Manganese in the structure of Sgrai With Cognate Dna and Manganese Bound (pdb 3dw9)

The binding sites of Manganese atom in the structure of Sgrai With Cognate Dna and Manganese Bound (pdb code 3dw9). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3dw9 structure was solved by P.W.DUNTEN, N.C.HORTON, E.J.LITTLE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 58.6-2.2 Space group P1211 a (A) 58.261 b (A) 117.101 c (A) 63.702 alpha (°) 90.00 beta (°) 112.96 gamma (°) 90.00 Rfactor (%) 17.4 Rfree (%) 24 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3dw9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3dw9. 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: Glu103, A: Asp188, A: Ala240, A: Phe241, A: Lys242, F: Da7, F: Dc8, F: Dc9, A: Hoh342, A: Hoh346, A: Hoh347, A: Hoh348, A: Hoh359, A: Hoh365, conact list: Atom Atom Distance (A) Mn OE2 A:Glu103 4.19 Mn CB A:Asp188 4.45 Mn OD2 A:Asp188 2.24 Mn OD1 A:Asp188 3.26 Mn CG A:Asp188 3.08 Mn C A:Ala240 4.70 Mn CA A:Ala240 4.95 Mn O A:Phe241 2.08 Mn N A:Phe241 3.82 Mn CB A:Phe241 4.25 Mn C A:Phe241 3.27 Mn CA A:Phe241 3.96 Mn N A:Lys242 4.37 Mn CG A:Lys242 4.57 Mn CA A:Lys242 4.75 Mn O3' F:Da7 4.51 Mn OP1 F:Dc8 2.26 Mn P F:Dc8 3.33 Mn OP2 F:Dc8 3.94 Mn C5' F:Dc8 4.06 Mn O5' F:Dc8 3.87 Mn OP2 F:Dc9 4.38 Mn O A:Hoh342 4.25 Mn O A:Hoh346 4.28 Mn O A:Hoh347 2.18 Mn O A:Hoh348 2.22 Mn O A:Hoh359 3.99 Mn O A:Hoh365 2.16 interactive model: Manganese binding site 2 out of 4 in 3dw9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3dw9. 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: Glu103, A: Asn149, A: Leu150, A: Pro151, A: Asp188, A: Leu189, A: Hoh345, A: Hoh346, conact list: Atom Atom Distance (A) Mn OE1 A:Glu103 2.02 Mn OE2 A:Glu103 3.95 Mn CD A:Glu103 3.23 Mn CG A:Glu103 4.21 Mn O A:Asn149 4.72 Mn CB A:Asn149 4.55 Mn ND2 A:Asn149 4.20 Mn C A:Asn149 4.00 Mn OD1 A:Asn149 2.27 Mn CG A:Asn149 3.46 Mn CA A:Asn149 4.45 Mn O A:Leu150 2.11 Mn N A:Leu150 3.40 Mn CB A:Leu150 4.46 Mn C A:Leu150 3.18 Mn CA A:Leu150 3.78 Mn N A:Pro151 4.31 Mn C A:Pro151 4.91 Mn CA A:Pro151 4.60 Mn O A:Asp188 2.54 Mn CB A:Asp188 3.99 Mn C A:Asp188 3.47 Mn CG A:Asp188 4.91 Mn CA A:Asp188 3.71 Mn N A:Leu189 4.73 Mn O A:Hoh345 2.52 Mn O A:Hoh346 3.75 interactive model: Manganese binding site 3 out of 4 in 3dw9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3dw9. 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: Glu103, B: Asp188, B: Ala240, B: Phe241, B: Lys242, E: Da7, E: Dc8, E: Dc9, E: Hoh20, E: Hoh21, E: Hoh38, B: Hoh344, B: Hoh347, B: Hoh357, conact list: Atom Atom Distance (A) Mn OE1 B:Glu103 4.01 Mn CD B:Glu103 4.91 Mn CB B:Asp188 4.35 Mn OD2 B:Asp188 3.25 Mn OD1 B:Asp188 2.06 Mn CG B:Asp188 2.98 Mn C B:Ala240 4.64 Mn CA B:Ala240 4.96 Mn O B:Phe241 2.10 Mn N B:Phe241 3.74 Mn CB B:Phe241 4.29 Mn C B:Phe241 3.30 Mn CA B:Phe241 3.97 Mn N B:Lys242 4.40 Mn CG B:Lys242 4.54 Mn CA B:Lys242 4.77 Mn O3' E:Da7 4.48 Mn OP1 E:Dc8 2.11 Mn P E:Dc8 3.26 Mn OP2 E:Dc8 3.92 Mn C5' E:Dc8 3.81 Mn O5' E:Dc8 3.79 Mn OP2 E:Dc9 4.47 Mn O E:Hoh20 4.18 Mn O E:Hoh21 3.92 Mn O E:Hoh38 2.16 Mn O B:Hoh344 4.09 Mn O B:Hoh347 2.33 Mn O B:Hoh357 2.45 interactive model: Manganese binding site 4 out of 4 in 3dw9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3dw9. 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: Glu103, B: Asn149, B: Leu150, B: Pro151, B: Pro187, B: Asp188, B: Leu189, E: Hoh21, E: Hoh22, B: Hoh345, B: Hoh375, B: Hoh455, conact list: Atom Atom Distance (A) Mn OE1 B:Glu103 4.10 Mn OE2 B:Glu103 2.11 Mn CD B:Glu103 3.35 Mn CG B:Glu103 4.32 Mn O B:Asn149 4.97 Mn CB B:Asn149 4.66 Mn ND2 B:Asn149 4.35 Mn C B:Asn149 4.11 Mn OD1 B:Asn149 2.37 Mn CG B:Asn149 3.60 Mn CA B:Asn149 4.48 Mn O B:Leu150 2.13 Mn N B:Leu150 3.34 Mn CB B:Leu150 4.40 Mn C B:Leu150 3.24 Mn CA B:Leu150 3.82 Mn N B:Pro151 4.37 Mn C B:Pro151 4.99 Mn CA B:Pro151 4.75 Mn O B:Pro187 4.72 Mn O B:Asp188 2.40 Mn N B:Asp188 4.79 Mn CB B:Asp188 3.83 Mn OD2 B:Asp188 4.84 Mn C B:Asp188 3.27 Mn CG B:Asp188 4.63 Mn CA B:Asp188 3.46 Mn N B:Leu189 4.54 Mn O E:Hoh21 3.80 Mn O E:Hoh22 3.71 Mn O B:Hoh345 2.50 Mn O B:Hoh375 2.59 Mn O B:Hoh455 4.14 interactive model: