Sodium in the structure of Crystal Structure Of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.51 Angstroms Resolution (pdb 2frs)

The binding sites of Sodium atom in the structure of Crystal Structure Of the F15W Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.51 Angstroms Resolution (pdb code 2frs). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2frs structure was solved by S.VAEZESLAMI, J.H.GEIGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.9-1.5 Space group P1 a (A) 34.582 b (A) 37.030 c (A) 58.693 alpha (°) 102.00 beta (°) 106.12 gamma (°) 93.00 Rfactor (%) 17.4 Rfree (%) 24 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2frs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2frs. 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: Gln74, A: Thr75, A: Val76, A: Gly78, A: Na503, A: Hoh585, A: Hoh623, A: Hoh698, A: Hoh700, A: Hoh715, A: Hoh729, conact list: Atom Atom Distance (A) Na O A:Gln74 3.32 Na N A:Gln74 4.70 Na OE1 A:Gln74 4.76 Na CB A:Gln74 3.33 Na CD A:Gln74 4.83 Na C A:Gln74 3.32 Na CG A:Gln74 4.63 Na CA A:Gln74 3.92 Na O A:Thr75 2.12 Na N A:Thr75 3.59 Na C A:Thr75 3.10 Na CA A:Thr75 3.94 Na O A:Val76 3.93 Na N A:Val76 3.94 Na C A:Val76 4.16 Na CA A:Val76 4.08 Na N A:Gly78 4.17 Na C A:Gly78 4.77 Na CA A:Gly78 4.01 Na NA A:Na503 3.04 Na O A:Hoh585 3.92 Na O A:Hoh623 3.88 Na O A:Hoh698 4.62 Na O A:Hoh698 4.45 Na O A:Hoh700 2.18 Na O A:Hoh715 4.29 Na O A:Hoh729 4.84 interactive model: Sodium binding site 2 out of 4 in 2frs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2frs. 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: Thr75, A: Leu99, A: Gly104, A: Pro105, A: Lys106, A: Thr107, A: Hoh649, A: Hoh658, A: Hoh659, A: Hoh716, conact list: Atom Atom Distance (A) Na CG2 A:Thr75 4.43 Na OG1 A:Thr75 4.90 Na CD1 A:Leu99 4.31 Na CD2 A:Leu99 4.70 Na CG A:Leu99 4.16 Na O A:Gly104 4.27 Na N A:Gly104 4.82 Na C A:Gly104 3.71 Na CA A:Gly104 3.96 Na O A:Pro105 2.06 Na N A:Pro105 3.47 Na CB A:Pro105 4.40 Na CD A:Pro105 3.58 Na C A:Pro105 3.21 Na CG A:Pro105 3.81 Na CA A:Pro105 3.91 Na N A:Lys106 4.25 Na C A:Lys106 4.46 Na CA A:Lys106 4.46 Na N A:Thr107 4.09 Na CB A:Thr107 4.34 Na CG2 A:Thr107 3.69 Na OG1 A:Thr107 3.93 Na CA A:Thr107 4.84 Na O A:Hoh649 3.40 Na O A:Hoh658 3.70 Na O A:Hoh659 3.68 Na O A:Hoh716 2.35 interactive model: Sodium binding site 3 out of 4 in 2frs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2frs. 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: Thr75, A: Val76, A: Asp77, A: Gly78, A: Na501, A: Hoh698, A: Hoh699, A: Hoh700, A: Hoh711, A: Hoh715, conact list: Atom Atom Distance (A) Na O A:Thr75 3.61 Na C A:Thr75 4.59 Na O A:Val76 2.29 Na N A:Val76 4.81 Na C A:Val76 3.35 Na CG1 A:Val76 4.97 Na CA A:Val76 3.98 Na N A:Asp77 4.40 Na C A:Asp77 4.44 Na CA A:Asp77 4.71 Na N A:Gly78 4.12 Na CA A:Gly78 4.26 Na NA A:Na501 3.04 Na O A:Hoh698 2.80 Na O A:Hoh698 3.74 Na O A:Hoh699 3.35 Na O A:Hoh700 2.16 Na O A:Hoh711 4.03 Na O A:Hoh711 3.83 Na O A:Hoh715 2.00 interactive model: Sodium binding site 4 out of 4 in 2frs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2frs. 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: Leu19, A: Lys20, A: Val21, A: Leu22, A: Gly23, A: Val24, A: Hoh564, A: Hoh573, conact list: Atom Atom Distance (A) Na O A:Leu19 3.99 Na O A:Lys20 3.30 Na C A:Lys20 4.19 Na CA A:Lys20 4.59 Na O A:Val21 4.94 Na C A:Val21 4.83 Na O A:Leu22 2.19 Na N A:Leu22 4.69 Na C A:Leu22 3.19 Na CA A:Leu22 4.54 Na O A:Gly23 2.63 Na N A:Gly23 3.60 Na C A:Gly23 3.08 Na CA A:Gly23 3.26 Na N A:Val24 4.09 Na C A:Val24 4.46 Na CA A:Val24 4.88 Na O A:Hoh564 4.91 Na O A:Hoh573 2.70 interactive model: