Sodium in the structure of Crystal Structure of Response Regulator Receiver Domain Protein (Chey- Like) From Methanospirillum Hungatei Jf-1 (pdb 3crn)

The binding sites of Sodium atom in the structure of Crystal Structure of Response Regulator Receiver Domain Protein (Chey- Like) From Methanospirillum Hungatei Jf-1 (pdb code 3crn). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3crn structure was solved by R.L.HINER, R.TORO, Y.PATSKOVSKY, J.FREEMAN, S.CHANG, D.SMITH, C.GROSHONG, S.R.WASSERMAN, J.M.SAUDER, S.K.BURLEY, S.C.ALMO, NEW YORK SGX RESEARCHCENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-1.6 Space group P212121 a (A) 51.930 b (A) 53.992 c (A) 92.681 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.3 Rfree (%) 22.4 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3crn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3crn. 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: Asp8, A: Asp9, A: Phd52, A: Lys54, A: Leu55, A: Hoh190, A: Hoh206, A: Hoh215, conact list: Atom Atom Distance (A) Na OD1 A:Asp8 4.02 Na N A:Asp9 4.59 Na CB A:Asp9 4.65 Na OD2 A:Asp9 3.58 Na OD1 A:Asp9 2.32 Na CG A:Asp9 3.30 Na OP1 A:Phd52 2.31 Na P A:Phd52 3.61 Na CB A:Phd52 4.64 Na OP2 A:Phd52 4.46 Na OD2 A:Phd52 2.42 Na OD1 A:Phd52 3.75 Na OP3 A:Phd52 4.70 Na CG A:Phd52 3.35 Na O A:Lys54 2.35 Na N A:Lys54 4.42 Na CB A:Lys54 3.96 Na C A:Lys54 3.29 Na CA A:Lys54 4.08 Na N A:Leu55 4.16 Na CD2 A:Leu55 4.89 Na CA A:Leu55 4.32 Na O A:Hoh190 4.02 Na O A:Hoh206 2.80 Na O A:Hoh215 2.46 interactive model: Sodium binding site 2 out of 4 in 3crn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3crn. 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: Asp8, B: Asp9, B: Phd52, B: Lys54, B: Leu55, B: Hoh161, B: Hoh170, B: Hoh171, B: Hoh215, conact list: Atom Atom Distance (A) Na OD1 B:Asp8 4.28 Na N B:Asp9 4.71 Na CB B:Asp9 4.69 Na OD2 B:Asp9 3.62 Na OD1 B:Asp9 2.32 Na CG B:Asp9 3.33 Na OP1 B:Phd52 2.21 Na P B:Phd52 3.53 Na CB B:Phd52 4.69 Na OP2 B:Phd52 4.42 Na OD2 B:Phd52 2.48 Na OD1 B:Phd52 3.72 Na OP3 B:Phd52 4.63 Na CG B:Phd52 3.38 Na O B:Lys54 2.42 Na N B:Lys54 4.44 Na CB B:Lys54 4.07 Na C B:Lys54 3.37 Na CA B:Lys54 4.14 Na N B:Leu55 4.25 Na CD2 B:Leu55 4.86 Na CA B:Leu55 4.41 Na O B:Hoh161 2.61 Na O B:Hoh170 2.36 Na O B:Hoh171 4.13 Na O B:Hoh215 4.79 interactive model: Sodium binding site 3 out of 4 in 3crn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3crn. 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: Leu92, A: Ala96, B: Leu92, B: Gly95, B: Ala96, B: Asp97, A: Hoh189, A: Hoh202, A: Hoh221, A: Hoh222, B: Hoh155, B: Hoh165, B: Hoh169, B: Hoh188, B: Hoh198, B: Hoh212, conact list: Atom Atom Distance (A) Na O A:Leu92 4.68 Na O A:Ala96 3.77 Na C A:Ala96 4.94 Na O B:Leu92 4.80 Na O B:Gly95 4.42 Na C B:Gly95 4.51 Na O B:Ala96 2.69 Na N B:Ala96 4.71 Na C B:Ala96 3.78 Na CA B:Ala96 4.89 Na O B:Asp97 4.99 Na N B:Asp97 4.40 Na C B:Asp97 4.88 Na OD1 B:Asp97 4.39 Na CG B:Asp97 4.94 Na CA B:Asp97 4.11 Na O A:Hoh189 4.20 Na O A:Hoh202 2.28 Na O A:Hoh221 4.84 Na O A:Hoh222 2.38 Na O B:Hoh155 4.11 Na O B:Hoh165 2.62 Na O B:Hoh169 2.25 Na O B:Hoh188 4.44 Na O B:Hoh198 2.34 Na O B:Hoh212 2.93 interactive model: Sodium binding site 4 out of 4 in 3crn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3crn. 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: His68, B: Pro72, B: Gly73, B: Mse74, B: Lys75, B: Lys76, B: Asp97, B: Hoh165, B: Hoh177, B: Hoh178, B: Hoh180, B: Hoh186, B: Hoh188, B: Hoh192, B: Hoh201, conact list: Atom Atom Distance (A) Na ND1 B:His68 4.74 Na CE1 B:His68 4.25 Na O B:Pro72 2.54 Na C B:Pro72 3.72 Na CA B:Pro72 4.85 Na O B:Gly73 4.20 Na N B:Gly73 4.40 Na C B:Gly73 4.12 Na CA B:Gly73 4.16 Na O B:Mse74 3.57 Na N B:Mse74 4.67 Na C B:Mse74 4.46 Na CE B:Lys75 4.96 Na CD B:Lys75 4.81 Na NZ B:Lys75 4.40 Na NZ B:Lys76 4.24 Na OD2 B:Asp97 4.21 Na OD1 B:Asp97 4.09 Na CG B:Asp97 4.58 Na O B:Hoh165 4.61 Na O B:Hoh177 4.73 Na O B:Hoh178 2.60 Na O B:Hoh180 2.55 Na O B:Hoh186 2.79 Na O B:Hoh188 4.28 Na O B:Hoh192 2.44 Na O B:Hoh201 2.31 interactive model: