Sodium in the structure of Fv Ige Spe-7 in Complex With Alizarin Red (pdb 1oar)

The binding sites of Sodium atom in the structure of Fv Ige Spe-7 in Complex With Alizarin Red (pdb code 1oar). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1oar structure was solved by L.C.JAMES, P.ROVERSI, D.TAWFIK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.7-2.2 Space group P212121 a (A) 78.917 b (A) 78.882 c (A) 169.036 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.5 Rfree (%) 24.1 Sodium Binding Sites: Sodium binding site 1 out of 6 in 1oar Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1oar. 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: L: Gln6, L: Glu7, L: Ser8, L: Gly102, L: Gly103, L: Thr104, L: Hoh2011, L: Hoh2012, L: Hoh2062, conact list: Atom Atom Distance (A) Na O L:Gln6 3.26 Na N L:Gln6 4.45 Na CB L:Gln6 4.18 Na C L:Gln6 4.03 Na CA L:Gln6 4.49 Na O L:Glu7 3.87 Na N L:Glu7 4.91 Na C L:Glu7 4.17 Na O L:Ser8 4.86 Na N L:Ser8 4.16 Na CB L:Ser8 4.61 Na C L:Ser8 4.86 Na CA L:Ser8 3.86 Na O L:Gly102 3.89 Na N L:Gly102 4.30 Na C L:Gly102 3.59 Na CA L:Gly102 3.82 Na O L:Gly103 2.78 Na N L:Gly103 3.77 Na C L:Gly103 3.83 Na CA L:Gly103 4.38 Na N L:Thr104 4.91 Na O L:Hoh2011 4.46 Na O L:Hoh2012 4.66 Na O L:Hoh2062 2.76 interactive model: Sodium binding site 2 out of 6 in 1oar Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1oar. 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: N: Ser8, N: Gly102, N: Gly103, J: Na903, N: Cl913, N: Hoh2010, N: Hoh2011, N: Hoh2012, N: Hoh2065, conact list: Atom Atom Distance (A) Na O N:Ser8 4.32 Na CB N:Ser8 4.74 Na OG N:Ser8 3.92 Na C N:Ser8 4.94 Na CA N:Ser8 4.74 Na O N:Gly102 4.35 Na O N:Gly103 4.36 Na NA J:Na903 4.31 Na CL N:Cl913 3.28 Na O N:Hoh2010 2.16 Na O N:Hoh2011 4.05 Na O N:Hoh2012 2.06 Na O N:Hoh2065 4.59 interactive model: Sodium binding site 3 out of 6 in 1oar Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1oar. 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: N: Gln6, N: Glu7, N: Ser8, N: Gly102, N: Gly103, N: Thr104, I: Na903, N: Hoh2010, N: Hoh2012, N: Hoh2064, conact list: Atom Atom Distance (A) Na O N:Gln6 3.27 Na N N:Gln6 4.47 Na CB N:Gln6 4.22 Na C N:Gln6 4.05 Na CA N:Gln6 4.52 Na O N:Glu7 3.91 Na N N:Glu7 4.93 Na C N:Glu7 4.19 Na O N:Ser8 4.88 Na N N:Ser8 4.17 Na CB N:Ser8 4.61 Na C N:Ser8 4.87 Na CA N:Ser8 3.87 Na O N:Gly102 3.90 Na N N:Gly102 4.30 Na C N:Gly102 3.61 Na CA N:Gly102 3.81 Na O N:Gly103 2.82 Na N N:Gly103 3.79 Na C N:Gly103 3.87 Na CA N:Gly103 4.41 Na N N:Thr104 4.95 Na NA I:Na903 4.31 Na O N:Hoh2010 4.46 Na O N:Hoh2012 4.66 Na O N:Hoh2064 2.76 interactive model: Sodium binding site 4 out of 6 in 1oar Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1oar. 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: H: Gly44, L: Glu40, L: Ile87, L: Phe89, L: Gly102, L: Cl913, H: Hoh2021, H: Hoh2026, L: Hoh2035, L: Hoh2063, conact list: Atom Atom Distance (A) Na CA H:Gly44 4.70 Na OE1 L:Glu40 4.65 Na CD1 L:Ile87 4.17 Na CG2 L:Ile87 4.36 Na CE2 L:Phe89 4.65 Na CZ L:Phe89 3.66 Na CE1 L:Phe89 4.27 Na O L:Gly102 4.57 Na CL L:Cl913 2.74 Na O H:Hoh2021 3.56 Na O H:Hoh2026 3.08 Na O L:Hoh2035 2.33 Na O L:Hoh2063 4.70 interactive model: Sodium binding site 5 out of 6 in 1oar Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1oar. 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: J: Tyr102, J: Gly103, M: Thr17, M: Val18, M: Thr19, M: Thr76, M: Cl913, M: Hoh2007, conact list: Atom Atom Distance (A) Na O J:Tyr102 2.95 Na CB J:Tyr102 3.97 Na C J:Tyr102 3.32 Na CA J:Tyr102 4.25 Na N J:Gly103 3.59 Na C J:Gly103 4.84 Na CA J:Gly103 3.57 Na O M:Thr17 3.83 Na CB M:Thr17 4.43 Na CG2 M:Thr17 3.47 Na C M:Thr17 3.90 Na CA M:Thr17 4.81 Na O M:Val18 4.11 Na N M:Val18 3.91 Na C M:Val18 3.54 Na CA M:Val18 3.76 Na N M:Thr19 3.29 Na CB M:Thr19 3.29 Na CG2 M:Thr19 4.67 Na OG1 M:Thr19 2.65 Na CA M:Thr19 3.87 Na CG2 M:Thr76 4.65 Na CL M:Cl913 3.32 Na O M:Hoh2007 2.89 interactive model: Sodium binding site 6 out of 6 in 1oar Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1oar. 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: J: Gly44, N: Glu40, N: Ile87, N: Phe89, N: Gly102, N: Cl913, J: Hoh2019, J: Hoh2024, N: Hoh2034, N: Hoh2065, conact list: Atom Atom Distance (A) Na CA J:Gly44 4.71 Na OE1 N:Glu40 4.65 Na CD1 N:Ile87 4.17 Na CG2 N:Ile87 4.36 Na CE2 N:Phe89 4.65 Na CZ N:Phe89 3.66 Na CE1 N:Phe89 4.27 Na O N:Gly102 4.57 Na CL N:Cl913 2.74 Na O J:Hoh2019 3.56 Na O J:Hoh2024 3.11 Na O N:Hoh2034 2.33 Na O N:Hoh2065 4.72 interactive model: