Magnesium in the structure of Structure of Hpoli With Dna and Dttp (pdb 2dpj)

The binding sites of Magnesium atom in the structure of Structure of Hpoli With Dna and Dttp (pdb code 2dpj). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2dpj structure was solved by D.T.NAIR, R.E.JOHNSON, L.PRAKASH, S.PRAKASH, A.K.AGGARWAL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.8-2.3 Space group P6522 a (A) 98.059 b (A) 98.059 c (A) 203.102 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.8 Rfree (%) 27.7 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2dpj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2dpj. 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: Asp34, A: Leu35, A: Asp36, A: Cys37, A: Phe38, A: Asp126, A: Mg872, A: Ttp875, A: Hoh929, A: Hoh932, conact list: Atom Atom Distance (A) Mg O A:Asp34 4.72 Mg CB A:Asp34 4.71 Mg OD2 A:Asp34 2.36 Mg C A:Asp34 4.27 Mg OD1 A:Asp34 3.88 Mg CG A:Asp34 3.48 Mg CA A:Asp34 4.86 Mg O A:Leu35 2.19 Mg N A:Leu35 3.82 Mg CB A:Leu35 4.65 Mg C A:Leu35 3.38 Mg CA A:Leu35 4.13 Mg N A:Asp36 4.42 Mg C A:Asp36 4.67 Mg CA A:Asp36 4.63 Mg N A:Cys37 4.45 Mg N A:Phe38 4.73 Mg CB A:Asp126 4.62 Mg OD2 A:Asp126 3.76 Mg OD1 A:Asp126 2.23 Mg CG A:Asp126 3.34 Mg MG A:Mg872 3.28 Mg PG A:Ttp875 3.44 Mg O3B A:Ttp875 3.77 Mg O2G A:Ttp875 4.61 Mg PA A:Ttp875 3.50 Mg O3G A:Ttp875 4.08 Mg O2A A:Ttp875 4.54 Mg O1B A:Ttp875 4.51 Mg PB A:Ttp875 3.23 Mg C5' A:Ttp875 4.30 Mg O5' A:Ttp875 4.44 Mg O2B A:Ttp875 2.14 Mg O3A A:Ttp875 3.70 Mg O1G A:Ttp875 2.29 Mg O1A A:Ttp875 2.31 Mg O A:Hoh929 3.64 Mg O A:Hoh932 3.74 interactive model: Magnesium binding site 2 out of 2 in 2dpj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2dpj. 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: P: Doc873, A: Asp34, A: Asp126, A: Glu127, A: Mg871, A: Ttp875, A: Hoh904, A: Hoh932, conact list: Atom Atom Distance (A) Mg C3' P:Doc873 3.80 Mg C2' P:Doc873 4.84 Mg C4' P:Doc873 4.85 Mg CB A:Asp34 4.55 Mg OD2 A:Asp34 3.03 Mg OD1 A:Asp34 2.65 Mg CG A:Asp34 3.15 Mg OD2 A:Asp126 3.33 Mg OD1 A:Asp126 3.87 Mg CG A:Asp126 4.06 Mg OE1 A:Glu127 4.46 Mg OE2 A:Glu127 2.50 Mg CD A:Glu127 3.37 Mg CG A:Glu127 3.62 Mg MG A:Mg871 3.28 Mg PA A:Ttp875 3.16 Mg O2A A:Ttp875 3.31 Mg C5' A:Ttp875 4.72 Mg O5' A:Ttp875 4.13 Mg O2B A:Ttp875 4.77 Mg O3A A:Ttp875 4.41 Mg O1G A:Ttp875 4.04 Mg O1A A:Ttp875 2.19 Mg O A:Hoh904 4.63 Mg O A:Hoh932 2.81 interactive model: