Magnesium in the structure of A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites (pdb 1dno)

The binding sites of Magnesium atom in the structure of A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites (pdb code 1dno). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1dno structure was solved by H.ROBINSON, Y.-G.GAO, R.SANISHVILI, A.JOACHIMIAK, A.H.-J.WANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.4 Space group P212121 a (A) 24.200 b (A) 42.656 c (A) 49.315 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 24.2 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1dno Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1dno. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: C2, A: G3, A: Dt4, B: Dt16, B: Da17, A: Hoh105, A: Hoh117, A: Hoh154, A: Hoh156, A: Hoh173, A: Hoh215, A: Hoh216, A: Hoh217, A: Hoh218, B: Hoh118, B: Hoh142, B: Hoh148, B: Hoh153, B: Hoh219, B: Hoh220, conact list: Atom Atom Distance (A) Mg C5 A:C2 5.00 Mg C4 A:C2 4.95 Mg N4 A:C2 4.64 Mg C6 A:G3 4.93 Mg N7 A:G3 4.48 Mg O6 A:G3 4.27 Mg O4 A:Dt4 4.17 Mg O4 B:Dt16 4.54 Mg N6 B:Da17 4.76 Mg O A:Hoh105 4.43 Mg O A:Hoh117 4.34 Mg O A:Hoh154 4.45 Mg O A:Hoh156 4.39 Mg O A:Hoh173 4.54 Mg O A:Hoh215 2.04 Mg O A:Hoh216 2.05 Mg O A:Hoh217 2.05 Mg O A:Hoh218 2.07 Mg O B:Hoh118 4.28 Mg O B:Hoh142 4.19 Mg O B:Hoh148 3.58 Mg O B:Hoh153 4.80 Mg O B:Hoh219 2.06 Mg O B:Hoh220 2.08 interactive model: Magnesium binding site 2 out of 4 in 1dno Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1dno. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dc18, B: Dg19, A: Hoh139, B: Hoh103, B: Hoh108, B: Hoh118, B: Hoh119, B: Hoh138, B: Hoh174, B: Hoh197, B: Hoh198, B: Hoh199, B: Hoh200, B: Hoh201, B: Hoh202, conact list: Atom Atom Distance (A) Mg C5 B:Dc18 4.55 Mg C4 B:Dc18 4.77 Mg N4 B:Dc18 4.10 Mg N7 B:Dg19 4.69 Mg O6 B:Dg19 4.33 Mg O A:Hoh139 4.48 Mg O B:Hoh103 4.52 Mg O B:Hoh108 4.09 Mg O B:Hoh118 4.23 Mg O B:Hoh119 4.09 Mg O B:Hoh138 4.09 Mg O B:Hoh174 4.30 Mg O B:Hoh197 2.07 Mg O B:Hoh198 2.06 Mg O B:Hoh199 2.07 Mg O B:Hoh200 2.06 Mg O B:Hoh201 2.06 Mg O B:Hoh202 2.06 interactive model: Magnesium binding site 3 out of 4 in 1dno Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1dno. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dt6, A: Da7, B: C12, B: G13, B: Dt14, A: Hoh105, A: Hoh111, A: Hoh156, A: Hoh179, A: Hoh205, B: Hoh144, B: Hoh153, B: Hoh169, B: Hoh181, B: Hoh203, B: Hoh204, B: Hoh206, B: Hoh207, B: Hoh208, conact list: Atom Atom Distance (A) Mg O4 A:Dt6 4.58 Mg N6 A:Da7 4.62 Mg C5 B:C12 4.96 Mg N4 B:C12 4.83 Mg N7 B:G13 4.66 Mg O6 B:G13 4.35 Mg O4 B:Dt14 4.07 Mg O A:Hoh105 4.00 Mg O A:Hoh111 4.78 Mg O A:Hoh156 4.56 Mg O A:Hoh179 4.44 Mg O A:Hoh205 2.06 Mg O B:Hoh144 4.22 Mg O B:Hoh153 4.43 Mg O B:Hoh169 4.24 Mg O B:Hoh181 3.91 Mg O B:Hoh203 2.05 Mg O B:Hoh204 2.06 Mg O B:Hoh206 2.06 Mg O B:Hoh207 2.07 Mg O B:Hoh208 2.05 interactive model: Magnesium binding site 4 out of 4 in 1dno Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1dno. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dc20, B: Hoh135, B: Hoh151, B: Hoh152, B: Hoh160, B: Hoh162, B: Hoh191, B: Hoh209, B: Hoh210, B: Hoh211, B: Hoh212, B: Hoh213, B: Hoh214, conact list: Atom Atom Distance (A) Mg OP1 B:Dc20 3.73 Mg P B:Dc20 4.96 Mg O3' B:Dc20 4.64 Mg C5' B:Dc20 4.56 Mg O5' B:Dc20 4.96 Mg O B:Hoh135 3.99 Mg O B:Hoh151 3.86 Mg O B:Hoh152 4.33 Mg O B:Hoh160 4.35 Mg O B:Hoh162 4.55 Mg O B:Hoh191 4.87 Mg O B:Hoh209 2.07 Mg O B:Hoh210 2.06 Mg O B:Hoh211 2.07 Mg O B:Hoh212 2.06 Mg O B:Hoh213 2.05 Mg O B:Hoh214 2.05 interactive model: