The binding sites of Yttrium atom in the structure of W. Succinogenes Nrfa Y218F Nitrite Complex (pdb code 3bnh). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom.
The 3bnh structure was solved by P.LUKAT, O.EINSLE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 29.5-1.8 | | Space group | I4122 | | a (A) | 120.768 | | b (A) | 120.768 | | c (A) | 186.466 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 17.7 | | Rfree (%) | 21.5 |
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Yttrium binding site 1 out of 3 in 3bnh
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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 3bnh. 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: Glu45, A: Glu52, A: Arg55, A: Act2, A: Hoh535, A: Hoh669, A: Hoh792, A: Hoh793, A: Hoh794, A: Hoh797, A: Hoh831, A: Hoh832, | conact list:
| Atom | Atom | Distance (A) | | Y | O A:Glu45 | 4.53 | | Y | O A:Glu52 | 4.49 | | Y | OE1 A:Glu52 | 2.33 | | Y | CB A:Glu52 | 4.79 | | Y | OE2 A:Glu52 | 3.87 | | Y | CD A:Glu52 | 3.44 | | Y | CG A:Glu52 | 4.70 | | Y | CA A:Glu52 | 4.83 | | Y | CD A:Arg55 | 4.42 | | Y | NH1 A:Arg55 | 4.73 | | Y | O A:Act2 | 3.97 | | Y | C A:Act2 | 4.77 | | Y | OXT A:Act2 | 4.65 | | Y | O A:Hoh535 | 4.90 | | Y | O A:Hoh669 | 2.46 | | Y | O A:Hoh792 | 2.39 | | Y | O A:Hoh793 | 2.56 | | Y | O A:Hoh794 | 2.41 | | Y | O A:Hoh797 | 2.51 | | Y | O A:Hoh831 | 4.35 | | Y | O A:Hoh832 | 4.35 |
| interactive model:
| Yttrium binding site 2 out of 3 in 3bnh
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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 3bnh. 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: Ala98, A: Pro99, A: Arg100, A: Hem512, A: Hem513, A: Hoh725, A: Hoh800, A: Hoh962, A: Hoh1000, A: Hoh1087, A: Hoh1124, | conact list:
| Atom | Atom | Distance (A) | | Y | C A:Ala98 | 4.80 | | Y | CB A:Ala98 | 4.49 | | Y | O A:Pro99 | 2.45 | | Y | N A:Pro99 | 4.26 | | Y | CB A:Pro99 | 4.52 | | Y | CD A:Pro99 | 4.18 | | Y | C A:Pro99 | 3.57 | | Y | CG A:Pro99 | 4.68 | | Y | CA A:Pro99 | 4.37 | | Y | N A:Arg100 | 4.52 | | Y | CA A:Arg100 | 4.52 | | Y | CGA A:Hem512 | 4.22 | | Y | CAA A:Hem512 | 4.81 | | Y | O2A A:Hem512 | 4.97 | | Y | O1A A:Hem512 | 3.00 | | Y | CBA A:Hem513 | 4.78 | | Y | CGA A:Hem513 | 3.45 | | Y | O2A A:Hem513 | 3.75 | | Y | O1A A:Hem513 | 2.42 | | Y | O A:Hoh725 | 2.70 | | Y | O A:Hoh800 | 3.01 | | Y | O A:Hoh962 | 3.95 | | Y | O A:Hoh1000 | 4.17 | | Y | O A:Hoh1087 | 4.00 | | Y | O A:Hoh1124 | 3.45 |
| interactive model:
| Yttrium binding site 3 out of 3 in 3bnh
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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 3bnh. 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: Lys344, A: Pro407, A: Glu408, A: So4509, A: Hem514, | conact list:
| Atom | Atom | Distance (A) | | Y | NZ A:Lys344 | 4.47 | | Y | CB A:Pro407 | 4.78 | | Y | CD A:Pro407 | 4.87 | | Y | CG A:Pro407 | 4.68 | | Y | OE1 A:Glu408 | 4.24 | | Y | CB A:Glu408 | 4.96 | | Y | OE2 A:Glu408 | 2.23 | | Y | CD A:Glu408 | 3.29 | | Y | CG A:Glu408 | 3.90 | | Y | S A:So4509 | 3.13 | | Y | O1 A:So4509 | 2.75 | | Y | O2 A:So4509 | 4.24 | | Y | O4 A:So4509 | 4.04 | | Y | O3 A:So4509 | 2.26 | | Y | CBA A:Hem514 | 4.12 | | Y | CGA A:Hem514 | 3.36 | | Y | O2A A:Hem514 | 4.11 | | Y | O1A A:Hem514 | 2.49 |
| interactive model:
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