The binding sites of Yttrium atom in the structure of Crystal Structure of B/Perth Neuraminidase D197E Mutant in Complex With Peramivir (pdb code 3k39). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom.
The 3k39 structure was solved by A.J.OAKLEY, J.L.MCKIMM-BRESCHKIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 55.9-2.5 | | Space group | P1 | | a (A) | 111.964 | | b (A) | 124.874 | | c (A) | 125.245 | | alpha (°) | 90.03 | | beta (°) | 92.11 | | gamma (°) | 91.27 | | Rfactor (%) | 19.8 | | Rfree (%) | 21.4 |
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Yttrium binding site 1 out of 4 in 3k39
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Yttrium in the PDB 3k39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu168, B: Glu168, C: Glu168, D: Glu168, C: Hoh2007, C: Hoh2013, C: Hoh2014, C: Hoh2017, | conact list:
| Atom | Atom | Distance (A) | | Y | OE1 A:Glu168 | 2.10 | | Y | CB A:Glu168 | 4.67 | | Y | OE2 A:Glu168 | 3.91 | | Y | CD A:Glu168 | 3.29 | | Y | CG A:Glu168 | 4.45 | | Y | OE1 B:Glu168 | 2.22 | | Y | CB B:Glu168 | 4.72 | | Y | OE2 B:Glu168 | 4.00 | | Y | CD B:Glu168 | 3.39 | | Y | CG B:Glu168 | 4.53 | | Y | OE1 C:Glu168 | 2.19 | | Y | CB C:Glu168 | 4.73 | | Y | OE2 C:Glu168 | 3.97 | | Y | CD C:Glu168 | 3.38 | | Y | CG C:Glu168 | 4.54 | | Y | OE1 D:Glu168 | 2.18 | | Y | CB D:Glu168 | 4.70 | | Y | OE2 D:Glu168 | 3.89 | | Y | CD D:Glu168 | 3.33 | | Y | CG D:Glu168 | 4.50 | | Y | O C:Hoh2007 | 2.16 | | Y | O C:Hoh2013 | 2.20 | | Y | O C:Hoh2014 | 2.29 | | Y | O C:Hoh2017 | 2.12 |
| interactive model:
| Yttrium binding site 2 out of 4 in 3k39
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Yttrium in the PDB 3k39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: Glu168, F: Glu168, G: Glu168, H: Glu168, E: Hoh2007, E: Hoh2068, E: Hoh2069, E: Hoh2070, | conact list:
| Atom | Atom | Distance (A) | | Y | OE1 E:Glu168 | 2.21 | | Y | CB E:Glu168 | 4.81 | | Y | OE2 E:Glu168 | 3.93 | | Y | CD E:Glu168 | 3.37 | | Y | CG E:Glu168 | 4.55 | | Y | OE1 F:Glu168 | 2.26 | | Y | CB F:Glu168 | 4.77 | | Y | OE2 F:Glu168 | 4.07 | | Y | CD F:Glu168 | 3.47 | | Y | CG F:Glu168 | 4.62 | | Y | OE1 G:Glu168 | 2.24 | | Y | CB G:Glu168 | 4.76 | | Y | OE2 G:Glu168 | 3.98 | | Y | CD G:Glu168 | 3.40 | | Y | CG G:Glu168 | 4.54 | | Y | OE1 H:Glu168 | 2.23 | | Y | CB H:Glu168 | 4.75 | | Y | OE2 H:Glu168 | 4.05 | | Y | CD H:Glu168 | 3.42 | | Y | CG H:Glu168 | 4.58 | | Y | O E:Hoh2007 | 2.45 | | Y | O E:Hoh2068 | 2.32 | | Y | O E:Hoh2069 | 2.32 | | Y | O E:Hoh2070 | 2.26 |
| interactive model:
| Yttrium binding site 3 out of 4 in 3k39
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Yttrium in the PDB 3k39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: I: Glu168, J: Glu168, K: Glu168, L: Glu168, J: Hoh2007, L: Hoh2007, L: Hoh2013, L: Hoh2014, | conact list:
| Atom | Atom | Distance (A) | | Y | OE1 I:Glu168 | 2.18 | | Y | CB I:Glu168 | 4.72 | | Y | OE2 I:Glu168 | 3.92 | | Y | CD I:Glu168 | 3.34 | | Y | CG I:Glu168 | 4.50 | | Y | OE1 J:Glu168 | 2.17 | | Y | CB J:Glu168 | 4.73 | | Y | OE2 J:Glu168 | 4.02 | | Y | CD J:Glu168 | 3.38 | | Y | CG J:Glu168 | 4.52 | | Y | OE1 K:Glu168 | 2.23 | | Y | CB K:Glu168 | 4.74 | | Y | OE2 K:Glu168 | 3.94 | | Y | CD K:Glu168 | 3.38 | | Y | CG K:Glu168 | 4.56 | | Y | OE1 L:Glu168 | 2.21 | | Y | CB L:Glu168 | 4.82 | | Y | OE2 L:Glu168 | 4.04 | | Y | CD L:Glu168 | 3.43 | | Y | CG L:Glu168 | 4.61 | | Y | O J:Hoh2007 | 2.36 | | Y | O L:Hoh2007 | 2.20 | | Y | O L:Hoh2013 | 2.23 | | Y | O L:Hoh2014 | 2.23 |
| interactive model:
| Yttrium binding site 4 out of 4 in 3k39
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Yttrium in the PDB 3k39. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: M: Glu168, N: Glu168, O: Glu168, P: Glu168, O: Hoh2007, O: Hoh2013, O: Hoh2014, O: Hoh2017, | conact list:
| Atom | Atom | Distance (A) | | Y | OE1 M:Glu168 | 2.21 | | Y | CB M:Glu168 | 4.73 | | Y | OE2 M:Glu168 | 3.98 | | Y | CD M:Glu168 | 3.40 | | Y | CG M:Glu168 | 4.55 | | Y | OE1 N:Glu168 | 2.28 | | Y | CB N:Glu168 | 4.79 | | Y | OE2 N:Glu168 | 4.04 | | Y | CD N:Glu168 | 3.44 | | Y | CG N:Glu168 | 4.61 | | Y | OE1 O:Glu168 | 2.18 | | Y | CB O:Glu168 | 4.82 | | Y | OE2 O:Glu168 | 4.01 | | Y | CD O:Glu168 | 3.40 | | Y | CG O:Glu168 | 4.57 | | Y | OE1 P:Glu168 | 2.24 | | Y | CB P:Glu168 | 4.71 | | Y | OE2 P:Glu168 | 4.02 | | Y | CD P:Glu168 | 3.42 | | Y | CG P:Glu168 | 4.56 | | Y | O O:Hoh2007 | 2.29 | | Y | O O:Hoh2013 | 2.28 | | Y | O O:Hoh2014 | 2.45 | | Y | O O:Hoh2017 | 2.28 |
| interactive model:
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