Magnesium in the structure of Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion (pdb 3oha)

The binding sites of Magnesium atom in the structure of Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8OXOG Lesion (pdb code 3oha). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3oha structure was solved by T.D.SILVERSTEIN, R.JAIN, A.K.AGGARWAL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.8-2.0 Space group C2221 a (A) 88.039 b (A) 227.635 c (A) 86.077 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.7 Rfree (%) 19.5 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3oha Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3oha. 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: Asp30, A: Met31, A: Asn32, A: Ala33, A: Phe34, A: Asp155, A: Dcp514, A: Mg519, A: Hoh756, A: Hoh797, A: Hoh972, conact list: Atom Atom Distance (A) Mg O A:Asp30 4.64 Mg CB A:Asp30 4.34 Mg OD2 A:Asp30 3.44 Mg C A:Asp30 4.25 Mg OD1 A:Asp30 1.96 Mg CG A:Asp30 3.03 Mg CA A:Asp30 4.75 Mg O A:Met31 2.21 Mg N A:Met31 4.04 Mg CB A:Met31 4.60 Mg C A:Met31 3.39 Mg CA A:Met31 4.22 Mg N A:Asn32 4.35 Mg C A:Asn32 4.62 Mg CA A:Asn32 4.47 Mg N A:Ala33 4.36 Mg N A:Phe34 4.69 Mg CB A:Phe34 4.81 Mg CB A:Asp155 4.54 Mg OD2 A:Asp155 3.63 Mg OD1 A:Asp155 2.20 Mg CG A:Asp155 3.27 Mg PG A:Dcp514 3.38 Mg O3B A:Dcp514 3.63 Mg O2G A:Dcp514 4.09 Mg PA A:Dcp514 3.25 Mg O3G A:Dcp514 2.09 Mg O2A A:Dcp514 4.50 Mg O1B A:Dcp514 4.53 Mg PB A:Dcp514 3.13 Mg C5' A:Dcp514 4.02 Mg O5' A:Dcp514 4.08 Mg O2B A:Dcp514 2.08 Mg O3A A:Dcp514 3.48 Mg O1G A:Dcp514 4.56 Mg O1A A:Dcp514 2.04 Mg MG A:Mg519 4.50 Mg O A:Hoh756 3.69 Mg O A:Hoh797 3.95 Mg O A:Hoh972 4.94 interactive model: Magnesium binding site 2 out of 2 in 3oha Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3oha. 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: Asp30, A: Ser153, A: Asp155, A: Glu156, A: Lys272, P: Doc11, A: Dcp514, A: Mg518, A: Hoh776, A: Hoh797, A: Hoh948, A: Hoh972, conact list: Atom Atom Distance (A) Mg OD2 A:Asp30 2.78 Mg OD1 A:Asp30 4.38 Mg CG A:Asp30 3.92 Mg OG A:Ser153 4.21 Mg OD2 A:Asp155 3.21 Mg OD1 A:Asp155 4.59 Mg CG A:Asp155 4.29 Mg OE1 A:Glu156 2.77 Mg CB A:Glu156 4.80 Mg OE2 A:Glu156 4.47 Mg CD A:Glu156 3.38 Mg CG A:Glu156 3.43 Mg NZ A:Lys272 4.18 Mg C3' P:Doc11 3.32 Mg O4' P:Doc11 4.83 Mg C5' P:Doc11 3.79 Mg C2' P:Doc11 4.43 Mg C4' P:Doc11 3.48 Mg O5' P:Doc11 4.87 Mg PA A:Dcp514 3.49 Mg O2A A:Dcp514 3.48 Mg C5' A:Dcp514 4.56 Mg O5' A:Dcp514 3.94 Mg O1A A:Dcp514 2.91 Mg MG A:Mg518 4.50 Mg O A:Hoh776 3.16 Mg O A:Hoh797 4.36 Mg O A:Hoh948 3.72 Mg O A:Hoh972 2.49 interactive model: