Magnesium in the structure of Dna Polymerase Eta in Complex With Undamaged Dna (pdb 3mfh)

The binding sites of Magnesium atom in the structure of Dna Polymerase Eta in Complex With Undamaged Dna (pdb code 3mfh). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3mfh structure was solved by T.D.SILVERSTEIN, R.E.JOHNSON, R.JAIN, L.PRAKASH, S.PRAKASH, A.K.AGGARWAL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group C2221 a (A) 88.745 b (A) 227.935 c (A) 85.967 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 22.7 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3mfh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3mfh. 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: Dtp514, A: Mg518, A: Hoh694, A: Hoh736, conact list: Atom Atom Distance (A) Mg O A:Asp30 4.68 Mg CB A:Asp30 4.37 Mg OD2 A:Asp30 3.52 Mg C A:Asp30 4.27 Mg OD1 A:Asp30 2.01 Mg CG A:Asp30 3.09 Mg CA A:Asp30 4.78 Mg O A:Met31 2.20 Mg N A:Met31 3.95 Mg CB A:Met31 4.64 Mg C A:Met31 3.39 Mg CA A:Met31 4.20 Mg N A:Asn32 4.38 Mg C A:Asn32 4.66 Mg CA A:Asn32 4.53 Mg N A:Ala33 4.40 Mg N A:Phe34 4.66 Mg CB A:Phe34 4.77 Mg CB A:Asp155 4.53 Mg OD2 A:Asp155 3.53 Mg OD1 A:Asp155 2.20 Mg CG A:Asp155 3.21 Mg PG A:Dtp514 3.34 Mg O3B A:Dtp514 3.58 Mg O2G A:Dtp514 4.60 Mg PA A:Dtp514 3.33 Mg O5' A:Dtp514 4.10 Mg O2B A:Dtp514 4.52 Mg O3A A:Dtp514 3.53 Mg O3G A:Dtp514 4.03 Mg O2A A:Dtp514 4.58 Mg O1B A:Dtp514 2.06 Mg PB A:Dtp514 3.12 Mg C5' A:Dtp514 3.94 Mg O1G A:Dtp514 2.12 Mg O1A A:Dtp514 2.12 Mg MG A:Mg518 4.61 Mg O A:Hoh694 3.69 Mg O A:Hoh736 3.90 interactive model: Magnesium binding site 2 out of 2 in 3mfh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3mfh. 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: Dtp514, A: Mg517, A: Hoh715, A: Hoh736, A: Hoh921, conact list: Atom Atom Distance (A) Mg OD2 A:Asp30 3.03 Mg OD1 A:Asp30 4.54 Mg CG A:Asp30 4.14 Mg OG A:Ser153 4.12 Mg OD2 A:Asp155 3.17 Mg OD1 A:Asp155 4.73 Mg CG A:Asp155 4.31 Mg OE1 A:Glu156 2.81 Mg CB A:Glu156 4.95 Mg OE2 A:Glu156 4.67 Mg CD A:Glu156 3.51 Mg CG A:Glu156 3.50 Mg NZ A:Lys272 4.81 Mg C3' P:Doc11 3.09 Mg O4' P:Doc11 4.65 Mg C5' P:Doc11 3.93 Mg C2' P:Doc11 4.51 Mg C4' P:Doc11 3.37 Mg O5' P:Doc11 4.82 Mg PA A:Dtp514 3.57 Mg O5' A:Dtp514 3.90 Mg O2A A:Dtp514 3.56 Mg C5' A:Dtp514 4.52 Mg O1A A:Dtp514 3.01 Mg MG A:Mg517 4.61 Mg O A:Hoh715 3.43 Mg O A:Hoh736 4.56 Mg O A:Hoh921 3.02 interactive model: