Manganese in the structure of Structure Of MN2+-Bound N-Terminal Domain Of Calmodulin in the Presence of ZN2+ (pdb 3uct)

The binding sites of Manganese atom in the structure of Structure Of MN2+-Bound N-Terminal Domain Of Calmodulin in the Presence of ZN2+ (pdb code 3uct). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3uct structure was solved by F.T.SENGUEN, Z.GRABAREK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.2-1.9 Space group P1211 a (A) 36.288 b (A) 35.463 c (A) 58.343 alpha (°) 90.00 beta (°) 93.12 gamma (°) 90.00 Rfactor (%) 20.2 Rfree (%) 23.4 Manganese Binding Sites: Manganese binding site 1 out of 6 in 3uct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3uct. 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: Asp20, A: Lys21, A: Asp22, A: Gly23, A: Asp24, A: Gly25, A: Thr26, A: Ile27, A: Mn102, A: Hoh91, A: Hoh92, A: Hoh93, A: Hoh95, A: Hoh137, A: Hoh138, conact list: Atom Atom Distance (A) Mn CB A:Asp20 4.06 Mn OD2 A:Asp20 4.07 Mn C A:Asp20 4.50 Mn OD1 A:Asp20 2.08 Mn CG A:Asp20 3.21 Mn CA A:Asp20 4.07 Mn N A:Lys21 4.87 Mn N A:Asp22 4.56 Mn CB A:Asp22 4.45 Mn OD2 A:Asp22 3.28 Mn C A:Asp22 4.78 Mn OD1 A:Asp22 2.14 Mn CG A:Asp22 3.06 Mn CA A:Asp22 4.83 Mn N A:Gly23 4.63 Mn N A:Asp24 4.07 Mn CB A:Asp24 4.35 Mn OD2 A:Asp24 3.39 Mn C A:Asp24 4.73 Mn OD1 A:Asp24 2.19 Mn CG A:Asp24 3.07 Mn CA A:Asp24 4.58 Mn N A:Gly25 4.55 Mn C A:Gly25 4.92 Mn O A:Thr26 2.21 Mn N A:Thr26 3.77 Mn CB A:Thr26 4.42 Mn OG1 A:Thr26 3.59 Mn C A:Thr26 3.34 Mn CA A:Thr26 4.00 Mn N A:Ile27 4.42 Mn CA A:Ile27 4.71 Mn MN A:Mn102 3.38 Mn O A:Hoh91 2.24 Mn O A:Hoh92 2.12 Mn O A:Hoh93 4.64 Mn O A:Hoh95 4.51 Mn O A:Hoh137 4.62 Mn O A:Hoh138 4.46 interactive model: Manganese binding site 2 out of 6 in 3uct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3uct. 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: Asp56, A: Asp58, A: Gly59, A: Asn60, A: Gly61, A: Thr62, A: Ile63, A: Glu67, A: Hoh106, A: Hoh119, A: Hoh120, A: Hoh123, conact list: Atom Atom Distance (A) Mn CB A:Asp56 4.22 Mn OD2 A:Asp56 3.96 Mn C A:Asp56 4.78 Mn OD1 A:Asp56 2.20 Mn CG A:Asp56 3.25 Mn CA A:Asp56 4.22 Mn N A:Asp58 4.70 Mn CB A:Asp58 4.54 Mn OD2 A:Asp58 3.41 Mn C A:Asp58 4.87 Mn OD1 A:Asp58 2.20 Mn CG A:Asp58 3.15 Mn CA A:Asp58 4.90 Mn N A:Gly59 4.46 Mn N A:Asn60 4.14 Mn CB A:Asn60 4.36 Mn ND2 A:Asn60 3.50 Mn C A:Asn60 4.71 Mn OD1 A:Asn60 2.19 Mn CG A:Asn60 3.09 Mn CA A:Asn60 4.61 Mn N A:Gly61 4.42 Mn C A:Gly61 4.85 Mn O A:Thr62 2.20 Mn N A:Thr62 3.74 Mn CB A:Thr62 4.59 Mn OG1 A:Thr62 3.86 Mn C A:Thr62 3.34 Mn CA A:Thr62 4.03 Mn N A:Ile63 4.42 Mn CD1 A:Ile63 4.76 Mn CA A:Ile63 4.77 Mn OE1 A:Glu67 4.91 Mn O A:Hoh106 2.19 Mn O A:Hoh119 4.11 Mn O A:Hoh120 4.07 Mn O A:Hoh123 2.18 interactive model: Manganese binding site 3 out of 6 in 3uct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3uct. 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: Asp22, A: Asp24, A: Thr26, A: Mn100, A: Hoh91, A: Hoh92, A: Hoh137, A: Hoh138, conact list: Atom Atom Distance (A) Mn CB A:Asp22 4.45 Mn OD2 A:Asp22 2.08 Mn OD1 A:Asp22 3.58 Mn CG A:Asp22 3.16 Mn CB A:Asp24 4.49 Mn OD2 A:Asp24 2.14 Mn OD1 A:Asp24 3.48 Mn CG A:Asp24 3.15 Mn O A:Thr26 4.81 Mn OG1 A:Thr26 3.88 Mn MN A:Mn100 3.38 Mn O A:Hoh91 4.40 Mn O A:Hoh92 2.27 Mn O A:Hoh137 2.14 Mn O A:Hoh138 2.20 interactive model: Manganese binding site 4 out of 6 in 3uct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3uct. 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: Phe19, A: Asp20, A: Lys21, A: Glu31, A: Hoh91, A: Hoh93, A: Hoh94, A: Hoh95, A: Hoh114, A: Hoh130, conact list: Atom Atom Distance (A) Mn O A:Phe19 2.22 Mn CB A:Phe19 4.14 Mn C A:Phe19 3.20 Mn CA A:Phe19 3.84 Mn N A:Asp20 4.22 Mn C A:Asp20 4.99 Mn CA A:Asp20 4.57 Mn N A:Lys21 4.29 Mn CB A:Lys21 4.89 Mn CG A:Lys21 4.74 Mn OE1 A:Glu31 3.44 Mn OE2 A:Glu31 2.14 Mn CD A:Glu31 3.13 Mn CG A:Glu31 4.50 Mn O A:Hoh91 4.03 Mn O A:Hoh93 2.25 Mn O A:Hoh94 2.21 Mn O A:Hoh95 4.41 Mn O A:Hoh114 2.22 Mn O A:Hoh130 4.37 interactive model: Manganese binding site 5 out of 6 in 3uct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3uct. 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: Glu45, B: Asp20, B: Lys21, B: Asp22, B: Gly23, B: Asp24, B: Gly25, B: Thr26, B: Ile27, B: Glu31, B: Zn102, A: Hoh110, B: Hoh85, B: Hoh92, conact list: Atom Atom Distance (A) Mn OE2 A:Glu45 4.25 Mn O B:Asp20 4.86 Mn CB B:Asp20 4.08 Mn OD2 B:Asp20 3.89 Mn C B:Asp20 4.34 Mn OD1 B:Asp20 2.06 Mn CG B:Asp20 3.14 Mn CA B:Asp20 4.07 Mn N B:Lys21 4.56 Mn N B:Asp22 4.34 Mn CB B:Asp22 4.51 Mn OD2 B:Asp22 3.57 Mn C B:Asp22 4.66 Mn OD1 B:Asp22 2.17 Mn CG B:Asp22 3.20 Mn CA B:Asp22 4.71 Mn N B:Gly23 4.35 Mn N B:Asp24 4.00 Mn CB B:Asp24 4.43 Mn OD2 B:Asp24 3.58 Mn C B:Asp24 4.79 Mn OD1 B:Asp24 2.14 Mn CG B:Asp24 3.16 Mn CA B:Asp24 4.59 Mn N B:Gly25 4.51 Mn C B:Gly25 4.97 Mn O B:Thr26 2.14 Mn N B:Thr26 3.85 Mn CB B:Thr26 4.56 Mn OG1 B:Thr26 3.87 Mn C B:Thr26 3.19 Mn CA B:Thr26 4.01 Mn N B:Ile27 4.13 Mn CA B:Ile27 4.24 Mn OE1 B:Glu31 4.62 Mn ZN B:Zn102 3.35 Mn O A:Hoh110 2.18 Mn O B:Hoh85 2.15 Mn O B:Hoh92 4.55 interactive model: Manganese binding site 6 out of 6 in 3uct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3uct. 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: Asp56, B: Ala57, B: Asp58, B: Gly59, B: Asn60, B: Gly61, B: Thr62, B: Ile63, B: Glu67, B: Hoh88, B: Hoh89, B: Hoh93, B: Hoh94, conact list: Atom Atom Distance (A) Mn CB B:Asp56 4.30 Mn OD2 B:Asp56 4.11 Mn C B:Asp56 4.58 Mn OD1 B:Asp56 2.16 Mn CG B:Asp56 3.34 Mn CA B:Asp56 4.12 Mn N B:Ala57 4.74 Mn N B:Asp58 4.46 Mn CB B:Asp58 4.55 Mn OD2 B:Asp58 3.59 Mn C B:Asp58 4.72 Mn OD1 B:Asp58 2.17 Mn CG B:Asp58 3.21 Mn CA B:Asp58 4.78 Mn N B:Gly59 4.50 Mn N B:Asn60 4.05 Mn CB B:Asn60 4.35 Mn ND2 B:Asn60 3.52 Mn C B:Asn60 4.86 Mn OD1 B:Asn60 2.17 Mn CG B:Asn60 3.09 Mn CA B:Asn60 4.61 Mn N B:Gly61 4.68 Mn O B:Thr62 2.22 Mn N B:Thr62 3.94 Mn CB B:Thr62 4.63 Mn OG1 B:Thr62 3.82 Mn C B:Thr62 3.39 Mn CA B:Thr62 4.15 Mn N B:Ile63 4.39 Mn CG2 B:Ile63 4.97 Mn CA B:Ile63 4.55 Mn OE1 B:Glu67 4.61 Mn O B:Hoh88 2.19 Mn O B:Hoh89 2.20 Mn O B:Hoh93 4.12 Mn O B:Hoh94 3.99 interactive model: