Sodium in the structure of Crystal Structure of Leut Bound to L-Selenomethionine and Sodium (pdb 3f4i)

The binding sites of Sodium atom in the structure of Crystal Structure of Leut Bound to L-Selenomethionine and Sodium (pdb code 3f4i). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3f4i 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) 31.1-1.9 Space group C121 a (A) 89.777 b (A) 86.703 c (A) 81.692 alpha (°) 90.00 beta (°) 95.85 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 21.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3f4i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3f4i. 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 2.46 Na C A:Gly20 3.56 Na CA A:Gly20 4.12 Na O A:Asn21 4.30 Na N A:Asn21 4.67 Na C A:Asn21 4.60 Na CA A:Asn21 4.95 Na O A:Ala22 4.75 Na C A:Ala22 4.68 Na O A:Val23 2.39 Na N A:Val23 4.39 Na CB A:Val23 4.78 Na C A:Val23 3.30 Na CA A:Val23 4.34 Na N A:Gly24 3.92 Na CA A:Gly24 3.70 Na O A:Phe350 4.45 Na O A:Ala351 2.49 Na C A:Ala351 3.54 Na CB A:Ala351 4.86 Na CA A:Ala351 4.01 Na O A:Gly352 4.77 Na N A:Gly352 4.70 Na C A:Gly352 4.87 Na O A:Thr354 4.06 Na N A:Thr354 4.14 Na CB A:Thr354 3.55 Na CG2 A:Thr354 4.88 Na OG1 A:Thr354 2.58 Na C A:Thr354 3.43 Na CA A:Thr354 3.86 Na N A:Ser355 3.07 Na CB A:Ser355 3.39 Na OG A:Ser355 2.71 Na CA A:Ser355 3.58 interactive model: Sodium binding site 2 out of 2 in 3f4i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3f4i. 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: Mse601, conact list: Atom Atom Distance (A) Na O A:Ala22 2.61 Na C A:Ala22 3.32 Na CB A:Ala22 4.49 Na CA A:Ala22 4.26 Na N A:Val23 3.88 Na C A:Val23 4.21 Na CA A:Val23 3.77 Na N A:Gly24 3.67 Na CA A:Gly24 4.75 Na C A:Gly26 4.70 Na CA A:Gly26 4.83 Na N A:Asn27 4.23 Na CB A:Asn27 4.54 Na ND2 A:Asn27 3.51 Na OD1 A:Asn27 2.48 Na CG A:Asn27 3.25 Na CA A:Asn27 4.76 Na O A:Phe253 4.78 Na O A:Thr254 2.57 Na N A:Thr254 4.68 Na CB A:Thr254 3.67 Na CG2 A:Thr254 4.66 Na OG1 A:Thr254 2.80 Na C A:Thr254 3.31 Na CA A:Thr254 3.36 Na N A:Leu255 4.59 Na CB A:Asn286 4.95 Na ND2 A:Asn286 3.63 Na OD1 A:Asn286 2.72 Na CG A:Asn286 3.53 Na OE2 A:Glu290 4.03 Na O A:Mse601 4.69 Na N A:Mse601 3.76 Na C A:Mse601 3.81 Na CA A:Mse601 4.40 Na OXT A:Mse601 2.81 interactive model: