The binding sites of Palladium atom in the structure of Crystal Structure of Fab F22-4 in Complex With A Shigella Flexneri 2A O-Ag Pentadecasaccharide (pdb code 3c6s). This binding sites where shown with 5.0 Angstroms radius around Palladium atom.
The 3c6s structure was solved by F.A.SAUL, B.VULLIEZ-LE-NORMAND, G.A.BENTLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 44.8-1.8 | | Space group | P1211 | | a (A) | 66.860 | | b (A) | 137.150 | | c (A) | 109.380 | | alpha (°) | 90.00 | | beta (°) | 94.97 | | gamma (°) | 90.00 | | Rfactor (%) | 19.1 | | Rfree (%) | 25.1 |
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Palladium binding site 1 out of 1 in 3c6s
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Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 3c6s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp1, A: Ile2, A: Val3, E: Asp1, E: Ile2, E: Lys27, E: Glu93, A: Hoh342, E: Hoh228, E: Hoh260, E: Hoh331, | conact list:
| Atom | Atom | Distance (A) | | Pd | O A:Asp1 | 2.20 | | Pd | N A:Asp1 | 2.33 | | Pd | CB A:Asp1 | 3.44 | | Pd | OD2 A:Asp1 | 4.20 | | Pd | C A:Asp1 | 2.84 | | Pd | OD1 A:Asp1 | 2.11 | | Pd | CG A:Asp1 | 3.04 | | Pd | CA A:Asp1 | 2.87 | | Pd | N A:Ile2 | 4.14 | | Pd | CA A:Ile2 | 4.89 | | Pd | CG2 A:Val3 | 4.69 | | Pd | O E:Asp1 | 2.27 | | Pd | N E:Asp1 | 2.31 | | Pd | CB E:Asp1 | 3.58 | | Pd | C E:Asp1 | 2.99 | | Pd | OD1 E:Asp1 | 4.77 | | Pd | CG E:Asp1 | 4.49 | | Pd | CA E:Asp1 | 3.05 | | Pd | N E:Ile2 | 4.28 | | Pd | CE E:Lys27 | 4.51 | | Pd | NZ E:Lys27 | 4.56 | | Pd | OE1 E:Glu93 | 4.43 | | Pd | OE2 E:Glu93 | 4.14 | | Pd | CD E:Glu93 | 4.73 | | Pd | O A:Hoh342 | 4.55 | | Pd | O E:Hoh228 | 4.30 | | Pd | O E:Hoh260 | 2.24 | | Pd | O E:Hoh331 | 4.82 |
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