Sodium in the structure of Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium (pdb 3f3e)

The binding sites of Sodium atom in the structure of Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium (pdb code 3f3e). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3f3e structure was solved by S.K.SINGH, C.L.PISCITELLI, A.YAMASHITA, E.GOUAUX, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 44.4-1.8 Space group C121 a (A) 89.361 b (A) 86.664 c (A) 81.382 alpha (°) 90.00 beta (°) 95.94 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 20.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3f3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3f3e. 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: Thr354, A: Ser355, conact list: Atom Atom Distance (A) Na O A:Gly20 2.31 Na C A:Gly20 3.43 Na CA A:Gly20 4.03 Na O A:Asn21 4.28 Na N A:Asn21 4.53 Na C A:Asn21 4.56 Na CA A:Asn21 4.81 Na O A:Ala22 5.00 Na C A:Ala22 4.77 Na O A:Val23 2.23 Na N A:Val23 4.31 Na CB A:Val23 4.80 Na C A:Val23 3.23 Na CA A:Val23 4.31 Na N A:Gly24 3.86 Na CA A:Gly24 3.61 Na O A:Phe350 4.42 Na O A:Ala351 2.36 Na C A:Ala351 3.44 Na CB A:Ala351 4.83 Na CA A:Ala351 3.97 Na O A:Gly352 4.60 Na N A:Gly352 4.57 Na C A:Gly352 4.71 Na CA A:Gly352 4.83 Na O A:Thr354 4.01 Na N A:Thr354 4.05 Na CB A:Thr354 3.43 Na CG2 A:Thr354 4.76 Na OG1 A:Thr354 2.40 Na C A:Thr354 3.32 Na CA A:Thr354 3.74 Na N A:Ser355 2.91 Na CB A:Ser355 3.29 Na OG A:Ser355 2.48 Na C A:Ser355 4.97 Na CA A:Ser355 3.49 interactive model: Sodium binding site 2 out of 2 in 3f3e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3f3e. 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: Phe253, A: Thr254, A: Leu255, A: Asn286, A: Glu290, A: Leu601, conact list: Atom Atom Distance (A) Na O A:Ala22 2.29 Na C A:Ala22 3.19 Na CB A:Ala22 4.43 Na CA A:Ala22 4.14 Na N A:Val23 3.89 Na C A:Val23 4.31 Na CA A:Val23 3.80 Na N A:Gly24 3.87 Na CA A:Gly24 4.95 Na C A:Gly26 4.78 Na CA A:Gly26 4.86 Na N A:Asn27 4.28 Na CB A:Asn27 4.51 Na ND2 A:Asn27 3.56 Na OD1 A:Asn27 2.31 Na CG A:Asn27 3.21 Na CA A:Asn27 4.78 Na O A:Phe253 4.72 Na O A:Thr254 2.39 Na N A:Thr254 4.64 Na CB A:Thr254 3.43 Na CG2 A:Thr254 4.52 Na OG1 A:Thr254 2.49 Na C A:Thr254 3.16 Na CA A:Thr254 3.25 Na N A:Leu255 4.43 Na CB A:Asn286 4.83 Na ND2 A:Asn286 3.60 Na OD1 A:Asn286 2.58 Na CG A:Asn286 3.42 Na OE2 A:Glu290 4.18 Na O A:Leu601 4.55 Na N A:Leu601 3.62 Na C A:Leu601 3.60 Na CA A:Leu601 4.17 Na OXT A:Leu601 2.59 interactive model: