Sodium in the structure of Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) (pdb 2ovl)

The binding sites of Sodium atom in the structure of Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) (pdb code 2ovl). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ovl structure was solved by K.N.RAO, S.K.BURLEY, S.SWAMINATHAN, NEW YORK SGX RESEARCHCENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.0-2.1 Space group P4212 a (A) 177.603 b (A) 177.603 c (A) 111.812 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.5 Rfree (%) 24.3 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2ovl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ovl. 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: Asp197, A: Asn199, A: Glu223, A: Glu224, A: Glu249, A: Hoh451, conact list: Atom Atom Distance (A) Na CB A:Asp197 4.72 Na OD2 A:Asp197 3.11 Na OD1 A:Asp197 2.75 Na CG A:Asp197 3.27 Na N A:Asn199 4.44 Na CB A:Asn199 4.62 Na ND2 A:Asn199 4.66 Na OD1 A:Asn199 3.21 Na CG A:Asn199 3.94 Na CA A:Asn199 4.13 Na O A:Glu223 4.86 Na OE1 A:Glu223 4.64 Na CB A:Glu223 4.60 Na OE2 A:Glu223 2.85 Na CD A:Glu223 3.53 Na C A:Glu223 4.81 Na CG A:Glu223 3.59 Na N A:Glu224 4.80 Na OE1 A:Glu224 4.32 Na CB A:Glu224 3.66 Na OE2 A:Glu224 2.51 Na CD A:Glu224 3.29 Na CG A:Glu224 3.58 Na CA A:Glu224 4.87 Na OE1 A:Glu249 2.68 Na OE2 A:Glu249 3.53 Na CD A:Glu249 3.18 Na CG A:Glu249 4.14 Na O A:Hoh451 3.70 interactive model: Sodium binding site 2 out of 4 in 2ovl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2ovl. 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: Lys168, B: Asp197, B: Asn199, B: Glu223, B: Glu224, B: Glu249, B: Hoh426, B: Hoh448, B: Hoh493, conact list: Atom Atom Distance (A) Na NZ B:Lys168 4.90 Na CB B:Asp197 4.46 Na OD2 B:Asp197 2.62 Na OD1 B:Asp197 2.71 Na CG B:Asp197 2.99 Na N B:Asn199 4.46 Na CB B:Asn199 4.68 Na ND2 B:Asn199 4.59 Na OD1 B:Asn199 3.22 Na CG B:Asn199 3.94 Na CA B:Asn199 4.24 Na OE1 B:Glu223 4.82 Na CB B:Glu223 4.57 Na OE2 B:Glu223 2.91 Na CD B:Glu223 3.67 Na C B:Glu223 4.97 Na CG B:Glu223 3.71 Na OE1 B:Glu224 4.39 Na CB B:Glu224 4.03 Na OE2 B:Glu224 2.33 Na CD B:Glu224 3.33 Na CG B:Glu224 3.76 Na OE1 B:Glu249 2.62 Na OE2 B:Glu249 3.46 Na CD B:Glu249 3.11 Na CG B:Glu249 4.09 Na O B:Hoh426 3.96 Na O B:Hoh448 3.81 Na O B:Hoh493 3.54 interactive model: Sodium binding site 3 out of 4 in 2ovl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2ovl. 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: C: Lys166, C: Lys168, C: Asp197, C: Glu223, C: Glu249, C: Glu270, C: His299, C: Glu319, C: Hoh427, conact list: Atom Atom Distance (A) Na CE C:Lys166 4.03 Na NZ C:Lys166 2.92 Na NZ C:Lys168 3.96 Na OD2 C:Asp197 3.21 Na CG C:Asp197 4.43 Na OE1 C:Glu223 4.52 Na OE2 C:Glu223 3.00 Na CD C:Glu223 4.10 Na OE1 C:Glu249 2.92 Na OE2 C:Glu249 4.08 Na CD C:Glu249 3.87 Na OE2 C:Glu270 4.10 Na NE2 C:His299 3.18 Na CB C:His299 4.65 Na ND1 C:His299 4.75 Na CD2 C:His299 2.64 Na CE1 C:His299 4.43 Na CG C:His299 3.86 Na OE1 C:Glu319 4.37 Na OE2 C:Glu319 2.95 Na CD C:Glu319 3.99 Na O C:Hoh427 3.97 interactive model: Sodium binding site 4 out of 4 in 2ovl Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2ovl. 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: Asp197, D: Asn199, D: Glu223, D: Glu224, D: Glu249, D: Hoh425, D: Hoh457, conact list: Atom Atom Distance (A) Na CB D:Asp197 4.57 Na OD2 D:Asp197 2.78 Na OD1 D:Asp197 2.70 Na CG D:Asp197 3.09 Na N D:Asn199 4.23 Na CB D:Asn199 4.49 Na ND2 D:Asn199 4.64 Na OD1 D:Asn199 3.10 Na CG D:Asn199 3.85 Na CA D:Asn199 3.96 Na O D:Glu223 4.83 Na OE1 D:Glu223 4.99 Na CB D:Glu223 4.70 Na OE2 D:Glu223 3.08 Na CD D:Glu223 3.83 Na C D:Glu223 4.88 Na CG D:Glu223 3.84 Na N D:Glu224 4.96 Na OE1 D:Glu224 4.48 Na CB D:Glu224 3.82 Na OE2 D:Glu224 2.57 Na CD D:Glu224 3.50 Na CG D:Glu224 3.96 Na OE1 D:Glu249 2.88 Na OE2 D:Glu249 3.36 Na CD D:Glu249 3.22 Na CG D:Glu249 4.26 Na O D:Hoh425 4.37 Na O D:Hoh457 3.42 interactive model: