Sodium in the structure of The Actinorhodin Ketosynthase/Chain Length Factor (pdb 1tqy)

The binding sites of Sodium atom in the structure of The Actinorhodin Ketosynthase/Chain Length Factor (pdb code 1tqy). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1tqy structure was solved by A.T.KEATINGE-CLAY, D.A.MALTBY, K.F.MEDZIHRADSZKY, C.KHOSLA, R.M.STROUD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.0 Space group H3 a (A) 262.700 b (A) 262.700 c (A) 224.030 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.3 Rfree (%) 25.3 Sodium Binding Sites: Sodium binding site 1 out of 4 in 1tqy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1tqy. 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: B: Pro13, B: Asn14, B: Gly31, B: Gln50, B: Ile51, B: Asp52, B: Hoh1112, B: Hoh1123, B: Hoh1161, B: Hoh1162, B: Hoh1205, B: Hoh1233, conact list: Atom Atom Distance (A) Na O B:Pro13 2.26 Na CB B:Pro13 4.10 Na C B:Pro13 3.30 Na CA B:Pro13 3.77 Na N B:Asn14 4.47 Na CA B:Asn14 4.85 Na O B:Gly31 3.31 Na C B:Gly31 3.95 Na CA B:Gly31 3.83 Na O B:Gln50 2.29 Na N B:Gln50 4.47 Na CB B:Gln50 4.93 Na C B:Gln50 3.51 Na CA B:Gln50 4.49 Na N B:Ile51 4.36 Na C B:Ile51 4.83 Na CA B:Ile51 4.33 Na N B:Asp52 4.36 Na OD2 B:Asp52 4.12 Na CG B:Asp52 4.76 Na O B:Hoh1112 2.34 Na O B:Hoh1123 4.89 Na O B:Hoh1161 2.99 Na O B:Hoh1162 4.36 Na O B:Hoh1205 4.49 Na O B:Hoh1233 1.92 interactive model: Sodium binding site 2 out of 4 in 1tqy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1tqy. 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: D: Pro13, D: Asn14, D: Gly31, D: Gln50, D: Ile51, D: Asp52, D: Hoh1100, D: Hoh1104, D: Hoh1153, D: Hoh1166, D: Hoh1192, D: Hoh1225, D: Hoh1260, conact list: Atom Atom Distance (A) Na O D:Pro13 2.36 Na CB D:Pro13 4.14 Na C D:Pro13 3.40 Na CA D:Pro13 3.89 Na N D:Asn14 4.54 Na CA D:Asn14 4.92 Na O D:Gly31 3.15 Na C D:Gly31 3.80 Na CA D:Gly31 3.72 Na O D:Gln50 2.51 Na N D:Gln50 4.50 Na C D:Gln50 3.71 Na CA D:Gln50 4.60 Na N D:Ile51 4.62 Na CA D:Ile51 4.58 Na N D:Asp52 4.51 Na OD2 D:Asp52 4.29 Na CG D:Asp52 4.86 Na O D:Hoh1100 2.35 Na O D:Hoh1104 1.96 Na O D:Hoh1153 4.47 Na O D:Hoh1166 4.91 Na O D:Hoh1192 2.51 Na O D:Hoh1225 4.50 Na O D:Hoh1260 4.18 interactive model: Sodium binding site 3 out of 4 in 1tqy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1tqy. 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: F: Pro13, F: Asn14, F: Gly31, F: Leu32, F: Gln50, F: Ile51, F: Asp52, F: Hoh1112, F: Hoh1135, F: Hoh1142, F: Hoh1154, F: Hoh1155, F: Hoh1241, conact list: Atom Atom Distance (A) Na O F:Pro13 2.37 Na CB F:Pro13 4.05 Na C F:Pro13 3.41 Na CA F:Pro13 3.87 Na N F:Asn14 4.58 Na O F:Gly31 3.05 Na C F:Gly31 3.67 Na CA F:Gly31 3.63 Na N F:Leu32 4.89 Na O F:Gln50 2.26 Na N F:Gln50 4.22 Na CB F:Gln50 4.80 Na C F:Gln50 3.47 Na CA F:Gln50 4.37 Na N F:Ile51 4.40 Na C F:Ile51 4.98 Na CA F:Ile51 4.48 Na N F:Asp52 4.53 Na OD2 F:Asp52 4.18 Na CG F:Asp52 4.76 Na O F:Hoh1112 2.29 Na O F:Hoh1135 2.42 Na O F:Hoh1142 4.80 Na O F:Hoh1154 2.50 Na O F:Hoh1155 4.69 Na O F:Hoh1241 4.91 interactive model: Sodium binding site 4 out of 4 in 1tqy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1tqy. 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: Pro13, H: Asn14, H: Gly31, H: Gln50, H: Ile51, H: Asp52, H: Hoh1125, H: Hoh1138, H: Hoh1141, H: Hoh1167, H: Hoh1176, H: Hoh1219, conact list: Atom Atom Distance (A) Na O H:Pro13 2.43 Na CB H:Pro13 4.02 Na C H:Pro13 3.37 Na CA H:Pro13 3.80 Na N H:Asn14 4.50 Na CA H:Asn14 4.94 Na O H:Gly31 3.06 Na C H:Gly31 3.79 Na CA H:Gly31 3.77 Na O H:Gln50 2.33 Na N H:Gln50 4.38 Na CB H:Gln50 4.94 Na C H:Gln50 3.56 Na CA H:Gln50 4.50 Na N H:Ile51 4.45 Na C H:Ile51 4.91 Na CA H:Ile51 4.44 Na N H:Asp52 4.40 Na OD2 H:Asp52 3.96 Na CG H:Asp52 4.68 Na O H:Hoh1125 2.36 Na O H:Hoh1138 4.92 Na O H:Hoh1141 4.81 Na O H:Hoh1167 4.60 Na O H:Hoh1176 2.48 Na O H:Hoh1219 4.86 interactive model: