.89 Ca O A:Ala140 4.00 Ca C A:Ala140 4.95 Ca O A:Asp141 2.32 Ca C A:Asp141 3.45 Ca CA A:Asp141 4.16 Ca N A:Ile142 4.48 Ca CA A:Ile142 4.72 Ca N A:Met143 4.69 Ca CG A:Met143 4.78 Ca O A:Gly171 4.37 Ca O A:Pro172 4.92 Ca C A:Pro172 4.65 Ca O A:Gly173 2.28 Ca N A:Gly173 4.28 Ca C A:Gly173 3.48 Ca CA A:Gly173 4.36 Ca O A:Ile174 4.13 Ca N A:Ile174 4.40 Ca C A:Ile174 4.01 Ca CA A:Ile174 4.43 Ca O A:Asn175 2.33 Ca N A:Asn175 4.13 Ca C A:Asn175 3.50 Ca CA A:Asn175 4.46 Ca N A:Gly176 4.35 Ca C A:Gly176 4.42 Ca CA A:Gly176 4.38 Ca N A:Asp177 4.09 Ca CB A:Asp177 4.56 Ca OD2 A:Asp177 3.85 Ca OD1 A:Asp177 2.37 Ca CG A:Asp177 3.39 Ca CA A:Asp177 4.67 Ca O A:Hoh306 2.32 Ca O A:Hoh307 2.31 Ca O A:Hoh317 4.68 Ca O A:Hoh330 4.55 Ca O A:Hoh338 4.49 interactive model: Calcium binding site 4 out of 6 in 1hy7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1hy7. 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: Asp658, B: Gly659, B: Pro660, B: Gly661, B: Asn662, B: Val663, B: Leu664, B: Asp681, B: Glu684, B: Hoh138, conact list: Atom Atom Distance (A) Ca O B:Asp658 4.71 Ca N B:Asp658 4.34 Ca CB B:Asp658 4.66 Ca OD2 B:Asp658 4.04 Ca C B:Asp658 4.25 Ca OD1 B:Asp658 2.32 Ca CG B:Asp658 3.50 Ca CA B:Asp658 4.62 Ca O B:Gly659 2.32 Ca N B:Gly659 4.08 Ca C B:Gly659 3.53 Ca CA B:Gly659 4.40 Ca O B:Pro660 4.69 Ca N B:Pro660 4.46 Ca C B:Pro660 4.15 Ca CA B:Pro660 4.48 Ca O B:Gly661 2.34 Ca N B:Gly661 3.86 Ca C B:Gly661 3.52 Ca CA B:Gly661 4.26 Ca O B:Asn662 4.61 Ca N B:Asn662 4.54 Ca CB B:Asn662 4.90 Ca C B:Asn662 4.20 Ca CA B:Asn662 4.75 Ca O B:Val663 2.30 Ca N B:Val663 3.86 Ca CB B:Val663 4.70 Ca C B:Val663 3.43 Ca CA B:Val663 4.16 Ca N B:Leu664 4.45 Ca CA B:Leu664 4.63 Ca CB B:Asp681 4.04 Ca OD2 B:Asp681 2.32 Ca OD1 B:Asp681 4.25 Ca CG B:Asp681 3.36 Ca OE1 B:Glu684 4.16 Ca OE2 B:Glu684 2.21 Ca CD B:Glu684 3.46 Ca CG B:Glu684 4.53 Ca O B:Hoh138 4.71 interactive model: Calcium binding site 5 out of 6 in 1hy7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 1hy7. 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: Thr605, B: Asp607, B: Asp682, B: Asp683, B: Glu684, B: Gln685, B: Trp686, A: Hoh357, A: Hoh364, B: Hoh20, B: Hoh36, B: Hoh52, conact list: Atom Atom Distance (A) Ca OG1 B:Thr605 4.10 Ca CB B:Asp607 4.38 Ca OD2 B:Asp607 2.45 Ca OD1 B:Asp607 2.58 Ca CG B:Asp607 2.89 Ca O B:Asp682 2.38 Ca CB B:Asp682 3.94 Ca OD2 B:Asp682 4.41 Ca C B:Asp682 3.34 Ca OD1 B:Asp682 2.39 Ca CG B:Asp682 3.44 Ca CA B:Asp682 3.79 Ca N B:Asp683 4.46 Ca C B:Asp683 4.65 Ca CA B:Asp683 4.76 Ca O B:Glu684 2.46 Ca N B:Glu684 4.42 Ca C B:Glu684 3.63 Ca CA B:Glu684 4.70 Ca N B:Gln685 4.39 Ca OE1 B:Gln685 4.84 Ca CA B:Gln685 4.24 Ca N B:Trp686 4.73 Ca CD1 B:Trp686 4.35 Ca NE1 B:Trp686 4.91 Ca O A:Hoh357 4.72 Ca O A:Hoh364 4.64 Ca O B:Hoh20 2.34 Ca O B:Hoh36 4.60 Ca O B:Hoh52 2.37 interactive model: Calcium binding site 6 out of 6 in 1hy7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 1hy7. 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: Trp592, B: Ala640, B: Asp641, B: Ile642, B: Met643, B: Gly671, B: Pro672, B: Gly673, B: Ile674, B: Asn675, B: Gly676, B: Asp677, B: Hoh12, B: Hoh51, B: Hoh64, B: Hoh98, B: Hoh272, conact list: Atom Atom Distance (A) Ca CH2 B:Trp592 4.86 Ca O B:Ala640 4.07 Ca O B:Asp641 2.29 Ca C B:Asp641 3.44 Ca CA B:Asp641 4.22 Ca N B:Ile642 4.45 Ca CA B:Ile642 4.65 Ca N B:Met643 4.68 Ca CG B:Met643 4.87 Ca O B:Gly671 4.40 Ca O B:Pro672 4.93 Ca C B:Pro672 4.66 Ca O B:Gly673 2.24 Ca N B:Gly673 4.31 Ca C B:Gly673 3.48 Ca CA B:Gly673 4.40 Ca O B:Ile674 4.12 Ca N B:Ile674 4.39 Ca C B:Ile674 4.00 Ca CA B:Ile674 4.42 Ca O B:Asn675 2.31 Ca N B:Asn675 4.16 Ca C B:Asn675 3.51 Ca CA B:Asn675 4.45 Ca N B:Gly676 4.41 Ca C B:Gly676 4.42 Ca CA B:Gly676 4.44 Ca N B:Asp677 4.05 Ca CB B:Asp677 4.53 Ca OD2 B:Asp677 3.84 Ca OD1 B:Asp677 2.35 Ca CG B:Asp677 3.38 Ca CA B:Asp677 4.66 Ca O B:Hoh12 2.36 Ca O B:Hoh51 4.78 Ca O B:Hoh64 2.36 Ca O B:Hoh98 4.45 Ca O B:Hoh272 4.53 interactive model: