Manganese in the structure of Structure of The Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between The Active Site And the Hrdc Domain; Protein in Complex With Mn, Zn, and Amp (pdb 2hbl)

The binding sites of Manganese atom in the structure of Structure of The Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between The Active Site And the Hrdc Domain; Protein in Complex With Mn, Zn, and Amp (pdb code 2hbl). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2hbl structure was solved by S.F.MIDTGAARD, J.ASSENHOLT, A.T.JONSTRUP, L.B.VAN, T.H.JENSEN, D.E.BRODERSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.9-2.3 Space group P3121 a (A) 110.846 b (A) 110.846 c (A) 79.873 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.9 Rfree (%) 29 Manganese Binding Sites: Manganese binding site 1 out of 1 in 2hbl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2hbl. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp238, A: Leu239, A: His291, A: Asp296, A: Zn1001, A: Amp2001, A: Hoh2004, A: Hoh2005, A: Hoh2006, A: Hoh2012, A: Hoh2046, A: Hoh2077, conact list: Atom Atom Distance (A) Mn CB A:Asp238 4.55 Mn OD2 A:Asp238 3.63 Mn OD1 A:Asp238 2.19 Mn CG A:Asp238 3.25 Mn CA A:Asp238 4.79 Mn O A:Leu239 3.94 Mn N A:Leu239 4.31 Mn C A:Leu239 4.95 Mn O A:His291 4.57 Mn OD2 A:Asp296 3.62 Mn OD1 A:Asp296 3.89 Mn CG A:Asp296 4.19 Mn ZN A:Zn1001 4.47 Mn P A:Amp2001 3.06 Mn O3P A:Amp2001 4.34 Mn C5' A:Amp2001 3.94 Mn O1P A:Amp2001 2.52 Mn O5' A:Amp2001 4.01 Mn O2P A:Amp2001 2.59 Mn O A:Hoh2004 2.01 Mn O A:Hoh2005 1.92 Mn O A:Hoh2006 1.83 Mn O A:Hoh2012 4.19 Mn O A:Hoh2046 4.68 Mn O A:Hoh2077 4.82 interactive model: