Sodium in the structure of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure (pdb 2v5c)

The binding sites of Sodium atom in the structure of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure (pdb code 2v5c). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2v5c structure was solved by E.FICKO-BLEAN, K.J.GREGG, J.J.ADAMS, J.H.HEHEMANN, S.J.SMITH, M.CZJZEK, A.B.BORASTON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 105.4-2.1 Space group I212121 a (A) 130.385 b (A) 150.046 c (A) 155.428 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 25.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2v5c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2v5c. 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: Met571, A: Gln575, A: Tyr583, A: Ala616, A: Leu617, A: Ser618, A: Phe619, A: Asp620, A: Cac1629, A: Hoh2571, conact list: Atom Atom Distance (A) Na CB A:Met571 4.55 Na CE A:Met571 4.29 Na CG A:Met571 4.69 Na SD A:Met571 3.57 Na OE1 A:Gln575 4.49 Na CD A:Gln575 4.98 Na CE2 A:Tyr583 4.92 Na CD1 A:Tyr583 4.91 Na CZ A:Tyr583 3.58 Na CE1 A:Tyr583 3.60 Na OH A:Tyr583 2.64 Na O A:Ala616 2.65 Na C A:Ala616 3.77 Na CA A:Ala616 4.99 Na O A:Leu617 3.04 Na N A:Leu617 4.30 Na C A:Leu617 3.60 Na CA A:Leu617 3.91 Na N A:Ser618 4.51 Na C A:Ser618 4.76 Na O A:Phe619 2.65 Na N A:Phe619 4.19 Na CB A:Phe619 4.77 Na C A:Phe619 3.79 Na CA A:Phe619 4.46 Na N A:Asp620 4.83 Na O2 A:Cac1629 4.61 Na AS A:Cac1629 4.89 Na C2 A:Cac1629 4.34 Na C1 A:Cac1629 4.94 Na O A:Hoh2571 2.86 interactive model: Sodium binding site 2 out of 2 in 2v5c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2v5c. 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: Met571, B: Gln575, B: Tyr583, B: Ala616, B: Leu617, B: Ser618, B: Phe619, B: Asp620, B: Hoh2191, B: Hoh2513, B: Hoh2556, conact list: Atom Atom Distance (A) Na CB B:Met571 4.99 Na CE B:Met571 3.59 Na SD B:Met571 4.28 Na NE2 B:Gln575 4.96 Na OE1 B:Gln575 3.54 Na CD B:Gln575 4.51 Na CE2 B:Tyr583 4.97 Na CD1 B:Tyr583 4.99 Na CZ B:Tyr583 3.65 Na CE1 B:Tyr583 3.67 Na OH B:Tyr583 2.72 Na O B:Ala616 2.55 Na C B:Ala616 3.70 Na CA B:Ala616 4.92 Na O B:Leu617 3.21 Na N B:Leu617 4.27 Na C B:Leu617 3.70 Na CA B:Leu617 3.94 Na N B:Ser618 4.61 Na C B:Ser618 4.69 Na O B:Phe619 2.41 Na N B:Phe619 3.89 Na CB B:Phe619 4.54 Na C B:Phe619 3.54 Na CA B:Phe619 4.16 Na N B:Asp620 4.65 Na CA B:Asp620 4.95 Na O B:Hoh2191 4.91 Na O B:Hoh2513 4.97 Na O B:Hoh2556 4.02 interactive model: