Magnesium in the structure of Crystal Structure Of D41N Variant of Human Mitochondrial 5' (3')-Deoxyribonucleotidase (Mdn) in Complex With 3'- Azidothymidine 5'-Monophosphate (pdb 2jau)

The binding sites of Magnesium atom in the structure of Crystal Structure Of D41N Variant of Human Mitochondrial 5' (3')-Deoxyribonucleotidase (Mdn) in Complex With 3'- Azidothymidine 5'-Monophosphate (pdb code 2jau). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2jau structure was solved by K.WALLDEN, B.RUZZENENTE, V.BIANCHI, P.NORDLUND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.8 Space group P43212 a (A) 73.590 b (A) 73.590 c (A) 105.740 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 21.4 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2jau Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2jau. 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: Met118, A: Ala119, A: Ser120, A: Leu121, A: Gln122, A: Asn123, A: Thr124, A: Asp125, A: Hoh2085, A: Hoh2091, A: Hoh2092, A: Hoh2093, A: Hoh2096, conact list: Atom Atom Distance (A) Mg O A:Met118 4.53 Mg O A:Ala119 2.42 Mg C A:Ala119 3.51 Mg CA A:Ala119 4.45 Mg O A:Ser120 4.34 Mg N A:Ser120 4.35 Mg C A:Ser120 4.02 Mg CA A:Ser120 4.42 Mg O A:Leu121 2.45 Mg N A:Leu121 3.97 Mg C A:Leu121 3.59 Mg CA A:Leu121 4.34 Mg N A:Gln122 4.61 Mg C A:Gln122 4.78 Mg CA A:Gln122 4.82 Mg N A:Asn123 4.78 Mg O A:Thr124 2.31 Mg N A:Thr124 3.85 Mg CB A:Thr124 4.09 Mg C A:Thr124 3.42 Mg CA A:Thr124 4.00 Mg N A:Asp125 4.54 Mg OD1 A:Asp125 4.78 Mg CA A:Asp125 4.90 Mg O A:Hoh2085 2.51 Mg O A:Hoh2091 2.67 Mg O A:Hoh2092 2.58 Mg O A:Hoh2093 4.53 Mg O A:Hoh2096 4.53 interactive model: Magnesium binding site 2 out of 2 in 2jau Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2jau. 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: Asn41, A: Met42, A: Asp43, A: Gly44, A: Val45, A: Phe75, A: Asp175, A: Asp176, A: Arg177, A: Po41229, A: Atm1230, A: Hoh2140, A: Hoh2141, A: Hoh2199, A: Hoh2202, conact list: Atom Atom Distance (A) Mg CB A:Asn41 4.38 Mg ND2 A:Asn41 3.63 Mg OD1 A:Asn41 2.00 Mg CG A:Asn41 3.11 Mg C A:Met42 4.90 Mg O A:Asp43 2.12 Mg N A:Asp43 4.20 Mg CB A:Asp43 4.16 Mg C A:Asp43 3.29 Mg CA A:Asp43 4.08 Mg N A:Gly44 4.33 Mg C A:Gly44 4.93 Mg CA A:Gly44 4.58 Mg CG2 A:Val45 4.80 Mg CZ A:Phe75 4.68 Mg CE1 A:Phe75 4.61 Mg OD2 A:Asp175 4.94 Mg OD1 A:Asp175 3.96 Mg CG A:Asp175 4.70 Mg N A:Asp176 4.46 Mg CB A:Asp176 4.54 Mg OD2 A:Asp176 3.59 Mg OD1 A:Asp176 2.16 Mg CG A:Asp176 3.21 Mg CA A:Asp176 4.96 Mg N A:Arg177 4.89 Mg O1 A:Po41229 4.19 Mg O2 A:Po41229 4.19 Mg P A:Po41229 3.63 Mg O4 A:Po41229 2.25 Mg O3 A:Po41229 4.65 Mg OP1 A:Atm1230 1.96 Mg P A:Atm1230 3.41 Mg OP2 A:Atm1230 4.22 Mg O5' A:Atm1230 4.25 Mg OP3 A:Atm1230 3.83 Mg O A:Hoh2140 2.13 Mg O A:Hoh2141 2.23 Mg O A:Hoh2199 4.42 Mg O A:Hoh2202 4.08 interactive model: