Manganese in the structure of Crystal Structure of Lactose Synthase Complex With Udp and Manganese (pdb 1nkh)

The binding sites of Manganese atom in the structure of Crystal Structure of Lactose Synthase Complex With Udp and Manganese (pdb code 1nkh). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1nkh structure was solved by B.RAMAKRISHNAN, P.K.QASBA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.7-2.0 Space group P1211 a (A) 55.469 b (A) 99.145 c (A) 102.261 alpha (°) 90.00 beta (°) 104.14 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 25.1 Manganese Binding Sites: Manganese binding site 1 out of 2 in 1nkh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1nkh. 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: Arg191, B: Asp252, B: Asp254, B: Met344, B: His347, B: Udp809, B: Hoh908, B: Hoh959, conact list: Atom Atom Distance (A) Mn CZ B:Arg191 4.97 Mn NH2 B:Arg191 4.39 Mn NH1 B:Arg191 4.52 Mn OD2 B:Asp252 4.99 Mn CB B:Asp254 4.59 Mn OD2 B:Asp254 2.27 Mn OD1 B:Asp254 3.51 Mn CG B:Asp254 3.23 Mn CE B:Met344 2.96 Mn CG B:Met344 3.80 Mn SD B:Met344 2.84 Mn NE2 B:His347 2.27 Mn ND1 B:His347 4.28 Mn CD2 B:His347 3.38 Mn CE1 B:His347 3.09 Mn CG B:His347 4.45 Mn O3B B:Udp809 4.47 Mn C3' B:Udp809 4.71 Mn PA B:Udp809 3.28 Mn O2A B:Udp809 4.11 Mn O1B B:Udp809 3.96 Mn PB B:Udp809 3.35 Mn O3' B:Udp809 3.95 Mn C5' B:Udp809 4.70 Mn O5' B:Udp809 4.45 Mn O2B B:Udp809 2.29 Mn O3A B:Udp809 3.31 Mn O1A B:Udp809 2.23 Mn O B:Hoh908 2.15 Mn O B:Hoh959 3.86 interactive model: Manganese binding site 2 out of 2 in 1nkh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1nkh. 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: D: Arg191, D: Asp254, D: Met344, D: His347, D: Udp810, D: Hoh902, D: Hoh919, conact list: Atom Atom Distance (A) Mn CZ D:Arg191 4.90 Mn NH2 D:Arg191 4.14 Mn NH1 D:Arg191 4.66 Mn CB D:Asp254 4.40 Mn OD2 D:Asp254 2.07 Mn OD1 D:Asp254 3.43 Mn CG D:Asp254 3.08 Mn CE D:Met344 3.41 Mn CG D:Met344 3.85 Mn SD D:Met344 2.80 Mn NE2 D:His347 2.38 Mn ND1 D:His347 4.44 Mn CD2 D:His347 3.39 Mn CE1 D:His347 3.30 Mn CG D:His347 4.52 Mn O3B D:Udp810 4.53 Mn C3' D:Udp810 4.69 Mn PA D:Udp810 3.24 Mn O2A D:Udp810 4.04 Mn O1B D:Udp810 3.84 Mn PB D:Udp810 3.36 Mn O3' D:Udp810 3.90 Mn C5' D:Udp810 4.64 Mn O5' D:Udp810 4.40 Mn O2B D:Udp810 2.27 Mn O3A D:Udp810 3.39 Mn O1A D:Udp810 2.15 Mn O D:Hoh902 2.30 Mn O D:Hoh919 3.82 interactive model: