Manganese in the structure of A Transient Unlocked Concanavalin A Structure With MN2+ Bound in the Transition Metal Ion Binding Site S1 and An Empty Calcium Binding Site S2 (pdb 1dq4)

The binding sites of Manganese atom in the structure of A Transient Unlocked Concanavalin A Structure With MN2+ Bound in the Transition Metal Ion Binding Site S1 and An Empty Calcium Binding Site S2 (pdb code 1dq4). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1dq4 structure was solved by J.BOUCKAERT, Y.DEWALLEF, F.POORTMANS, L.WYNS, R.LORIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.9 Space group P21212 a (A) 60.890 b (A) 85.014 c (A) 91.620 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 24.6 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1dq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1dq4. 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: Glu8, A: Asp10, A: His24, A: Val32, A: Ser34, A: Hoh308, conact list: Atom Atom Distance (A) Mn OE1 A:Glu8 3.32 Mn OE2 A:Glu8 2.64 Mn CD A:Glu8 3.35 Mn CG A:Glu8 4.81 Mn CB A:Asp10 4.75 Mn OD2 A:Asp10 3.33 Mn OD1 A:Asp10 2.97 Mn CG A:Asp10 3.43 Mn NE2 A:His24 2.43 Mn ND1 A:His24 4.40 Mn CD2 A:His24 3.62 Mn CE1 A:His24 3.14 Mn CG A:His24 4.65 Mn O A:Val32 4.49 Mn OG A:Ser34 3.80 Mn O A:Hoh308 2.28 interactive model: Manganese binding site 2 out of 4 in 1dq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1dq4. 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: Lys59, A: Asp80, A: Asp82, A: Asn83, conact list: Atom Atom Distance (A) Mn NZ A:Lys59 4.35 Mn CB A:Asp80 4.57 Mn OD2 A:Asp80 2.31 Mn OD1 A:Asp80 3.29 Mn CG A:Asp80 3.15 Mn N A:Asp82 4.78 Mn CB A:Asp82 2.88 Mn OD2 A:Asp82 3.20 Mn C A:Asp82 4.67 Mn OD1 A:Asp82 4.33 Mn CG A:Asp82 3.32 Mn CA A:Asp82 4.27 Mn N A:Asn83 4.81 Mn ND2 A:Asn83 4.29 Mn OD1 A:Asn83 4.53 Mn CG A:Asn83 4.60 interactive model: Manganese binding site 3 out of 4 in 1dq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1dq4. 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: Glu8, B: Asp10, B: His24, B: Val32, B: Ser34, conact list: Atom Atom Distance (A) Mn OE1 B:Glu8 3.53 Mn OE2 B:Glu8 2.96 Mn CD B:Glu8 3.63 Mn CB B:Asp10 4.78 Mn OD2 B:Asp10 3.29 Mn OD1 B:Asp10 2.93 Mn CG B:Asp10 3.42 Mn NE2 B:His24 2.22 Mn ND1 B:His24 4.15 Mn CD2 B:His24 3.48 Mn CE1 B:His24 2.87 Mn CG B:His24 4.46 Mn O B:Val32 4.68 Mn OG B:Ser34 3.94 interactive model: Manganese binding site 4 out of 4 in 1dq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1dq4. 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: Lys59, B: Asp80, B: Asp82, B: Asn83, conact list: Atom Atom Distance (A) Mn NZ B:Lys59 4.57 Mn CB B:Asp80 4.56 Mn OD2 B:Asp80 2.25 Mn OD1 B:Asp80 3.46 Mn CG B:Asp80 3.20 Mn N B:Asp82 4.88 Mn CB B:Asp82 3.00 Mn OD2 B:Asp82 3.47 Mn C B:Asp82 4.63 Mn OD1 B:Asp82 4.59 Mn CG B:Asp82 3.56 Mn CA B:Asp82 4.34 Mn N B:Asn83 4.72 Mn ND2 B:Asn83 4.03 Mn OD1 B:Asn83 4.26 Mn CG B:Asn83 4.35 interactive model: