Sodium in the structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I (pdb 3fc3)

The binding sites of Sodium atom in the structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I (pdb code 3fc3). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3fc3 structure was solved by M.SOKOLOWSKA, H.CZAPINSKA, M.BOCHTLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.7-1.8 Space group H32 a (A) 90.089 b (A) 90.089 c (A) 334.254 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.1 Rfree (%) 20.5 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3fc3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3fc3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp148, A: His149, A: Arg157, A: Asn165, A: Leu168, A: Asp173, C: Dg2, C: Dt3, D: Dg2, D: Da3, A: Hoh439, A: Hoh515, A: Hoh516, conact list: Atom Atom Distance (A) Na CB A:Asp148 3.98 Na OD2 A:Asp148 4.30 Na C A:Asp148 4.60 Na OD1 A:Asp148 2.21 Na CG A:Asp148 3.32 Na CA A:Asp148 4.06 Na O A:His149 4.09 Na N A:His149 4.06 Na NH2 A:Arg157 3.93 Na O A:Asn165 4.61 Na CB A:Asn165 4.65 Na ND2 A:Asn165 3.77 Na OD1 A:Asn165 2.31 Na CG A:Asn165 3.34 Na CA A:Asn165 4.93 Na CD1 A:Leu168 4.73 Na OD2 A:Asp173 4.40 Na OD1 A:Asp173 4.86 Na C3' C:Dg2 3.53 Na O3' C:Dg2 2.75 Na O4' C:Dg2 4.95 Na C5' C:Dg2 4.74 Na C2' C:Dg2 4.96 Na C4' C:Dg2 3.85 Na OP1 C:Dt3 2.39 Na P C:Dt3 3.07 Na OP2 C:Dt3 4.42 Na O5' C:Dt3 3.72 Na C3' D:Dg2 3.62 Na O3' D:Dg2 2.47 Na O4' D:Dg2 4.91 Na C5' D:Dg2 4.85 Na C2' D:Dg2 4.91 Na C4' D:Dg2 3.91 Na OP1 D:Da3 2.67 Na P D:Da3 3.14 Na OP2 D:Da3 4.42 Na O5' D:Da3 3.86 Na O A:Hoh439 2.39 Na O A:Hoh515 4.56 Na O A:Hoh516 2.58 interactive model: Sodium binding site 2 out of 3 in 3fc3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3fc3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp148, B: His149, B: Arg157, B: Asn165, B: Leu168, B: Asp173, C: Dg2, C: Dt3, D: Dg2, D: Da3, B: Hoh208, B: Hoh466, C: Hoh212, conact list: Atom Atom Distance (A) Na CB B:Asp148 4.09 Na OD2 B:Asp148 4.34 Na C B:Asp148 4.64 Na OD1 B:Asp148 2.27 Na CG B:Asp148 3.40 Na CA B:Asp148 4.09 Na O B:His149 4.11 Na N B:His149 4.10 Na NH2 B:Arg157 4.00 Na O B:Asn165 4.55 Na CB B:Asn165 4.64 Na ND2 B:Asn165 3.74 Na OD1 B:Asn165 2.28 Na CG B:Asn165 3.32 Na CA B:Asn165 4.94 Na CD1 B:Leu168 4.86 Na OD2 B:Asp173 4.39 Na OD1 B:Asp173 4.78 Na C3' C:Dg2 3.49 Na O3' C:Dg2 2.73 Na O4' C:Dg2 4.95 Na C5' C:Dg2 4.72 Na C2' C:Dg2 4.93 Na C4' C:Dg2 3.84 Na OP1 C:Dt3 2.35 Na P C:Dt3 3.04 Na OP2 C:Dt3 4.38 Na O5' C:Dt3 3.71 Na C3' D:Dg2 3.59 Na O3' D:Dg2 2.45 Na O4' D:Dg2 4.93 Na C5' D:Dg2 4.85 Na C2' D:Dg2 4.89 Na C4' D:Dg2 3.91 Na OP1 D:Da3 2.62 Na P D:Da3 3.10 Na OP2 D:Da3 4.39 Na O5' D:Da3 3.84 Na O B:Hoh208 2.31 Na O B:Hoh466 2.45 Na O C:Hoh212 4.55 interactive model: Sodium binding site 3 out of 3 in 3fc3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3fc3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Tyr57, B: Arg58, B: Tyr63, B: Hoh198, B: Hoh482, conact list: Atom Atom Distance (A) Na O B:Tyr57 2.32 Na CB B:Tyr57 4.10 Na C B:Tyr57 3.45 Na CA B:Tyr57 4.27 Na N B:Arg58 4.38 Na CG B:Arg58 4.87 Na CA B:Arg58 4.56 Na CE2 B:Tyr63 3.62 Na CD2 B:Tyr63 4.96 Na CZ B:Tyr63 3.39 Na CE1 B:Tyr63 4.61 Na OH B:Tyr63 2.44 Na O B:Hoh198 2.42 Na O B:Hoh482 4.90 interactive model: