Magnesium in the structure of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed With Udp (pdb 3fbb)

The binding sites of Magnesium atom in the structure of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed With Udp (pdb code 3fbb). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3fbb 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) 28.6-2.4 Space group C2221 a (A) 79.676 b (A) 152.899 c (A) 184.534 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 22.7 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 3fbb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3fbb. 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: Asp115, A: Udp201, A: Hoh141, A: Hoh171, conact list: Atom Atom Distance (A) Mg NE2 A:His53 4.71 Mg CE1 A:His53 4.63 Mg CZ A:Arg86 4.50 Mg NH2 A:Arg86 3.52 Mg NH1 A:Arg86 4.77 Mg OD2 A:Asp115 3.69 Mg CG A:Asp115 4.56 Mg O3B A:Udp201 2.50 Mg PA A:Udp201 4.03 Mg O2A A:Udp201 4.97 Mg O1B A:Udp201 4.74 Mg PB A:Udp201 3.90 Mg C5' A:Udp201 4.99 Mg O2B A:Udp201 4.66 Mg O3A A:Udp201 4.43 Mg O1A A:Udp201 2.65 Mg O A:Hoh141 4.98 Mg O A:Hoh171 2.52 interactive model: Magnesium binding site 2 out of 6 in 3fbb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3fbb. 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: His112, B: Asp115, B: Udp201, B: Hoh173, B: Hoh178, conact list: Atom Atom Distance (A) Mg NE2 B:His53 4.00 Mg CE1 B:His53 4.58 Mg NH2 B:Arg86 3.92 Mg CE1 B:His112 4.74 Mg OD2 B:Asp115 3.90 Mg CG B:Asp115 4.63 Mg O3B B:Udp201 2.59 Mg PA B:Udp201 4.04 Mg O1B B:Udp201 5.00 Mg PB B:Udp201 3.95 Mg C5' B:Udp201 4.44 Mg O5' B:Udp201 4.76 Mg O2B B:Udp201 4.55 Mg O3A B:Udp201 4.42 Mg O1A B:Udp201 2.70 Mg O B:Hoh173 4.53 Mg O B:Hoh178 4.19 interactive model: Magnesium binding site 3 out of 6 in 3fbb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3fbb. 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: C: His53, C: Arg86, C: Asp115, C: Udp201, C: Hoh181, conact list: Atom Atom Distance (A) Mg NE2 C:His53 4.84 Mg CZ C:Arg86 4.10 Mg NH2 C:Arg86 3.42 Mg NH1 C:Arg86 4.06 Mg CB C:Asp115 4.57 Mg OD2 C:Asp115 3.40 Mg CG C:Asp115 4.23 Mg O3B C:Udp201 2.36 Mg PA C:Udp201 4.05 Mg O2A C:Udp201 4.98 Mg O1B C:Udp201 4.72 Mg PB C:Udp201 3.76 Mg O2B C:Udp201 4.40 Mg O3A C:Udp201 4.34 Mg O1A C:Udp201 2.78 Mg O C:Hoh181 3.87 interactive model: Magnesium binding site 4 out of 6 in 3fbb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3fbb. 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: D: His53, D: Arg86, D: Asp115, D: Udp201, conact list: Atom Atom Distance (A) Mg NE2 D:His53 4.58 Mg CE1 D:His53 4.51 Mg CZ D:Arg86 4.54 Mg NH2 D:Arg86 3.91 Mg NH1 D:Arg86 4.35 Mg OD2 D:Asp115 3.47 Mg CG D:Asp115 4.46 Mg O3B D:Udp201 2.51 Mg PA D:Udp201 3.85 Mg O2A D:Udp201 4.85 Mg O1B D:Udp201 4.74 Mg PB D:Udp201 3.86 Mg C5' D:Udp201 4.87 Mg O5' D:Udp201 4.78 Mg O2B D:Udp201 4.67 Mg O3A D:Udp201 4.27 Mg O1A D:Udp201 2.48 interactive model: Magnesium binding site 5 out of 6 in 3fbb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3fbb. 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: E: His53, E: Arg86, E: Asp115, E: Udp201, E: Hoh151, conact list: Atom Atom Distance (A) Mg NE2 E:His53 5.00 Mg CZ E:Arg86 4.27 Mg NH2 E:Arg86 3.63 Mg NH1 E:Arg86 4.20 Mg CB E:Asp115 4.66 Mg OD2 E:Asp115 3.37 Mg CG E:Asp115 4.29 Mg O3B E:Udp201 2.50 Mg PA E:Udp201 3.93 Mg O2A E:Udp201 4.77 Mg O1B E:Udp201 4.84 Mg PB E:Udp201 3.84 Mg O2B E:Udp201 4.49 Mg O3A E:Udp201 4.30 Mg O1A E:Udp201 2.60 Mg O E:Hoh151 4.82 interactive model: Magnesium binding site 6 out of 6 in 3fbb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3fbb. 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: F: Arg86, F: Asp115, F: Udp201, conact list: Atom Atom Distance (A) Mg CZ F:Arg86 3.94 Mg NH2 F:Arg86 3.34 Mg NH1 F:Arg86 3.93 Mg CB F:Asp115 4.15 Mg OD2 F:Asp115 3.06 Mg OD1 F:Asp115 4.83 Mg CG F:Asp115 3.85 Mg O3B F:Udp201 2.56 Mg PA F:Udp201 4.24 Mg O1B F:Udp201 4.60 Mg PB F:Udp201 3.98 Mg O2B F:Udp201 4.89 Mg O3A F:Udp201 4.56 Mg O1A F:Udp201 2.96 interactive model: