Sodium in the structure of Crystal Structure of Leut-F253A Bound to L-Leucine From Lipid Bicelles (pdb 4fxz)

The binding sites of Sodium atom in the structure of Crystal Structure of Leut-F253A Bound to L-Leucine From Lipid Bicelles (pdb code 4fxz). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 4fxz structure was solved by H.WANG, E.GOUAUX, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.3-2.6 Space group C121 a (A) 122.140 b (A) 89.888 c (A) 81.262 alpha (°) 90.00 beta (°) 102.95 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 22 Sodium Binding Sites: Sodium binding site 1 out of 2 in 4fxz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 4fxz. 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: Ala22, A: Val23, A: Gly24, A: Gly26, A: Asn27, A: Ala253, A: Thr254, A: Leu255, A: Asn286, A: Glu290, A: Leu601, conact list: Atom Atom Distance (A) Na O A:Ala22 2.27 Na C A:Ala22 3.08 Na CB A:Ala22 4.36 Na CA A:Ala22 4.04 Na N A:Val23 3.74 Na C A:Val23 4.31 Na CA A:Val23 3.77 Na N A:Gly24 3.86 Na CA A:Gly24 4.94 Na C A:Gly26 4.95 Na N A:Asn27 4.65 Na CB A:Asn27 4.60 Na ND2 A:Asn27 3.32 Na OD1 A:Asn27 2.35 Na CG A:Asn27 3.17 Na O A:Ala253 4.88 Na O A:Thr254 2.36 Na N A:Thr254 4.60 Na CB A:Thr254 3.36 Na CG2 A:Thr254 4.45 Na OG1 A:Thr254 2.42 Na C A:Thr254 3.12 Na CA A:Thr254 3.20 Na N A:Leu255 4.40 Na CB A:Asn286 4.77 Na ND2 A:Asn286 3.63 Na OD1 A:Asn286 2.43 Na CG A:Asn286 3.37 Na OE2 A:Glu290 4.22 Na O A:Leu601 2.61 Na N A:Leu601 3.81 Na C A:Leu601 3.65 Na CA A:Leu601 4.30 Na OXT A:Leu601 4.53 interactive model: Sodium binding site 2 out of 2 in 4fxz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 4fxz. 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: Gly20, A: Asn21, A: Ala22, A: Val23, A: Gly24, A: Phe350, A: Ala351, A: Gly352, A: Leu353, A: Thr354, A: Ser355, conact list: Atom Atom Distance (A) Na O A:Gly20 2.19 Na C A:Gly20 3.38 Na CA A:Gly20 4.17 Na O A:Asn21 4.13 Na N A:Asn21 4.40 Na C A:Asn21 4.40 Na CA A:Asn21 4.60 Na O A:Ala22 5.00 Na C A:Ala22 4.87 Na O A:Val23 2.37 Na N A:Val23 4.60 Na C A:Val23 3.35 Na CA A:Val23 4.50 Na N A:Gly24 3.90 Na CA A:Gly24 3.66 Na O A:Phe350 4.61 Na O A:Ala351 2.30 Na C A:Ala351 3.37 Na CB A:Ala351 4.66 Na CA A:Ala351 3.93 Na O A:Gly352 4.70 Na N A:Gly352 4.50 Na C A:Gly352 4.74 Na CA A:Gly352 4.88 Na C A:Leu353 4.85 Na O A:Thr354 3.66 Na N A:Thr354 3.96 Na CB A:Thr354 3.15 Na CG2 A:Thr354 4.56 Na OG1 A:Thr354 2.37 Na C A:Thr354 2.99 Na CA A:Thr354 3.50 Na N A:Ser355 2.57 Na CB A:Ser355 3.21 Na OG A:Ser355 2.38 Na C A:Ser355 4.71 Na CA A:Ser355 3.21 interactive model: