Sodium in the structure of Crystal Structure of Leut Bound to L-Methionine and Sodium (pdb 3f3d)

The binding sites of Sodium atom in the structure of Crystal Structure of Leut Bound to L-Methionine and Sodium (pdb code 3f3d). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3f3d 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) 44.0-2.3 Space group C121 a (A) 88.333 b (A) 86.636 c (A) 81.166 alpha (°) 90.00 beta (°) 95.57 gamma (°) 90.00 Rfactor (%) 19.7 Rfree (%) 22.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3f3d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3f3d. 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 2.20 Na C A:Gly20 3.36 Na CA A:Gly20 4.02 Na O A:Asn21 4.35 Na N A:Asn21 4.46 Na C A:Asn21 4.58 Na CA A:Asn21 4.83 Na C A:Ala22 4.87 Na O A:Val23 2.09 Na N A:Val23 4.35 Na CB A:Val23 4.74 Na C A:Val23 3.14 Na CA A:Val23 4.23 Na N A:Gly24 3.82 Na CA A:Gly24 3.69 Na O A:Phe350 4.46 Na O A:Ala351 2.36 Na C A:Ala351 3.46 Na CB A:Ala351 4.84 Na CA A:Ala351 4.00 Na O A:Gly352 4.85 Na N A:Gly352 4.60 Na C A:Gly352 4.86 Na CA A:Gly352 4.95 Na O A:Thr354 4.18 Na N A:Thr354 4.16 Na CB A:Thr354 3.40 Na CG2 A:Thr354 4.69 Na OG1 A:Thr354 2.37 Na C A:Thr354 3.48 Na CA A:Thr354 3.82 Na N A:Ser355 3.10 Na CB A:Ser355 3.51 Na OG A:Ser355 2.60 Na CA A:Ser355 3.72 interactive model: Sodium binding site 2 out of 2 in 3f3d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3f3d. 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: Met601, conact list: Atom Atom Distance (A) Na O A:Ala22 2.12 Na C A:Ala22 3.12 Na CB A:Ala22 4.45 Na CA A:Ala22 4.13 Na N A:Val23 3.83 Na C A:Val23 4.26 Na CA A:Val23 3.79 Na N A:Gly24 3.75 Na CA A:Gly24 4.82 Na C A:Gly26 4.75 Na CA A:Gly26 4.82 Na N A:Asn27 4.26 Na CB A:Asn27 4.50 Na ND2 A:Asn27 3.63 Na OD1 A:Asn27 2.22 Na CG A:Asn27 3.21 Na CA A:Asn27 4.80 Na O A:Phe253 4.75 Na O A:Thr254 2.38 Na N A:Thr254 4.71 Na CB A:Thr254 3.61 Na CG2 A:Thr254 4.64 Na OG1 A:Thr254 2.68 Na C A:Thr254 3.22 Na CA A:Thr254 3.36 Na N A:Leu255 4.49 Na CB A:Asn286 4.95 Na ND2 A:Asn286 3.88 Na OD1 A:Asn286 2.63 Na CG A:Asn286 3.59 Na OE2 A:Glu290 4.10 Na O A:Met601 4.69 Na N A:Met601 3.66 Na C A:Met601 3.78 Na CA A:Met601 4.33 Na OXT A:Met601 2.79 interactive model: