Magnesium in the structure of Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex (pdb 3k5l)

The binding sites of Magnesium atom in the structure of Crystal Structure of E.Coli Pol II-Abasic Dna-Datp Lt(0, 3) Ternary Complex (pdb code 3k5l). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3k5l structure was solved by W.YANG, F.WANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.4-2.7 Space group P212121 a (A) 79.974 b (A) 101.198 c (A) 121.717 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.4 Rfree (%) 24.1 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3k5l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3k5l. 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: Asp419, A: Tyr420, A: Lys421, A: Ser422, A: Leu423, A: Asp547, A: Dtp914, A: Mg1002, conact list: Atom Atom Distance (A) Mg O A:Asp419 4.89 Mg CB A:Asp419 4.28 Mg OD2 A:Asp419 3.86 Mg C A:Asp419 4.31 Mg OD1 A:Asp419 2.01 Mg CG A:Asp419 3.19 Mg CA A:Asp419 4.80 Mg O A:Tyr420 1.87 Mg N A:Tyr420 3.78 Mg CB A:Tyr420 4.48 Mg C A:Tyr420 3.07 Mg CA A:Tyr420 3.93 Mg N A:Lys421 4.06 Mg C A:Lys421 4.54 Mg CA A:Lys421 4.29 Mg N A:Ser422 4.19 Mg N A:Leu423 4.60 Mg CB A:Leu423 4.99 Mg CB A:Asp547 4.28 Mg OD2 A:Asp547 2.05 Mg OD1 A:Asp547 3.52 Mg CG A:Asp547 3.07 Mg PG A:Dtp914 3.39 Mg O3B A:Dtp914 3.84 Mg O2G A:Dtp914 4.00 Mg PA A:Dtp914 3.43 Mg O5' A:Dtp914 4.33 Mg O2B A:Dtp914 4.74 Mg O3A A:Dtp914 3.89 Mg O3G A:Dtp914 4.66 Mg O2A A:Dtp914 4.52 Mg O1B A:Dtp914 2.31 Mg PB A:Dtp914 3.33 Mg C5' A:Dtp914 3.98 Mg O1G A:Dtp914 2.22 Mg O1A A:Dtp914 2.15 Mg MG A:Mg1002 4.52 interactive model: Magnesium binding site 2 out of 2 in 3k5l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3k5l. 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: Asp419, A: Asp545, A: Asp547, A: Ser548, P: Doc913, A: Dtp914, A: Mg1001, A: Hoh804, conact list: Atom Atom Distance (A) Mg OD2 A:Asp419 2.80 Mg OD1 A:Asp419 3.98 Mg CG A:Asp419 3.77 Mg O A:Asp545 3.90 Mg N A:Asp547 4.51 Mg CB A:Asp547 4.85 Mg OD2 A:Asp547 4.25 Mg C A:Asp547 4.70 Mg OD1 A:Asp547 2.54 Mg CG A:Asp547 3.69 Mg CA A:Asp547 4.86 Mg N A:Ser548 4.49 Mg CB A:Ser548 4.17 Mg OG A:Ser548 4.26 Mg CA A:Ser548 4.96 Mg C3' P:Doc913 3.29 Mg C5' P:Doc913 3.96 Mg C2' P:Doc913 4.22 Mg C4' P:Doc913 4.14 Mg O5' P:Doc913 4.06 Mg PA A:Dtp914 3.85 Mg O5' A:Dtp914 3.87 Mg O2A A:Dtp914 3.84 Mg C5' A:Dtp914 4.46 Mg O1A A:Dtp914 3.24 Mg MG A:Mg1001 4.52 Mg O A:Hoh804 3.56 interactive model: