Sodium in the structure of Structure of Human Guanosine Monophosphate Reductase GMPR1 in Complex With Gmp (pdb 2ble)

The binding sites of Sodium atom in the structure of Structure of Human Guanosine Monophosphate Reductase GMPR1 in Complex With Gmp (pdb code 2ble). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ble structure was solved by G.BUNKOCZI, A.HARONITI, S.NG, F.VON DELFT, U.OPPERMANN, C.ARROWSMITH, M.SUNDSTROM, A.EDWARDS, O.GILEADI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.9 Space group P4212 a (A) 117.780 b (A) 117.780 c (A) 54.420 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 22.8 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2ble Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ble. 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: Thr57, A: Val58, A: Ser246, A: Gly247, A: Cys251, A: Lys264, A: Leu265, A: Phe266, A: Val295, A: Hoh2102, conact list: Atom Atom Distance (A) Na O A:Thr57 4.65 Na CB A:Thr57 3.49 Na CG2 A:Thr57 4.26 Na OG1 A:Thr57 3.32 Na C A:Thr57 4.64 Na CA A:Thr57 4.71 Na CG1 A:Val58 4.33 Na CB A:Ser246 3.73 Na OG A:Ser246 4.86 Na C A:Ser246 3.95 Na CA A:Ser246 3.68 Na N A:Gly247 3.29 Na CA A:Gly247 4.26 Na CB A:Cys251 3.88 Na SG A:Cys251 3.87 Na CB A:Lys264 4.76 Na CD A:Lys264 4.69 Na O A:Leu265 4.21 Na C A:Leu265 4.76 Na N A:Phe266 4.90 Na CB A:Phe266 4.25 Na CE2 A:Phe266 4.65 Na CD2 A:Phe266 3.78 Na CG A:Phe266 4.44 Na CA A:Phe266 4.45 Na CG1 A:Val295 4.84 Na O A:Hoh2102 3.08 interactive model: Sodium binding site 2 out of 3 in 2ble Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2ble. 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: Ser105, A: Gly106, A: Gln107, A: Phe141, A: Na1346, A: Hoh2017, A: Hoh2047, conact list: Atom Atom Distance (A) Na O A:Ser105 2.73 Na C A:Ser105 3.95 Na CA A:Ser105 4.98 Na N A:Gly106 4.73 Na C A:Gly106 4.45 Na CA A:Gly106 4.55 Na N A:Gln107 4.28 Na CA A:Gln107 4.87 Na CD1 A:Phe141 4.44 Na CE1 A:Phe141 4.75 Na NA A:Na1346 0.00 Na NA A:Na1346 2.07 Na O A:Hoh2017 4.63 Na O A:Hoh2047 4.76 interactive model: Sodium binding site 3 out of 3 in 2ble Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2ble. 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: Ser105, A: Leu110, A: Phe141, A: Leu144, A: Na1346, conact list: Atom Atom Distance (A) Na O A:Ser105 4.40 Na CD2 A:Leu110 4.80 Na CD1 A:Phe141 4.41 Na CE1 A:Phe141 4.82 Na CD2 A:Leu144 3.87 Na NA A:Na1346 2.07 Na NA A:Na1346 0.00 interactive model: