The binding sites of Yttrium atom in the structure of Engineered Human Lipocalin 2 in Complex With Y-Dtpa (pdb code 3dsz). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom.
The 3dsz structure was solved by A.EICHINGER, A.SKERRA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 40.0-2.0 | | Space group | P41212 | | a (A) | 82.350 | | b (A) | 82.350 | | c (A) | 115.128 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 21.3 | | Rfree (%) | 23 |
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Yttrium binding site 1 out of 2 in 3dsz
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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 3dsz. 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: Gln33, A: Liz187, A: Hoh189, A: Hoh190, A: Hoh193, | conact list:
| Atom | Atom | Distance (A) | | Y | NE2 A:Gln33 | 4.25 | | Y | O5 A:Liz187 | 2.31 | | Y | N3 A:Liz187 | 2.60 | | Y | N2 A:Liz187 | 2.52 | | Y | C18 A:Liz187 | 4.80 | | Y | C11 A:Liz187 | 3.36 | | Y | C1 A:Liz187 | 3.24 | | Y | O8 A:Liz187 | 4.33 | | Y | O1 A:Liz187 | 2.40 | | Y | O3 A:Liz187 | 2.35 | | Y | C8 A:Liz187 | 3.33 | | Y | C2 A:Liz187 | 3.38 | | Y | C6 A:Liz187 | 3.23 | | Y | O10 A:Liz187 | 4.55 | | Y | C5 A:Liz187 | 3.15 | | Y | O9 A:Liz187 | 2.51 | | Y | C25 A:Liz187 | 4.83 | | Y | C4 A:Liz187 | 3.51 | | Y | C13 A:Liz187 | 3.36 | | Y | C10 A:Liz187 | 3.35 | | Y | O7 A:Liz187 | 2.40 | | Y | O4 A:Liz187 | 4.49 | | Y | C9 A:Liz187 | 3.34 | | Y | C12 A:Liz187 | 3.35 | | Y | C14 A:Liz187 | 3.44 | | Y | N1 A:Liz187 | 2.66 | | Y | O2 A:Liz187 | 4.41 | | Y | C7 A:Liz187 | 3.19 | | Y | C3 A:Liz187 | 3.31 | | Y | C15 A:Liz187 | 4.77 | | Y | O6 A:Liz187 | 4.35 | | Y | O A:Hoh189 | 2.86 | | Y | O A:Hoh190 | 4.77 | | Y | O A:Hoh193 | 4.74 |
| interactive model:
| Yttrium binding site 2 out of 2 in 3dsz
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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 3dsz. 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: B: Gln33, B: Liz187, B: Hoh223, B: Hoh224, B: Hoh231, B: Hoh237, B: Hoh296, | conact list:
| Atom | Atom | Distance (A) | | Y | NE2 B:Gln33 | 4.52 | | Y | O5 B:Liz187 | 2.42 | | Y | N3 B:Liz187 | 2.60 | | Y | N2 B:Liz187 | 2.49 | | Y | C18 B:Liz187 | 4.79 | | Y | C11 B:Liz187 | 3.30 | | Y | C1 B:Liz187 | 3.21 | | Y | O8 B:Liz187 | 4.34 | | Y | O1 B:Liz187 | 2.36 | | Y | O3 B:Liz187 | 2.29 | | Y | C8 B:Liz187 | 3.32 | | Y | C2 B:Liz187 | 3.38 | | Y | C6 B:Liz187 | 3.22 | | Y | O10 B:Liz187 | 4.58 | | Y | C5 B:Liz187 | 3.19 | | Y | O9 B:Liz187 | 2.51 | | Y | C25 B:Liz187 | 4.77 | | Y | C4 B:Liz187 | 3.46 | | Y | C13 B:Liz187 | 3.32 | | Y | C10 B:Liz187 | 3.39 | | Y | O7 B:Liz187 | 2.46 | | Y | O4 B:Liz187 | 4.43 | | Y | C9 B:Liz187 | 3.36 | | Y | C12 B:Liz187 | 3.31 | | Y | C14 B:Liz187 | 3.41 | | Y | N1 B:Liz187 | 2.62 | | Y | O2 B:Liz187 | 4.37 | | Y | C7 B:Liz187 | 3.21 | | Y | C3 B:Liz187 | 3.24 | | Y | C15 B:Liz187 | 4.74 | | Y | O6 B:Liz187 | 4.39 | | Y | O B:Hoh223 | 2.74 | | Y | O B:Hoh224 | 4.99 | | Y | O B:Hoh231 | 4.64 | | Y | O B:Hoh237 | 4.88 | | Y | O B:Hoh296 | 4.74 |
| interactive model:
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