Manganese in the structure of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex With Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser (pdb 3cu0)

The binding sites of Manganese atom in the structure of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex With Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser (pdb code 3cu0). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3cu0 structure was solved by Y.TONE, L.C.PEDERSEN, T.YAMAMOTO, H.KITAGAWA, J.NISHIHARA-SHIMIZU, J.TAMURA, M.NEGISHI, K.SUGAHARA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 23.6-1.9 Space group P1211 a (A) 57.047 b (A) 48.399 c (A) 103.708 alpha (°) 90.00 beta (°) 92.40 gamma (°) 90.00 Rfactor (%) 21 Rfree (%) 23.4 Manganese Binding Sites: Manganese binding site 1 out of 2 in 3cu0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3cu0. 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: Asp194, A: Asp196, A: Asn197, A: His308, A: Thr309, A: Arg310, A: Udp501, A: Hoh504, A: Hoh505, A: Hoh522, A: Hoh547, conact list: Atom Atom Distance (A) Mn CB A:Asp194 4.50 Mn OD1 A:Asp194 4.43 Mn CG A:Asp194 4.96 Mn N A:Asp196 4.93 Mn CB A:Asp196 4.03 Mn OD2 A:Asp196 2.18 Mn OD1 A:Asp196 2.26 Mn CG A:Asp196 2.52 Mn CA A:Asp196 4.89 Mn OD1 A:Asn197 4.29 Mn CG A:Asn197 4.97 Mn NE2 A:His308 4.27 Mn CD2 A:His308 4.98 Mn CE1 A:His308 4.34 Mn O A:Thr309 4.35 Mn CD A:Arg310 4.92 Mn CG A:Arg310 4.19 Mn NH1 A:Arg310 4.39 Mn O3B A:Udp501 2.29 Mn PA A:Udp501 3.32 Mn O2A A:Udp501 2.27 Mn O1B A:Udp501 3.73 Mn PB A:Udp501 3.15 Mn C5' A:Udp501 4.86 Mn O5' A:Udp501 4.60 Mn O2B A:Udp501 4.46 Mn O3A A:Udp501 3.37 Mn O1A A:Udp501 4.14 Mn O A:Hoh504 2.25 Mn O A:Hoh505 2.32 Mn O A:Hoh522 4.79 Mn O A:Hoh547 4.08 interactive model: Manganese binding site 2 out of 2 in 3cu0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3cu0. 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: Asp194, B: Asp196, B: Asn197, B: His308, B: Thr309, B: Arg310, A: Udp503, A: Hoh514, B: Hoh505, B: Hoh506, B: Hoh542, conact list: Atom Atom Distance (A) Mn CB B:Asp194 4.59 Mn OD1 B:Asp194 4.51 Mn N B:Asp196 4.96 Mn CB B:Asp196 4.09 Mn OD2 B:Asp196 2.33 Mn OD1 B:Asp196 2.21 Mn CG B:Asp196 2.58 Mn CA B:Asp196 4.92 Mn OD1 B:Asn197 4.23 Mn CG B:Asn197 4.92 Mn NE2 B:His308 4.21 Mn ND1 B:His308 4.88 Mn CD2 B:His308 4.96 Mn CE1 B:His308 4.18 Mn O B:Thr309 4.33 Mn CD B:Arg310 4.93 Mn CG B:Arg310 4.20 Mn NH1 B:Arg310 3.98 Mn O3B A:Udp503 2.08 Mn PA A:Udp503 3.37 Mn O2A A:Udp503 2.33 Mn O1B A:Udp503 4.01 Mn PB A:Udp503 3.15 Mn C5' A:Udp503 4.86 Mn O5' A:Udp503 4.62 Mn O2B A:Udp503 4.33 Mn O3A A:Udp503 3.37 Mn O1A A:Udp503 4.20 Mn O A:Hoh514 4.02 Mn O B:Hoh505 2.24 Mn O B:Hoh506 2.28 Mn O B:Hoh542 4.79 interactive model: