Magnesium in the structure of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed With Gdp (pdb 3ejm)

The binding sites of Magnesium atom in the structure of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed With Gdp (pdb code 3ejm). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3ejm structure was solved by S.JEUDY, A.LARTIGUE, J.M.CLAVERIE, C.ABERGEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 23.0-1.9 Space group P63 a (A) 70.153 b (A) 70.153 c (A) 104.937 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.3 Rfree (%) 21.2 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 3ejm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3ejm. 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: His53, A: Arg86, A: His116, A: Ala117, A: Asp119, A: Gdp201, A: Hoh214, A: Hoh230, A: Hoh234, A: Hoh240, A: Hoh251, A: Hoh308, conact list: Atom Atom Distance (A) Mg NE2 A:His53 4.65 Mg CZ A:Arg86 4.79 Mg NH2 A:Arg86 4.70 Mg NH1 A:Arg86 4.23 Mg ND1 A:His116 4.66 Mg CE1 A:His116 4.34 Mg O A:Ala117 4.98 Mg CB A:Asp119 4.71 Mg OD2 A:Asp119 4.00 Mg CG A:Asp119 4.59 Mg O3B A:Gdp201 4.24 Mg PA A:Gdp201 3.57 Mg O2A A:Gdp201 4.61 Mg O1B A:Gdp201 2.43 Mg PB A:Gdp201 3.57 Mg C5' A:Gdp201 4.50 Mg O5' A:Gdp201 4.55 Mg O2B A:Gdp201 4.79 Mg O3A A:Gdp201 3.89 Mg O1A A:Gdp201 2.33 Mg O A:Hoh214 3.97 Mg O A:Hoh230 4.03 Mg O A:Hoh234 4.90 Mg O A:Hoh240 2.57 Mg O A:Hoh251 4.72 Mg O A:Hoh308 2.36 interactive model: Magnesium binding site 2 out of 2 in 3ejm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3ejm. 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: B: His53, B: Arg86, B: His116, B: Ala117, B: Asp119, B: Gdp202, B: Hoh213, B: Hoh224, B: Hoh256, B: Hoh279, B: Hoh306, B: Hoh322, conact list: Atom Atom Distance (A) Mg NE2 B:His53 4.76 Mg CZ B:Arg86 4.66 Mg NH2 B:Arg86 4.57 Mg NH1 B:Arg86 4.12 Mg ND1 B:His116 4.72 Mg CE1 B:His116 4.32 Mg O B:Ala117 4.94 Mg CB B:Asp119 4.67 Mg OD2 B:Asp119 4.03 Mg CG B:Asp119 4.54 Mg O3B B:Gdp202 4.34 Mg PA B:Gdp202 3.65 Mg O2A B:Gdp202 4.59 Mg O1B B:Gdp202 2.50 Mg PB B:Gdp202 3.69 Mg C5' B:Gdp202 4.69 Mg O5' B:Gdp202 4.72 Mg O2B B:Gdp202 4.87 Mg O3A B:Gdp202 4.00 Mg O1A B:Gdp202 2.36 Mg O B:Hoh213 3.93 Mg O B:Hoh224 4.80 Mg O B:Hoh256 4.16 Mg O B:Hoh279 3.47 Mg O B:Hoh306 2.70 Mg O B:Hoh322 2.35 interactive model: