Cadmium in the structure of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas At 2.8 Angstroms Resolution (pdb 1c1j)

The binding sites of Cadmium atom in the structure of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas At 2.8 Angstroms Resolution (pdb code 1c1j). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1c1j structure was solved by H.-L.ZHANG, Y.-Q.ZHANG, S.-Y.SONG, Y.ZHOU, Z.-J.LIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.8 Space group C121 a (A) 100.180 b (A) 54.010 c (A) 108.490 alpha (°) 90.00 beta (°) 111.59 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 28.2 Cadmium Binding Sites: Cadmium binding site 1 out of 6 in 1c1j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1c1j. 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: Phe5, A: Tyr28, A: Gly30, A: Cys45, A: His48, A: Asp49, A: Bog600, A: Hoh603, A: Hoh604, conact list: Atom Atom Distance (A) Cd CE2 A:Phe5 4.69 Cd O A:Tyr28 4.65 Cd O A:Gly30 3.87 Cd N A:Gly30 4.40 Cd C A:Gly30 4.63 Cd CA A:Gly30 4.95 Cd O A:Cys45 4.24 Cd CA A:Cys45 4.99 Cd O A:His48 4.78 Cd NE2 A:His48 4.51 Cd CB A:His48 4.01 Cd ND1 A:His48 2.62 Cd CD2 A:His48 4.66 Cd C A:His48 4.51 Cd CE1 A:His48 3.38 Cd CG A:His48 3.64 Cd CA A:His48 4.92 Cd N A:Asp49 4.45 Cd CB A:Asp49 4.91 Cd OD2 A:Asp49 2.83 Cd OD1 A:Asp49 4.53 Cd CG A:Asp49 3.91 Cd CA A:Asp49 4.72 Cd C8' A:Bog600 4.84 Cd O A:Hoh603 2.72 Cd O A:Hoh604 2.86 interactive model: Cadmium binding site 2 out of 6 in 1c1j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1c1j. 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: Phe24, A: Tyr25, A: Gly26, A: Cys27, A: Tyr28, A: Cys29, A: Arg34, A: Tyr120, A: Asp122, A: Hoh610, conact list: Atom Atom Distance (A) Cd O A:Phe24 4.22 Cd C A:Phe24 4.55 Cd CA A:Phe24 4.92 Cd O A:Tyr25 4.03 Cd C A:Tyr25 4.66 Cd O A:Gly26 2.97 Cd C A:Gly26 3.90 Cd O A:Cys27 4.38 Cd N A:Cys27 4.38 Cd C A:Cys27 4.27 Cd CA A:Cys27 4.09 Cd N A:Tyr28 4.87 Cd O A:Cys29 4.42 Cd NH1 A:Arg34 4.76 Cd O A:Tyr120 3.71 Cd C A:Tyr120 4.82 Cd OD2 A:Asp122 4.41 Cd OD1 A:Asp122 3.10 Cd CG A:Asp122 4.09 Cd O A:Hoh610 3.26 interactive model: Cadmium binding site 3 out of 6 in 1c1j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1c1j. 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: Phe5, B: Tyr28, B: Cys29, B: Ser31, B: Gly32, B: Cys45, B: His48, B: Asp49, B: Bog601, B: Hoh610, conact list: Atom Atom Distance (A) Cd CE2 B:Phe5 4.80 Cd O B:Tyr28 4.69 Cd O B:Cys29 3.80 Cd C B:Cys29 4.85 Cd N B:Ser31 4.82 Cd CA B:Ser31 4.64 Cd N B:Gly32 4.89 Cd O B:Cys45 4.29 Cd CA B:Cys45 5.00 Cd O B:His48 4.94 Cd NE2 B:His48 4.60 Cd CB B:His48 4.07 Cd ND1 B:His48 2.75 Cd CD2 B:His48 4.74 Cd C B:His48 4.64 Cd CE1 B:His48 3.49 Cd CG B:His48 3.73 Cd N B:Asp49 4.55 Cd CB B:Asp49 4.95 Cd OD2 B:Asp49 2.85 Cd OD1 B:Asp49 4.48 Cd CG B:Asp49 3.91 Cd CA B:Asp49 4.80 Cd C6 B:Bog601 4.03 Cd C5 B:Bog601 4.72 Cd C4 B:Bog601 4.18 Cd O4 B:Bog601 3.63 Cd O6 B:Bog601 3.66 Cd O B:Hoh610 2.96 interactive model: Cadmium binding site 4 out of 6 in 1c1j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1c1j. 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: C: Phe5, C: Cys45, C: His48, C: Asp49, C: Hoh141, C: Hoh143, C: Hoh144, conact list: Atom Atom Distance (A) Cd CE2 C:Phe5 4.73 Cd O C:Cys45 4.21 Cd O C:His48 4.60 Cd NE2 C:His48 4.40 Cd CB C:His48 3.92 Cd ND1 C:His48 2.51 Cd CD2 C:His48 4.54 Cd C C:His48 4.38 Cd CE1 C:His48 3.27 Cd CG C:His48 3.53 Cd CA C:His48 4.81 Cd N C:Asp49 4.36 Cd CB C:Asp49 4.89 Cd OD2 C:Asp49 2.85 Cd OD1 C:Asp49 4.63 Cd CG C:Asp49 3.95 Cd CA C:Asp49 4.64 Cd O C:Hoh141 4.24 Cd O C:Hoh143 3.33 Cd O C:Hoh144 2.78 interactive model: Cadmium binding site 5 out of 6 in 1c1j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1c1j. 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: D: Phe5, D: Tyr28, D: Gly30, D: Cys45, D: His48, D: Asp49, D: Hoh136, D: Hoh147, conact list: Atom Atom Distance (A) Cd CE2 D:Phe5 4.57 Cd O D:Tyr28 4.79 Cd O D:Gly30 4.60 Cd N D:Gly30 4.72 Cd O D:Cys45 4.33 Cd O D:His48 4.83 Cd NE2 D:His48 4.38 Cd CB D:His48 3.95 Cd ND1 D:His48 2.53 Cd CD2 D:His48 4.53 Cd C D:His48 4.54 Cd CE1 D:His48 3.26 Cd CG D:His48 3.54 Cd CA D:His48 4.91 Cd N D:Asp49 4.50 Cd OD2 D:Asp49 3.04 Cd OD1 D:Asp49 4.72 Cd CG D:Asp49 4.09 Cd CA D:Asp49 4.80 Cd O D:Hoh136 2.87 Cd O D:Hoh147 2.48 interactive model: Cadmium binding site 6 out of 6 in 1c1j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 1c1j. 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: D: Phe24, D: Tyr25, D: Gly26, D: Cys27, D: Cys29, D: Ser31, D: Arg34, D: Tyr120, D: Asp122, conact list: Atom Atom Distance (A) Cd O D:Phe24 4.20 Cd C D:Phe24 4.57 Cd CA D:Phe24 4.83 Cd O D:Tyr25 4.40 Cd C D:Tyr25 4.88 Cd O D:Gly26 3.35 Cd C D:Gly26 4.19 Cd O D:Cys27 4.53 Cd N D:Cys27 4.69 Cd C D:Cys27 4.54 Cd CA D:Cys27 4.45 Cd O D:Cys29 4.04 Cd OG D:Ser31 4.53 Cd CZ D:Arg34 4.56 Cd NH2 D:Arg34 4.80 Cd NH1 D:Arg34 4.36 Cd O D:Tyr120 3.79 Cd C D:Tyr120 4.93 Cd OD2 D:Asp122 4.25 Cd OD1 D:Asp122 3.01 Cd CG D:Asp122 3.99 interactive model: