Sodium in the structure of Chaperone Complex (pdb 3cqx)

The binding sites of Sodium atom in the structure of Chaperone Complex (pdb code 3cqx). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3cqx structure was solved by Z.XU, J.C.NIX, S.MISRA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 43.1-2.3 Space group P212121 a (A) 52.846 b (A) 105.808 c (A) 210.683 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.2 Rfree (%) 25.6 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3cqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3cqx. 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: Leu73, A: Ile74, A: Gly75, A: Arg76, A: Arg100, A: Pro116, A: Glu117, A: Ala157, conact list: Atom Atom Distance (A) Na O A:Leu73 4.15 Na C A:Leu73 4.78 Na O A:Ile74 4.98 Na N A:Ile74 4.72 Na CB A:Ile74 4.84 Na C A:Ile74 3.81 Na CG1 A:Ile74 4.50 Na CA A:Ile74 3.85 Na N A:Gly75 2.84 Na C A:Gly75 4.39 Na CA A:Gly75 3.62 Na O A:Arg76 4.69 Na N A:Arg76 4.36 Na CZ A:Arg100 4.84 Na NE A:Arg100 4.95 Na NH2 A:Arg100 3.81 Na N A:Pro116 4.70 Na CB A:Pro116 3.85 Na CD A:Pro116 3.87 Na CG A:Pro116 3.84 Na CA A:Pro116 4.84 Na N A:Glu117 4.55 Na OE1 A:Glu117 4.58 Na OE2 A:Glu117 2.89 Na CD A:Glu117 4.02 Na CB A:Ala157 4.26 interactive model: Sodium binding site 2 out of 4 in 3cqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3cqx. 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: Lys71, A: Arg72, A: Leu73, A: Ile74, A: Gly75, A: Arg76, A: Phe150, A: Gln154, conact list: Atom Atom Distance (A) Na O A:Lys71 2.96 Na C A:Lys71 4.06 Na O A:Arg72 3.64 Na N A:Arg72 4.62 Na C A:Arg72 3.73 Na CA A:Arg72 4.22 Na O A:Leu73 4.35 Na N A:Leu73 4.07 Na C A:Leu73 3.97 Na CA A:Leu73 4.41 Na O A:Ile74 2.82 Na N A:Ile74 3.80 Na CB A:Ile74 4.58 Na CG2 A:Ile74 3.70 Na C A:Ile74 3.77 Na CA A:Ile74 4.18 Na N A:Gly75 4.90 Na CB A:Arg76 4.98 Na CD A:Arg76 3.83 Na CZ A:Arg76 3.92 Na CG A:Arg76 3.83 Na NE A:Arg76 3.22 Na NH2 A:Arg76 4.07 Na NH1 A:Arg76 4.95 Na CE2 A:Phe150 4.00 Na CD2 A:Phe150 4.92 Na CZ A:Phe150 3.86 Na CE1 A:Phe150 4.69 Na OE1 A:Gln154 2.92 Na CB A:Gln154 4.70 Na CD A:Gln154 3.83 Na CG A:Gln154 4.01 interactive model: Sodium binding site 3 out of 4 in 3cqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3cqx. 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: Ile29, A: Ala30, A: Asn31, A: Asp32, A: Ile130, A: Ala131, A: Ala133, A: Tyr134, A: Hoh526, conact list: Atom Atom Distance (A) Na CG2 A:Ile29 4.08 Na O A:Ala30 2.92 Na C A:Ala30 4.07 Na O A:Asn31 4.67 Na N A:Asn31 4.61 Na C A:Asn31 4.34 Na CA A:Asn31 4.13 Na N A:Asp32 4.72 Na O A:Ile130 2.91 Na CB A:Ile130 4.34 Na CG2 A:Ile130 3.59 Na C A:Ile130 3.76 Na CG1 A:Ile130 4.97 Na CA A:Ile130 3.93 Na N A:Ala131 4.99 Na N A:Ala133 4.96 Na C A:Ala133 4.42 Na CB A:Ala133 3.60 Na CA A:Ala133 4.54 Na N A:Tyr134 4.14 Na CB A:Tyr134 4.41 Na CA A:Tyr134 4.68 Na O A:Hoh526 4.84 interactive model: Sodium binding site 4 out of 4 in 3cqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3cqx. 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: Arg262, A: Asp285, D: Cys142, D: Val159, D: Gln167, D: Lys168, D: Lys171, D: Hoh505, D: Hoh507, conact list: Atom Atom Distance (A) Na NH2 A:Arg262 4.41 Na CB A:Asp285 3.82 Na OD2 A:Asp285 2.84 Na OD1 A:Asp285 4.93 Na CG A:Asp285 3.74 Na O D:Cys142 3.32 Na CB D:Cys142 3.49 Na SG D:Cys142 4.30 Na C D:Cys142 3.99 Na CA D:Cys142 3.91 Na CG1 D:Val159 4.39 Na O D:Gln167 3.07 Na OE1 D:Gln167 4.51 Na CB D:Gln167 3.81 Na C D:Gln167 3.62 Na CG D:Gln167 4.78 Na CA D:Gln167 4.11 Na N D:Lys168 4.43 Na CA D:Lys168 4.81 Na N D:Lys171 4.86 Na CB D:Lys171 3.72 Na CD D:Lys171 3.96 Na CG D:Lys171 4.40 Na CA D:Lys171 4.83 Na O D:Hoh505 4.33 Na O D:Hoh507 3.05 interactive model: