Cadmium in the structure of Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed With Its Endogenous Inhibitor Penw (pdb 1kug)

The binding sites of Cadmium atom in the structure of Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed With Its Endogenous Inhibitor Penw (pdb code 1kug). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1kug structure was solved by K.F.HUANG, S.H.CHIOU, T.P.KO, A.H.J.WANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 1.4-1.4 Space group P41212 a (A) 61.151 b (A) 61.151 c (A) 131.193 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 20.2 Cadmium Binding Sites: Cadmium binding site 1 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His144, A: Glu145, A: His148, A: His154, A: Met167, B: Trp253, A: Hoh416, A: Hoh508, B: Hoh412, B: Hoh413, B: Hoh682, B: Hoh842, conact list: Atom Atom Distance (A) Cd NE2 A:His144 2.28 Cd ND1 A:His144 4.40 Cd CD2 A:His144 3.25 Cd CE1 A:His144 3.28 Cd CG A:His144 4.41 Cd OE1 A:Glu145 4.78 Cd OE2 A:Glu145 4.75 Cd NE2 A:His148 2.23 Cd ND1 A:His148 4.33 Cd CD2 A:His148 3.21 Cd CE1 A:His148 3.21 Cd CG A:His148 4.36 Cd NE2 A:His154 2.18 Cd ND1 A:His154 4.28 Cd CD2 A:His154 3.14 Cd CE1 A:His154 3.18 Cd CG A:His154 4.30 Cd CE A:Met167 4.90 Cd N B:Trp253 4.81 Cd CB B:Trp253 4.71 Cd CD1 B:Trp253 4.09 Cd C B:Trp253 2.69 Cd CG B:Trp253 4.48 Cd CA B:Trp253 4.16 Cd O B:Trp253 2.46 Cd NE1 B:Trp253 4.72 Cd OXT B:Trp253 2.26 Cd O A:Hoh416 4.19 Cd O A:Hoh508 4.23 Cd O B:Hoh412 4.83 Cd O B:Hoh413 2.42 Cd O B:Hoh682 4.33 Cd O B:Hoh842 4.30 interactive model: Cadmium binding site 2 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His36, A: Hoh348, A: Hoh349, A: Hoh429, A: Hoh904, conact list: Atom Atom Distance (A) Cd NE2 A:His36 4.47 Cd CB A:His36 3.60 Cd ND1 A:His36 2.38 Cd CD2 A:His36 4.50 Cd CE1 A:His36 3.34 Cd CG A:His36 3.36 Cd CA A:His36 4.81 Cd O A:Hoh348 2.41 Cd O A:Hoh349 2.36 Cd O A:Hoh429 4.38 Cd O A:Hoh904 0.60 interactive model: Cadmium binding site 3 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg4, A: Asp181, A: Asp185, A: Hoh391, A: Hoh431, A: Hoh432, A: Hoh433, A: Hoh825, conact list: Atom Atom Distance (A) Cd NH2 A:Arg4 4.75 Cd O A:Asp181 4.31 Cd CB A:Asp181 4.34 Cd OD2 A:Asp181 2.28 Cd C A:Asp181 4.91 Cd OD1 A:Asp181 2.60 Cd CG A:Asp181 2.79 Cd CB A:Asp185 4.34 Cd OD2 A:Asp185 2.32 Cd OD1 A:Asp185 2.68 Cd CG A:Asp185 2.85 Cd O A:Hoh391 4.06 Cd O A:Hoh431 2.31 Cd O A:Hoh432 4.71 Cd O A:Hoh433 2.33 Cd O A:Hoh825 4.06 interactive model: Cadmium binding site 4 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His18, A: Thr22, A: Glu63, A: Hoh327, A: Hoh330, A: Hoh425, A: Hoh437, A: Hoh466, A: Hoh467, A: Hoh583, A: Hoh597, A: Hoh721, A: Hoh821, A: Hoh914, conact list: Atom Atom Distance (A) Cd NE2 A:His18 2.29 Cd ND1 A:His18 4.35 Cd CD2 A:His18 3.32 Cd CE1 A:His18 3.20 Cd CG A:His18 4.44 Cd OG1 A:Thr22 4.31 Cd O A:Glu63 4.63 Cd O A:Hoh327 4.51 Cd O A:Hoh330 4.77 Cd O A:Hoh425 3.83 Cd O A:Hoh437 4.25 Cd O A:Hoh466 4.55 Cd O A:Hoh467 4.62 Cd O A:Hoh583 2.49 Cd O A:Hoh597 3.60 Cd O A:Hoh721 2.30 Cd O A:Hoh821 2.34 Cd O A:Hoh914 3.11 interactive model: Cadmium binding site 5 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gln3, A: Gln7, A: Asn50, A: Hoh317, A: Hoh319, A: Hoh320, A: Hoh438, A: Hoh568, A: Hoh664, A: Hoh666, A: Hoh724, A: Hoh818, conact list: Atom Atom Distance (A) Cd NE2 A:Gln3 4.35 Cd NE2 A:Gln7 3.61 Cd OE1 A:Gln7 2.23 Cd CB A:Gln7 4.82 Cd CD A:Gln7 3.22 Cd CG A:Gln7 4.54 Cd O A:Asn50 4.90 Cd CB A:Asn50 4.60 Cd ND2 A:Asn50 3.70 Cd OD1 A:Asn50 2.18 Cd CG A:Asn50 3.26 Cd CA A:Asn50 4.84 Cd O A:Hoh317 4.27 Cd O A:Hoh319 2.56 Cd O A:Hoh320 2.56 Cd O A:Hoh438 2.43 Cd O A:Hoh568 4.48 Cd O A:Hoh664 4.15 Cd O A:Hoh666 2.29 Cd O A:Hoh724 4.10 Cd O A:Hoh818 4.52 interactive model: Cadmium binding site 6 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly116, A: Met118, A: Phe190, A: Asp194, A: Pro196, A: Hoh442, A: Hoh514, A: Hoh571, A: Hoh633, A: Hoh634, A: Hoh638, A: Hoh659, A: Hoh879, A: Hoh880, conact list: Atom Atom Distance (A) Cd O A:Gly116 4.23 Cd O A:Met118 4.29 Cd CZ A:Phe190 4.92 Cd CE1 A:Phe190 4.86 Cd CB A:Asp194 4.13 Cd OD2 A:Asp194 2.23 Cd OD1 A:Asp194 2.34 Cd CG A:Asp194 2.61 Cd CA A:Asp194 4.96 Cd CB A:Pro196 4.50 Cd CD A:Pro196 4.99 Cd O A:Hoh442 2.81 Cd O A:Hoh514 4.84 Cd O A:Hoh571 2.22 Cd O A:Hoh633 3.69 Cd O A:Hoh634 4.87 Cd O A:Hoh638 4.19 Cd O A:Hoh659 4.79 Cd O A:Hoh879 3.70 Cd O A:Hoh880 4.32 interactive model: Cadmium binding site 7 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala202, A: Pro203, A: Hoh746, A: Hoh747, A: Hoh813, A: Hoh837, A: Hoh916, conact list: Atom Atom Distance (A) Cd O A:Ala202 4.79 Cd O A:Pro203 2.33 Cd N A:Pro203 4.96 Cd CB A:Pro203 4.89 Cd C A:Pro203 2.69 Cd CA A:Pro203 4.21 Cd OXT A:Pro203 2.40 Cd O A:Hoh746 1.83 Cd O A:Hoh747 2.09 Cd O A:Hoh813 4.75 Cd O A:Hoh837 1.98 Cd O A:Hoh916 4.60 interactive model: Cadmium binding site 8 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His131, A: Ser132, A: Hoh344, A: Hoh353, A: Hoh354, A: Hoh355, A: Hoh356, A: Hoh424, A: Hoh483, A: Hoh486, A: Hoh608, A: Hoh717, A: Hoh718, conact list: Atom Atom Distance (A) Cd O A:His131 2.54 Cd NE2 A:His131 4.33 Cd CB A:His131 3.54 Cd ND1 A:His131 2.23 Cd CD2 A:His131 4.37 Cd C A:His131 3.42 Cd CE1 A:His131 3.20 Cd CG A:His131 3.24 Cd CA A:His131 4.14 Cd N A:Ser132 4.27 Cd CB A:Ser132 4.15 Cd OG A:Ser132 5.00 Cd CA A:Ser132 4.48 Cd O A:Hoh344 4.83 Cd O A:Hoh353 3.84 Cd O A:Hoh354 2.36 Cd O A:Hoh355 2.55 Cd O A:Hoh356 2.36 Cd O A:Hoh424 2.43 Cd O A:Hoh483 4.59 Cd O A:Hoh486 4.34 Cd O A:Hoh608 4.95 Cd O A:Hoh717 4.23 Cd O A:Hoh718 4.19 interactive model: Cadmium binding site 9 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys160, A: Lys161, A: Cys162, A: Asp181, A: Hoh380, A: Hoh386, A: Hoh550, A: Hoh551, A: Hoh552, A: Hoh836, A: Hoh884, A: Hoh885, conact list: Atom Atom Distance (A) Cd CB A:Cys160 4.79 Cd N A:Lys161 4.51 Cd N A:Cys162 4.90 Cd N A:Asp181 4.57 Cd CB A:Asp181 4.06 Cd CA A:Asp181 4.94 Cd O A:Hoh380 2.58 Cd O A:Hoh386 2.33 Cd O A:Hoh550 2.50 Cd O A:Hoh551 1.88 Cd O A:Hoh552 2.30 Cd O A:Hoh836 2.05 Cd O A:Hoh884 4.07 Cd O A:Hoh885 3.13 interactive model: Cadmium binding site 10 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu85, A: Arg86, A: Cd991, A: Hoh455, A: Hoh512, A: Hoh613, A: Hoh617, A: Hoh618, A: Hoh748, A: Hoh803, conact list: Atom Atom Distance (A) Cd O A:Glu85 4.79 Cd OE1 A:Glu85 2.27 Cd OE2 A:Glu85 2.43 Cd CD A:Glu85 2.68 Cd C A:Glu85 4.95 Cd CG A:Glu85 4.23 Cd N A:Arg86 4.99 Cd CB A:Arg86 4.92 Cd CA A:Arg86 4.72 Cd CD A:Cd991 4.65 Cd O A:Hoh455 4.62 Cd O A:Hoh512 4.81 Cd O A:Hoh613 4.32 Cd O A:Hoh617 2.52 Cd O A:Hoh618 2.62 Cd O A:Hoh748 4.22 Cd O A:Hoh803 4.49 interactive model: Cadmium binding site 11 out of 11 in 1kug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 1kug. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu85, A: Glu121, A: Cd990, A: Hoh455, A: Hoh774, A: Hoh803, A: Hoh852, conact list: Atom Atom Distance (A) Cd OE1 A:Glu85 4.79 Cd OE2 A:Glu85 2.74 Cd CD A:Glu85 3.70 Cd CG A:Glu85 3.93 Cd OE1 A:Glu121 2.20 Cd CB A:Glu121 4.82 Cd OE2 A:Glu121 3.48 Cd CD A:Glu121 3.17 Cd CG A:Glu121 4.53 Cd CD A:Cd990 4.65 Cd O A:Hoh455 2.49 Cd O A:Hoh774 4.92 Cd O A:Hoh803 1.93 Cd O A:Hoh852 4.17 interactive model: