Manganese in the structure of Crystal Structure of Activated Chey Bound to Xe (pdb 1zdm)

The binding sites of Manganese atom in the structure of Crystal Structure of Activated Chey Bound to Xe (pdb code 1zdm). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1zdm structure was solved by T.J.LOWERY, M.DOUCLEFF, E.J.RUIZ, S.M.RUBIN, A.PINES, D.E.WEMMER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.4 Space group P212121 a (A) 53.730 b (A) 53.820 c (A) 161.170 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.4 Rfree (%) 26.7 Manganese Binding Sites: Manganese binding site 1 out of 2 in 1zdm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1zdm. 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: Asp12, A: Asp13, A: Phe14, A: Bfd57, A: Asn59, A: Met60, A: Lys109, A: Hoh196, A: Hoh221, A: Hoh269, conact list: Atom Atom Distance (A) Mn OD2 A:Asp12 4.82 Mn OD1 A:Asp12 3.99 Mn CG A:Asp12 4.64 Mn N A:Asp13 4.42 Mn CB A:Asp13 4.46 Mn OD2 A:Asp13 3.24 Mn OD1 A:Asp13 2.19 Mn CG A:Asp13 3.06 Mn CA A:Asp13 4.97 Mn CE2 A:Phe14 4.27 Mn CD2 A:Phe14 4.00 Mn CB A:Bfd57 4.52 Mn BE A:Bfd57 3.34 Mn OD2 A:Bfd57 2.15 Mn OD1 A:Bfd57 3.62 Mn F2 A:Bfd57 4.46 Mn F3 A:Bfd57 4.10 Mn CG A:Bfd57 3.21 Mn F1 A:Bfd57 2.08 Mn O A:Asn59 2.37 Mn N A:Asn59 4.42 Mn CB A:Asn59 4.30 Mn ND2 A:Asn59 4.82 Mn C A:Asn59 3.53 Mn CG A:Asn59 4.95 Mn CA A:Asn59 4.25 Mn N A:Met60 4.60 Mn CG A:Met60 4.29 Mn CA A:Met60 4.85 Mn NZ A:Lys109 4.73 Mn O A:Hoh196 2.51 Mn O A:Hoh221 2.29 Mn O A:Hoh269 4.31 interactive model: Manganese binding site 2 out of 2 in 1zdm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1zdm. 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: B: Asp12, B: Asp13, B: Phe14, B: Bfd57, B: Asn59, B: Met60, B: Lys109, B: Hoh195, B: Hoh220, B: Hoh228, B: Hoh236, B: Hoh251, conact list: Atom Atom Distance (A) Mn OD1 B:Asp12 4.32 Mn CG B:Asp12 4.96 Mn N B:Asp13 4.72 Mn CB B:Asp13 4.55 Mn OD2 B:Asp13 3.35 Mn OD1 B:Asp13 2.31 Mn CG B:Asp13 3.17 Mn CE2 B:Phe14 4.22 Mn CD2 B:Phe14 4.00 Mn CB B:Bfd57 4.66 Mn BE B:Bfd57 3.44 Mn OD2 B:Bfd57 2.32 Mn OD1 B:Bfd57 3.78 Mn F2 B:Bfd57 4.41 Mn F3 B:Bfd57 4.30 Mn CG B:Bfd57 3.38 Mn F1 B:Bfd57 2.12 Mn O B:Asn59 2.28 Mn N B:Asn59 4.47 Mn CB B:Asn59 4.21 Mn ND2 B:Asn59 4.34 Mn C B:Asn59 3.45 Mn CG B:Asn59 4.52 Mn CA B:Asn59 4.21 Mn N B:Met60 4.50 Mn CG B:Met60 4.38 Mn CA B:Met60 4.75 Mn NZ B:Lys109 4.88 Mn O B:Hoh195 2.43 Mn O B:Hoh220 3.37 Mn O B:Hoh228 2.31 Mn O B:Hoh236 3.89 Mn O B:Hoh251 4.25 interactive model: