Cadmium in the structure of 18-K C-Terminally Trunucated Small Subunit of Calpain (pdb 1np8)

The binding sites of Cadmium atom in the structure of 18-K C-Terminally Trunucated Small Subunit of Calpain (pdb code 1np8). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1np8 structure was solved by E.K.LEINALA, J.S.ARTHUR, P.GROCHULSKI, P.L.DAVIES, J.S.ELCE, Z.JIA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.0 Space group P212121 a (A) 58.040 b (A) 67.570 c (A) 75.070 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 23.9 Cadmium Binding Sites: Cadmium binding site 1 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1np8. 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: Glu30, A: Asp68, A: Ser69, A: Asp70, A: Thr71, A: Thr72, A: Gly73, A: Lys74, A: Leu75, A: Gly76, A: Glu79, A: Hoh778, conact list: Atom Atom Distance (A) Cd OE1 A:Glu30 4.26 Cd OE2 A:Glu30 4.25 Cd CD A:Glu30 4.60 Cd O A:Asp68 4.82 Cd CB A:Asp68 4.19 Cd OD2 A:Asp68 4.32 Cd C A:Asp68 4.46 Cd OD1 A:Asp68 2.27 Cd CG A:Asp68 3.42 Cd CA A:Asp68 4.15 Cd N A:Ser69 4.90 Cd N A:Asp70 4.38 Cd CB A:Asp70 4.48 Cd OD2 A:Asp70 3.43 Cd C A:Asp70 4.69 Cd OD1 A:Asp70 2.30 Cd CG A:Asp70 3.17 Cd CA A:Asp70 4.72 Cd N A:Thr71 4.56 Cd C A:Thr71 4.97 Cd N A:Thr72 3.85 Cd CB A:Thr72 3.66 Cd CG2 A:Thr72 3.85 Cd OG1 A:Thr72 2.53 Cd C A:Thr72 4.83 Cd CA A:Thr72 4.30 Cd N A:Gly73 4.65 Cd O A:Lys74 2.26 Cd N A:Lys74 4.32 Cd C A:Lys74 3.47 Cd CA A:Lys74 4.55 Cd N A:Leu75 4.24 Cd CD1 A:Leu75 4.99 Cd C A:Leu75 4.57 Cd CA A:Leu75 4.18 Cd N A:Gly76 4.06 Cd OE1 A:Glu79 2.14 Cd CB A:Glu79 4.97 Cd OE2 A:Glu79 2.93 Cd CD A:Glu79 2.85 Cd CG A:Glu79 4.27 Cd O A:Hoh778 2.42 interactive model: Cadmium binding site 2 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1np8. 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: Asp100, A: Asn108, A: Glu109, A: Hoh720, A: Hoh723, A: Hoh769, A: Hoh771, A: Hoh774, A: Hoh805, conact list: Atom Atom Distance (A) Cd CB A:Asp100 3.64 Cd OD2 A:Asp100 2.31 Cd OD1 A:Asp100 4.24 Cd CG A:Asp100 3.23 Cd CA A:Asp100 4.96 Cd CB A:Asn108 4.68 Cd ND2 A:Asn108 4.48 Cd OE1 A:Glu109 4.97 Cd OE2 A:Glu109 4.12 Cd CD A:Glu109 4.38 Cd CG A:Glu109 4.56 Cd O A:Hoh720 4.26 Cd O A:Hoh723 4.63 Cd O A:Hoh769 2.45 Cd O A:Hoh771 2.39 Cd O A:Hoh774 2.37 Cd O A:Hoh805 4.26 interactive model: Cadmium binding site 3 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1np8. 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: Asp98, A: Thr99, A: Asp100, A: Arg101, A: Ser102, A: Gly103, A: Thr104, A: Ile105, A: Gly106, A: Glu109, A: Asn139, A: Hoh720, A: Hoh774, conact list: Atom Atom Distance (A) Cd O A:Asp98 4.80 Cd CB A:Asp98 3.87 Cd OD2 A:Asp98 4.16 Cd C A:Asp98 4.29 Cd OD1 A:Asp98 2.07 Cd CG A:Asp98 3.20 Cd CA A:Asp98 3.82 Cd N A:Thr99 4.69 Cd N A:Asp100 4.40 Cd CB A:Asp100 4.49 Cd OD2 A:Asp100 3.47 Cd C A:Asp100 4.75 Cd OD1 A:Asp100 2.20 Cd CG A:Asp100 3.15 Cd CA A:Asp100 4.77 Cd N A:Arg101 4.56 Cd N A:Ser102 3.93 Cd CB A:Ser102 3.48 Cd OG A:Ser102 2.33 Cd C A:Ser102 4.87 Cd CA A:Ser102 4.30 Cd N A:Gly103 4.76 Cd O A:Thr104 2.38 Cd N A:Thr104 4.32 Cd CB A:Thr104 4.88 Cd OG1 A:Thr104 4.05 Cd C A:Thr104 3.50 Cd CA A:Thr104 4.46 Cd N A:Ile105 4.31 Cd C A:Ile105 4.67 Cd CA A:Ile105 4.26 Cd N A:Gly106 4.15 Cd OE1 A:Glu109 2.29 Cd OE2 A:Glu109 2.68 Cd CD A:Glu109 2.84 Cd CG A:Glu109 4.33 Cd OD1 A:Asn139 4.48 Cd O A:Hoh720 2.21 Cd O A:Hoh774 4.91 interactive model: Cadmium binding site 4 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1np8. 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: Leu24, A: Ala25, A: Gly26, A: Asp28, A: Met29, A: Glu30, A: Val31, A: Ser32, A: Glu35, A: Hoh726, A: Hoh732, A: Hoh772, A: Hoh810, A: Hoh817, conact list: Atom Atom Distance (A) Cd O A:Leu24 4.53 Cd O A:Ala25 2.19 Cd C A:Ala25 3.20 Cd CB A:Ala25 4.48 Cd CA A:Ala25 3.79 Cd N A:Gly26 4.28 Cd C A:Gly26 4.80 Cd CA A:Gly26 4.59 Cd N A:Asp28 4.58 Cd CB A:Asp28 4.50 Cd OD2 A:Asp28 3.27 Cd OD1 A:Asp28 2.23 Cd CG A:Asp28 3.09 Cd CA A:Asp28 4.91 Cd N A:Met29 4.76 Cd O A:Glu30 2.37 Cd N A:Glu30 4.27 Cd C A:Glu30 3.62 Cd CA A:Glu30 4.61 Cd N A:Val31 4.48 Cd C A:Val31 4.85 Cd CA A:Val31 4.47 Cd N A:Ser32 4.31 Cd CB A:Ser32 4.82 Cd OG A:Ser32 4.80 Cd OE1 A:Glu35 2.44 Cd OE2 A:Glu35 2.36 Cd CD A:Glu35 2.71 Cd CG A:Glu35 4.20 Cd O A:Hoh726 2.52 Cd O A:Hoh732 4.36 Cd O A:Hoh772 2.25 Cd O A:Hoh810 4.74 Cd O A:Hoh817 4.59 interactive model: Cadmium binding site 5 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1np8. 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: Asp53, A: Gly54, A: Asp141, A: Asp143, A: Asn144, A: Hoh713, A: Hoh717, A: Hoh725, A: Hoh729, A: Hoh755, A: Hoh757, A: Hoh765, A: Hoh773, B: Hoh239, conact list: Atom Atom Distance (A) Cd N A:Asp53 4.28 Cd CB A:Asp53 4.47 Cd OD2 A:Asp53 3.53 Cd OD1 A:Asp53 2.14 Cd CG A:Asp53 3.15 Cd CA A:Asp53 4.90 Cd O A:Gly54 4.93 Cd CB A:Asp141 4.22 Cd OD2 A:Asp141 2.52 Cd OD1 A:Asp141 2.22 Cd CG A:Asp141 2.71 Cd N A:Asp143 4.94 Cd CB A:Asp143 4.31 Cd OD2 A:Asp143 2.13 Cd C A:Asp143 4.82 Cd OD1 A:Asp143 3.06 Cd CG A:Asp143 2.90 Cd CA A:Asp143 4.93 Cd N A:Asn144 4.13 Cd CB A:Asn144 4.32 Cd ND2 A:Asn144 3.96 Cd OD1 A:Asn144 2.47 Cd CG A:Asn144 3.33 Cd CA A:Asn144 4.71 Cd O A:Hoh713 4.55 Cd O A:Hoh717 3.71 Cd O A:Hoh725 3.30 Cd O A:Hoh729 2.32 Cd O A:Hoh755 4.52 Cd O A:Hoh757 4.42 Cd O A:Hoh765 5.00 Cd O A:Hoh773 2.34 Cd O B:Hoh239 4.45 interactive model: Cadmium binding site 6 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 1np8. 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: Asp27, A: Hoh768, A: Hoh776, A: Hoh791, conact list: Atom Atom Distance (A) Cd CB A:Asp27 4.49 Cd OD2 A:Asp27 3.12 Cd OD1 A:Asp27 2.26 Cd CG A:Asp27 3.03 Cd O A:Hoh768 2.41 Cd O A:Hoh776 2.19 Cd O A:Hoh791 4.26 interactive model: Cadmium binding site 7 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 1np8. 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: His47, A: Asp49, A: Gln91, A: Lys95, B: His624, A: Hoh777, B: Hoh140, conact list: Atom Atom Distance (A) Cd NE2 A:His47 4.44 Cd CB A:His47 3.32 Cd ND1 A:His47 2.32 Cd CD2 A:His47 4.37 Cd C A:His47 4.74 Cd CE1 A:His47 3.37 Cd CG A:His47 3.18 Cd CA A:His47 4.08 Cd N A:Asp49 4.95 Cd CB A:Asp49 4.19 Cd OD2 A:Asp49 2.19 Cd OD1 A:Asp49 2.52 Cd CG A:Asp49 2.68 Cd NE2 A:Gln91 4.78 Cd CE A:Lys95 4.57 Cd CD A:Lys95 4.74 Cd NZ A:Lys95 4.20 Cd NE2 B:His624 4.30 Cd CE1 B:His624 4.61 Cd O A:Hoh777 2.67 Cd O B:Hoh140 3.15 interactive model: Cadmium binding site 8 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 1np8. 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: B: Glu530, B: Asp568, B: Ser569, B: Asp570, B: Thr571, B: Thr572, B: Gly573, B: Lys574, B: Leu575, B: Gly576, B: Glu579, B: Hoh112, conact list: Atom Atom Distance (A) Cd OE1 B:Glu530 4.08 Cd OE2 B:Glu530 4.30 Cd CD B:Glu530 4.55 Cd O B:Asp568 4.92 Cd CB B:Asp568 4.09 Cd OD2 B:Asp568 4.24 Cd C B:Asp568 4.53 Cd OD1 B:Asp568 2.28 Cd CG B:Asp568 3.36 Cd CA B:Asp568 4.14 Cd N B:Ser569 4.95 Cd N B:Asp570 4.45 Cd CB B:Asp570 4.45 Cd OD2 B:Asp570 3.36 Cd C B:Asp570 4.66 Cd OD1 B:Asp570 2.22 Cd CG B:Asp570 3.10 Cd CA B:Asp570 4.76 Cd N B:Thr571 4.48 Cd C B:Thr571 4.85 Cd N B:Thr572 3.74 Cd CB B:Thr572 3.44 Cd CG2 B:Thr572 3.84 Cd OG1 B:Thr572 2.15 Cd C B:Thr572 4.71 Cd CA B:Thr572 4.15 Cd N B:Gly573 4.52 Cd O B:Lys574 2.36 Cd N B:Lys574 4.32 Cd C B:Lys574 3.58 Cd CA B:Lys574 4.64 Cd N B:Leu575 4.35 Cd C B:Leu575 4.62 Cd CA B:Leu575 4.22 Cd N B:Gly576 4.02 Cd CA B:Gly576 4.96 Cd OE1 B:Glu579 2.18 Cd CB B:Glu579 4.98 Cd OE2 B:Glu579 3.07 Cd CD B:Glu579 2.97 Cd CG B:Glu579 4.41 Cd O B:Hoh112 2.23 interactive model: Cadmium binding site 9 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 1np8. 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: B: Asp598, B: Thr599, B: Asp600, B: Arg601, B: Ser602, B: Gly603, B: Thr604, B: Ile605, B: Gly606, B: Glu609, B: Asn639, B: Hoh138, conact list: Atom Atom Distance (A) Cd O B:Asp598 4.88 Cd CB B:Asp598 3.92 Cd OD2 B:Asp598 4.03 Cd C B:Asp598 4.33 Cd OD1 B:Asp598 1.98 Cd CG B:Asp598 3.13 Cd CA B:Asp598 3.85 Cd N B:Thr599 4.68 Cd N B:Asp600 4.41 Cd CB B:Asp600 4.50 Cd OD2 B:Asp600 3.42 Cd C B:Asp600 4.80 Cd OD1 B:Asp600 2.25 Cd CG B:Asp600 3.14 Cd CA B:Asp600 4.79 Cd N B:Arg601 4.69 Cd N B:Ser602 3.96 Cd CB B:Ser602 3.50 Cd OG B:Ser602 2.30 Cd C B:Ser602 4.84 Cd CA B:Ser602 4.29 Cd N B:Gly603 4.79 Cd O B:Thr604 2.36 Cd N B:Thr604 4.30 Cd CB B:Thr604 4.96 Cd OG1 B:Thr604 4.19 Cd C B:Thr604 3.43 Cd CA B:Thr604 4.43 Cd N B:Ile605 4.21 Cd C B:Ile605 4.59 Cd CA B:Ile605 4.15 Cd N B:Gly606 4.13 Cd OE1 B:Glu609 2.14 Cd OE2 B:Glu609 2.63 Cd CD B:Glu609 2.70 Cd CG B:Glu609 4.17 Cd OD1 B:Asn639 4.37 Cd O B:Hoh138 2.14 interactive model: Cadmium binding site 10 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 1np8. 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: B: Leu524, B: Ala525, B: Gly526, B: Asp528, B: Met529, B: Glu530, B: Val531, B: Ser532, B: Glu535, B: Lys574, B: Hoh61, B: Hoh142, B: Hoh184, B: Hoh186, B: Hoh187, conact list: Atom Atom Distance (A) Cd O B:Leu524 4.69 Cd O B:Ala525 2.18 Cd C B:Ala525 3.26 Cd CB B:Ala525 4.54 Cd CA B:Ala525 3.84 Cd N B:Gly526 4.37 Cd C B:Gly526 4.77 Cd CA B:Gly526 4.67 Cd N B:Asp528 4.51 Cd CB B:Asp528 4.46 Cd OD2 B:Asp528 3.19 Cd OD1 B:Asp528 2.27 Cd CG B:Asp528 3.05 Cd CA B:Asp528 4.84 Cd N B:Met529 4.72 Cd O B:Glu530 2.37 Cd N B:Glu530 4.22 Cd C B:Glu530 3.60 Cd CA B:Glu530 4.54 Cd N B:Val531 4.49 Cd C B:Val531 4.84 Cd CA B:Val531 4.46 Cd N B:Ser532 4.31 Cd CB B:Ser532 4.83 Cd OG B:Ser532 4.71 Cd OE1 B:Glu535 2.52 Cd OE2 B:Glu535 2.26 Cd CD B:Glu535 2.71 Cd CG B:Glu535 4.21 Cd CD B:Lys574 4.65 Cd O B:Hoh61 4.47 Cd O B:Hoh142 2.17 Cd O B:Hoh184 4.60 Cd O B:Hoh186 2.47 Cd O B:Hoh187 4.99 interactive model: Cadmium binding site 11 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 1np8. 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: B: Asp553, B: Asp641, B: Asp643, B: Asn644, B: Hoh38, B: Hoh42, B: Hoh118, B: Hoh119, B: Hoh209, conact list: Atom Atom Distance (A) Cd N B:Asp553 4.27 Cd CB B:Asp553 4.53 Cd OD2 B:Asp553 3.38 Cd OD1 B:Asp553 2.32 Cd CG B:Asp553 3.16 Cd CA B:Asp553 4.92 Cd CB B:Asp641 4.35 Cd OD2 B:Asp641 2.67 Cd OD1 B:Asp641 2.33 Cd CG B:Asp641 2.85 Cd N B:Asp643 4.85 Cd CB B:Asp643 4.15 Cd OD2 B:Asp643 2.07 Cd C B:Asp643 4.75 Cd OD1 B:Asp643 2.81 Cd CG B:Asp643 2.74 Cd CA B:Asp643 4.80 Cd N B:Asn644 4.09 Cd CB B:Asn644 4.31 Cd ND2 B:Asn644 3.81 Cd OD1 B:Asn644 2.48 Cd CG B:Asn644 3.27 Cd CA B:Asn644 4.71 Cd O B:Hoh38 3.87 Cd O B:Hoh42 4.92 Cd O B:Hoh118 4.40 Cd O B:Hoh119 2.17 Cd O B:Hoh209 3.16 interactive model: Cadmium binding site 12 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 1np8. 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: B: His547, B: Asp549, B: Leu550, B: Gln591, B: Lys595, conact list: Atom Atom Distance (A) Cd NE2 B:His547 4.27 Cd CB B:His547 3.47 Cd ND1 B:His547 2.29 Cd CD2 B:His547 4.27 Cd C B:His547 4.91 Cd CE1 B:His547 3.23 Cd CG B:His547 3.17 Cd CA B:His547 4.26 Cd CB B:Asp549 4.34 Cd OD2 B:Asp549 2.73 Cd OD1 B:Asp549 2.30 Cd CG B:Asp549 2.85 Cd CG B:Leu550 4.76 Cd NE2 B:Gln591 4.92 Cd CE B:Lys595 3.01 Cd CD B:Lys595 3.52 Cd CG B:Lys595 4.66 Cd NZ B:Lys595 2.68 interactive model: Cadmium binding site 13 out of 13 in 1np8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cadmium in the PDB 1np8. 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: Lys95, B: Gln623, B: His624, B: Met628, B: Hoh148, B: Hoh198, conact list: Atom Atom Distance (A) Cd CE A:Lys95 4.77 Cd NZ A:Lys95 4.87 Cd OE1 B:Gln623 4.62 Cd NE2 B:His624 4.49 Cd N B:His624 4.65 Cd CB B:His624 3.60 Cd ND1 B:His624 2.41 Cd CD2 B:His624 4.51 Cd C B:His624 4.99 Cd CE1 B:His624 3.37 Cd CG B:His624 3.37 Cd CA B:His624 3.83 Cd CG B:Met628 4.59 Cd SD B:Met628 3.52 Cd O B:Hoh148 2.57 Cd O B:Hoh198 2.34 interactive model: