Sodium in the structure of The Crystal Structure of the Inorganic Triphosphatase NE1496 (pdb 3typ)

The binding sites of Sodium atom in the structure of The Crystal Structure of the Inorganic Triphosphatase NE1496 (pdb code 3typ). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3typ structure was solved by V.V.LUNIN, T.SKARINA, O.ONOPRIYENKO, T.A.BINKOWSKI, A.JOACHIMIAK, A.M.EDWARDS, A.SAVCHENKO, MIDWEST CENTER FOR STRUCTURAL GENOMICS(MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.6-1.9 Space group P3221 a (A) 52.282 b (A) 52.282 c (A) 252.484 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.3 Rfree (%) 27 Sodium Binding Sites: Sodium binding site 1 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3typ. 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: Ala12, A: Pro129, A: Pro130, A: Trp131, A: Phe132, A: Gly133, A: Hoh173, A: Hoh186, A: Hoh195, A: Hoh229, A: Hoh240, A: Hoh246, A: Hoh250, A: Hoh272, conact list: Atom Atom Distance (A) Na CB A:Ala12 4.38 Na O A:Pro129 4.42 Na O A:Pro130 2.56 Na C A:Pro130 3.57 Na CA A:Pro130 4.08 Na N A:Trp131 4.63 Na C A:Trp131 4.54 Na CA A:Trp131 4.93 Na O A:Phe132 2.28 Na N A:Phe132 4.20 Na CB A:Phe132 4.96 Na C A:Phe132 3.51 Na CA A:Phe132 4.44 Na N A:Gly133 4.38 Na C A:Gly133 4.95 Na CA A:Gly133 4.38 Na O A:Hoh173 2.53 Na O A:Hoh186 2.22 Na O A:Hoh195 4.12 Na O A:Hoh229 4.34 Na O A:Hoh240 2.34 Na O A:Hoh246 2.35 Na O A:Hoh250 3.27 Na O A:Hoh272 4.60 interactive model: Sodium binding site 2 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3typ. 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: Gly80, A: Arg81, A: Arg82, A: His106, A: Leu147, A: Ala148, A: Leu149, A: Ser150, A: Ile151, A: Hoh177, A: Hoh179, A: Hoh182, A: Hoh283, conact list: Atom Atom Distance (A) Na O A:Gly80 2.56 Na N A:Gly80 4.94 Na C A:Gly80 3.20 Na CA A:Gly80 3.96 Na N A:Arg81 3.89 Na C A:Arg81 4.52 Na CA A:Arg81 4.03 Na O A:Arg82 4.21 Na N A:Arg82 4.05 Na NE2 A:His106 3.86 Na CD2 A:His106 4.73 Na CE1 A:His106 4.61 Na O A:Leu147 4.21 Na O A:Ala148 2.31 Na C A:Ala148 3.49 Na CA A:Ala148 4.48 Na O A:Leu149 4.21 Na N A:Leu149 4.25 Na C A:Leu149 3.92 Na CA A:Leu149 4.16 Na O A:Ser150 2.31 Na N A:Ser150 4.01 Na OG A:Ser150 4.70 Na C A:Ser150 3.55 Na CA A:Ser150 4.46 Na N A:Ile151 4.46 Na CG2 A:Ile151 4.49 Na CA A:Ile151 4.50 Na O A:Hoh177 2.35 Na O A:Hoh179 4.49 Na O A:Hoh182 2.49 Na O A:Hoh283 4.30 interactive model: Sodium binding site 3 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3typ. 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: Gly105, A: His106, A: Leu107, A: Ser108, A: Pro109, A: Hoh193, A: Hoh202, A: Hoh248, A: Hoh261, A: Hoh265, conact list: Atom Atom Distance (A) Na O A:Gly105 4.46 Na O A:His106 2.45 Na CB A:His106 4.64 Na C A:His106 3.39 Na CA A:His106 3.94 Na O A:Leu107 4.83 Na N A:Leu107 4.41 Na C A:Leu107 4.40 Na CA A:Leu107 4.70 Na O A:Ser108 2.36 Na N A:Ser108 4.26 Na CB A:Ser108 4.76 Na C A:Ser108 3.56 Na CA A:Ser108 4.37 Na N A:Pro109 4.51 Na CD A:Pro109 4.52 Na O A:Hoh193 2.55 Na O A:Hoh202 4.99 Na O A:Hoh248 4.24 Na O A:Hoh261 2.56 Na O A:Hoh265 2.44 interactive model: Sodium binding site 4 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3typ. 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: Asp94, A: Gly95, A: Hoh234, A: Hoh354, conact list: Atom Atom Distance (A) Na O A:Asp94 2.56 Na CB A:Asp94 4.43 Na C A:Asp94 3.50 Na CA A:Asp94 4.05 Na N A:Gly95 4.54 Na CA A:Gly95 4.89 Na O A:Hoh234 4.36 Na O A:Hoh354 2.11 interactive model: Sodium binding site 5 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3typ. 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: Ala12, B: Pro129, B: Pro130, B: Trp131, B: Phe132, B: Gly133, B: Hoh174, B: Hoh176, B: Hoh178, B: Hoh230, B: Hoh242, B: Hoh252, B: Hoh290, conact list: Atom Atom Distance (A) Na CB B:Ala12 4.39 Na O B:Pro129 4.31 Na O B:Pro130 2.60 Na C B:Pro130 3.57 Na CA B:Pro130 4.04 Na N B:Trp131 4.63 Na C B:Trp131 4.57 Na CA B:Trp131 4.96 Na O B:Phe132 2.21 Na N B:Phe132 4.19 Na CB B:Phe132 4.93 Na C B:Phe132 3.46 Na CA B:Phe132 4.41 Na N B:Gly133 4.34 Na C B:Gly133 4.95 Na CA B:Gly133 4.36 Na O B:Hoh174 2.28 Na O B:Hoh176 2.24 Na O B:Hoh178 4.19 Na O B:Hoh230 4.33 Na O B:Hoh242 2.42 Na O B:Hoh252 4.56 Na O B:Hoh290 2.17 interactive model: Sodium binding site 6 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3typ. 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: Gly80, B: Arg81, B: Arg82, B: His106, B: Leu147, B: Ala148, B: Leu149, B: Ser150, B: Ile151, B: Hoh163, B: Hoh167, B: Hoh193, B: Hoh312, conact list: Atom Atom Distance (A) Na O B:Gly80 2.62 Na N B:Gly80 4.98 Na C B:Gly80 3.24 Na CA B:Gly80 4.04 Na N B:Arg81 3.88 Na C B:Arg81 4.42 Na CA B:Arg81 3.98 Na O B:Arg82 4.12 Na N B:Arg82 3.90 Na C B:Arg82 4.99 Na NE2 B:His106 3.86 Na CD2 B:His106 4.75 Na CE1 B:His106 4.60 Na O B:Leu147 4.16 Na O B:Ala148 2.24 Na C B:Ala148 3.40 Na CA B:Ala148 4.32 Na O B:Leu149 4.27 Na N B:Leu149 4.23 Na C B:Leu149 4.00 Na CA B:Leu149 4.23 Na O B:Ser150 2.33 Na N B:Ser150 4.04 Na OG B:Ser150 4.79 Na C B:Ser150 3.57 Na CA B:Ser150 4.47 Na N B:Ile151 4.54 Na CA B:Ile151 4.76 Na O B:Hoh163 2.39 Na O B:Hoh167 2.45 Na O B:Hoh193 4.47 Na O B:Hoh312 4.37 interactive model: Sodium binding site 7 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3typ. 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: Gly105, B: His106, B: Leu107, B: Ser108, B: Pro109, B: Hoh196, B: Hoh244, B: Hoh259, conact list: Atom Atom Distance (A) Na O B:Gly105 4.38 Na O B:His106 2.47 Na CB B:His106 4.66 Na C B:His106 3.40 Na CA B:His106 3.94 Na O B:Leu107 4.77 Na N B:Leu107 4.40 Na C B:Leu107 4.35 Na CA B:Leu107 4.69 Na O B:Ser108 2.33 Na N B:Ser108 4.16 Na CB B:Ser108 4.70 Na C B:Ser108 3.51 Na CA B:Ser108 4.31 Na N B:Pro109 4.46 Na CD B:Pro109 4.39 Na O B:Hoh196 2.48 Na O B:Hoh244 4.92 Na O B:Hoh259 2.52 interactive model: Sodium binding site 8 out of 8 in 3typ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3typ. 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: Asp94, B: Gly95, B: Hoh206, B: Hoh331, conact list: Atom Atom Distance (A) Na O B:Asp94 2.53 Na CB B:Asp94 4.56 Na C B:Asp94 3.49 Na CA B:Asp94 4.09 Na N B:Gly95 4.52 Na CA B:Gly95 4.88 Na O B:Hoh206 4.30 Na O B:Hoh331 2.15 interactive model: