Sodium in the structure of Crystal Structure of Leut Bound to L-Tryptophan and Sodium (pdb 3f3a)

The binding sites of Sodium atom in the structure of Crystal Structure of Leut Bound to L-Tryptophan and Sodium (pdb code 3f3a). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3f3a 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) 48.2-2.0 Space group C121 a (A) 88.566 b (A) 85.218 c (A) 82.274 alpha (°) 90.00 beta (°) 93.33 gamma (°) 90.00 Rfactor (%) 19.8 Rfree (%) 22.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3f3a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3f3a. 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 3.47 Na CA A:Gly20 4.22 Na O A:Asn21 4.03 Na N A:Asn21 4.45 Na C A:Asn21 4.30 Na CA A:Asn21 4.51 Na N A:Ala22 4.98 Na C A:Ala22 4.78 Na O A:Val23 2.27 Na N A:Val23 4.33 Na CB A:Val23 4.70 Na C A:Val23 3.35 Na CA A:Val23 4.30 Na N A:Gly24 4.14 Na CA A:Gly24 4.10 Na O A:Phe350 4.43 Na O A:Ala351 2.32 Na C A:Ala351 3.45 Na CB A:Ala351 4.92 Na CA A:Ala351 4.08 Na O A:Gly352 4.48 Na N A:Gly352 4.54 Na C A:Gly352 4.66 Na CA A:Gly352 4.76 Na O A:Thr354 4.03 Na N A:Thr354 4.15 Na CB A:Thr354 3.47 Na CG2 A:Thr354 4.79 Na OG1 A:Thr354 2.43 Na C A:Thr354 3.42 Na CA A:Thr354 3.83 Na N A:Ser355 3.08 Na CB A:Ser355 3.30 Na OG A:Ser355 2.28 Na CA A:Ser355 3.60 interactive model: Sodium binding site 2 out of 2 in 3f3a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3f3a. 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: Asn27, A: Phe253, A: Thr254, A: Leu255, A: Asn286, A: Glu290, A: Trp601, A: Hoh539, conact list: Atom Atom Distance (A) Na O A:Ala22 2.42 Na C A:Ala22 3.21 Na CB A:Ala22 4.26 Na CA A:Ala22 4.14 Na N A:Val23 3.84 Na C A:Val23 4.39 Na CA A:Val23 3.82 Na N A:Gly24 3.97 Na N A:Asn27 4.76 Na CB A:Asn27 4.73 Na ND2 A:Asn27 3.62 Na OD1 A:Asn27 2.59 Na CG A:Asn27 3.41 Na O A:Phe253 4.81 Na O A:Thr254 2.49 Na N A:Thr254 4.69 Na CB A:Thr254 3.57 Na CG2 A:Thr254 4.47 Na OG1 A:Thr254 2.68 Na C A:Thr254 3.23 Na CA A:Thr254 3.33 Na N A:Leu255 4.49 Na CB A:Asn286 4.64 Na ND2 A:Asn286 3.55 Na OD1 A:Asn286 2.40 Na CG A:Asn286 3.29 Na OE1 A:Glu290 4.15 Na N A:Trp601 3.49 Na C A:Trp601 3.44 Na CA A:Trp601 4.04 Na O A:Trp601 4.28 Na OXT A:Trp601 2.58 Na O A:Hoh539 3.90 interactive model: