Cadmium in the structure of Structure of Streptococcal Pyrogenic Exotoxin A (pdb 1fnv)

The binding sites of Cadmium atom in the structure of Structure of Streptococcal Pyrogenic Exotoxin A (pdb code 1fnv). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1fnv structure was solved by C.A.EARHART, G.M.VATH, M.ROGGIANI, P.M.SCHLIEVERT, D.H.OHLENDORF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.6 Space group P21212 a (A) 105.480 b (A) 130.710 c (A) 84.520 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.3 Rfree (%) 30.4 Cadmium Binding Sites: Cadmium binding site 1 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1fnv. 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: Lys57, A: Cys90, A: Ala93, A: Cd223, C: Cd224, A: Cd225, conact list: Atom Atom Distance (A) Cd CE A:Lys57 4.82 Cd CB A:Cys90 3.16 Cd SG A:Cys90 3.30 Cd CA A:Cys90 4.67 Cd CB A:Ala93 4.69 Cd CD A:Cd223 3.53 Cd CD C:Cd224 4.31 Cd CD A:Cd225 4.26 interactive model: Cadmium binding site 2 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1fnv. 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: Asp39, A: Cys90, A: Cd222, C: Cd224, A: Cd225, conact list: Atom Atom Distance (A) Cd CB A:Asp39 3.93 Cd OD2 A:Asp39 2.51 Cd OD1 A:Asp39 4.25 Cd CG A:Asp39 3.38 Cd CB A:Cys90 4.97 Cd SG A:Cys90 4.36 Cd CD A:Cd222 3.53 Cd CD C:Cd224 3.59 Cd CD A:Cd225 3.14 interactive model: Cadmium binding site 3 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1fnv. 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: Asp39, A: Leu89, A: Cys90, A: Glu91, C: Glu691, A: Cd222, A: Cd223, A: Cd225, conact list: Atom Atom Distance (A) Cd OD2 A:Asp39 4.26 Cd O A:Leu89 4.56 Cd CB A:Cys90 3.17 Cd SG A:Cys90 2.00 Cd C A:Cys90 4.81 Cd CA A:Cys90 3.88 Cd N A:Glu91 4.69 Cd OE1 C:Glu691 2.85 Cd OE2 C:Glu691 1.97 Cd CD C:Glu691 2.75 Cd CG C:Glu691 4.22 Cd CD A:Cd222 4.31 Cd CD A:Cd223 3.59 Cd CD A:Cd225 4.36 interactive model: Cadmium binding site 4 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1fnv. 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: Cys90, A: Cd222, A: Cd223, C: Cd224, conact list: Atom Atom Distance (A) Cd SG A:Cys90 4.58 Cd CD A:Cd222 4.26 Cd CD A:Cd223 3.14 Cd CD C:Cd224 4.36 interactive model: Cadmium binding site 5 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1fnv. 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: Cys390, B: Ala393, B: Cd523, B: Cd524, B: Cd525, conact list: Atom Atom Distance (A) Cd CB B:Cys390 3.23 Cd SG B:Cys390 3.33 Cd CA B:Cys390 4.75 Cd CB B:Ala393 4.97 Cd CD B:Cd523 3.84 Cd CD B:Cd524 4.40 Cd CD B:Cd525 4.11 interactive model: Cadmium binding site 6 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 1fnv. 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: Asp339, B: Cys390, B: Cd522, B: Cd524, B: Cd525, conact list: Atom Atom Distance (A) Cd CB B:Asp339 3.74 Cd OD2 B:Asp339 2.18 Cd OD1 B:Asp339 3.74 Cd CG B:Asp339 2.99 Cd SG B:Cys390 4.18 Cd CD B:Cd522 3.84 Cd CD B:Cd524 3.86 Cd CD B:Cd525 3.59 interactive model: Cadmium binding site 7 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 1fnv. 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: Asp339, B: Leu389, B: Cys390, B: Glu391, D: Glu991, B: Cd522, B: Cd523, B: Cd525, conact list: Atom Atom Distance (A) Cd OD2 B:Asp339 4.51 Cd O B:Leu389 4.64 Cd CB B:Cys390 3.30 Cd SG B:Cys390 1.56 Cd C B:Cys390 4.81 Cd CA B:Cys390 3.98 Cd N B:Glu391 4.54 Cd OE1 D:Glu991 2.41 Cd OE2 D:Glu991 1.90 Cd CD D:Glu991 2.45 Cd CG D:Glu991 3.96 Cd CD B:Cd522 4.40 Cd CD B:Cd523 3.86 Cd CD B:Cd525 4.55 interactive model: Cadmium binding site 8 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 1fnv. 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: Cys390, B: Cd522, B: Cd523, B: Cd524, conact list: Atom Atom Distance (A) Cd SG B:Cys390 4.77 Cd CD B:Cd522 4.11 Cd CD B:Cd523 3.59 Cd CD B:Cd524 4.55 interactive model: Cadmium binding site 9 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 1fnv. 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: Lys657, C: Cys690, C: Ala693, C: Cd823, C: Cd824, C: Cd825, conact list: Atom Atom Distance (A) Cd CE C:Lys657 4.69 Cd CB C:Cys690 3.06 Cd SG C:Cys690 3.18 Cd CA C:Cys690 4.58 Cd CB C:Ala693 4.97 Cd CD C:Cd823 3.67 Cd CD C:Cd824 4.23 Cd CD C:Cd825 3.63 interactive model: Cadmium binding site 10 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 1fnv. 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: Asp639, C: Cys690, C: Cd822, C: Cd824, C: Cd825, conact list: Atom Atom Distance (A) Cd CB C:Asp639 3.78 Cd OD2 C:Asp639 2.22 Cd OD1 C:Asp639 4.15 Cd CG C:Asp639 3.20 Cd SG C:Cys690 4.25 Cd CD C:Cd822 3.67 Cd CD C:Cd824 3.91 Cd CD C:Cd825 2.89 interactive model: Cadmium binding site 11 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 1fnv. 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: Glu91, C: Asp639, C: Leu689, C: Cys690, C: Glu691, C: Cd822, C: Cd823, C: Cd825, conact list: Atom Atom Distance (A) Cd OE1 A:Glu91 2.49 Cd OE2 A:Glu91 1.83 Cd CD A:Glu91 2.46 Cd CG A:Glu91 3.95 Cd OD2 C:Asp639 4.76 Cd O C:Leu689 4.72 Cd N C:Cys690 4.98 Cd CB C:Cys690 3.07 Cd SG C:Cys690 1.53 Cd C C:Cys690 4.64 Cd CA C:Cys690 3.78 Cd N C:Glu691 4.44 Cd CD C:Cd822 4.23 Cd CD C:Cd823 3.91 Cd CD C:Cd825 3.81 interactive model: Cadmium binding site 12 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 1fnv. 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: Asp639, C: Cys690, C: Cd822, C: Cd823, C: Cd824, conact list: Atom Atom Distance (A) Cd OD2 C:Asp639 4.71 Cd SG C:Cys690 3.84 Cd CD C:Cd822 3.63 Cd CD C:Cd823 2.89 Cd CD C:Cd824 3.81 interactive model: Cadmium binding site 13 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Cadmium in the PDB 1fnv. 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: Cys990, D: Cd1123, D: Cd1124, D: Cd1125, conact list: Atom Atom Distance (A) Cd CB D:Cys990 3.19 Cd SG D:Cys990 3.31 Cd CA D:Cys990 4.71 Cd CD D:Cd1123 3.78 Cd CD D:Cd1124 4.26 Cd CD D:Cd1125 3.80 interactive model: Cadmium binding site 14 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Cadmium in the PDB 1fnv. 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: Asp939, D: Cys990, D: Cd1122, D: Cd1124, D: Cd1125, conact list: Atom Atom Distance (A) Cd CB D:Asp939 3.93 Cd OD2 D:Asp939 2.48 Cd OD1 D:Asp939 4.12 Cd CG D:Asp939 3.30 Cd SG D:Cys990 4.31 Cd CD D:Cd1122 3.78 Cd CD D:Cd1124 3.99 Cd CD D:Cd1125 3.10 interactive model: Cadmium binding site 15 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Cadmium in the PDB 1fnv. 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: Glu391, D: Asp939, D: Leu989, D: Cys990, D: Glu991, D: Cd1122, D: Cd1123, D: Cd1125, conact list: Atom Atom Distance (A) Cd OE1 B:Glu391 2.39 Cd CB B:Glu391 4.96 Cd OE2 B:Glu391 1.90 Cd CD B:Glu391 2.46 Cd CG B:Glu391 3.98 Cd OD2 D:Asp939 4.79 Cd O D:Leu989 4.52 Cd CB D:Cys990 3.11 Cd SG D:Cys990 1.39 Cd C D:Cys990 4.70 Cd CA D:Cys990 3.86 Cd N D:Glu991 4.49 Cd CD D:Cd1122 4.26 Cd CD D:Cd1123 3.99 Cd CD D:Cd1125 4.13 interactive model: Cadmium binding site 16 out of 16 in 1fnv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Cadmium in the PDB 1fnv. 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: Cys990, D: Cd1122, D: Cd1123, D: Cd1124, conact list: Atom Atom Distance (A) Cd SG D:Cys990 4.25 Cd CD D:Cd1122 3.80 Cd CD D:Cd1123 3.10 Cd CD D:Cd1124 4.13 interactive model: