Sodium in the structure of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida (pdb 1u7h)

The binding sites of Sodium atom in the structure of Structure and A Proposed Mechanism For Ornithine Cyclodeaminase From Pseudomonas Putida (pdb code 1u7h). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1u7h structure was solved by S.ALAM, J.L.GOODMAN, S.WANG, F.J.RUZICKA, P.A.FREY, J.E.WEDEKIND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-1.8 Space group P212121 a (A) 69.900 b (A) 78.600 c (A) 119.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.8 Rfree (%) 18.1 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1u7h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1u7h. 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: Ala224, A: Val225, A: Gly226, A: Gly227, A: Asp228, A: Glu234, A: Glu258, A: Asp292, A: Ser293, A: Val294, A: Nad802, A: Hoh992, A: Hoh993, A: Hoh994, conact list: Atom Atom Distance (A) Na O A:Ala224 2.55 Na C A:Ala224 3.28 Na CB A:Ala224 4.34 Na CA A:Ala224 4.41 Na O A:Val225 3.35 Na N A:Val225 3.67 Na C A:Val225 3.31 Na CA A:Val225 3.52 Na O A:Gly226 4.99 Na N A:Gly226 3.86 Na C A:Gly226 4.16 Na CA A:Gly226 4.53 Na O A:Gly227 2.44 Na N A:Gly227 3.45 Na C A:Gly227 3.44 Na CA A:Gly227 3.81 Na N A:Asp228 4.63 Na OE1 A:Glu234 4.66 Na OE2 A:Glu258 4.42 Na CG A:Glu258 4.78 Na C A:Asp292 4.73 Na OD1 A:Asp292 4.30 Na O A:Ser293 2.41 Na N A:Ser293 3.99 Na CB A:Ser293 4.69 Na C A:Ser293 3.49 Na CA A:Ser293 4.19 Na N A:Val294 4.51 Na CG1 A:Val294 4.53 Na CA A:Val294 4.70 Na N7N A:Nad802 4.84 Na O A:Hoh992 2.54 Na O A:Hoh993 4.60 Na O A:Hoh994 2.52 interactive model: Sodium binding site 2 out of 2 in 1u7h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1u7h. 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: Ala224, B: Val225, B: Gly226, B: Gly227, B: Asp228, B: Glu234, B: Glu258, B: Asp292, B: Ser293, B: Val294, B: Nad801, B: Hoh1104, B: Hoh1105, B: Hoh1106, conact list: Atom Atom Distance (A) Na O B:Ala224 2.55 Na C B:Ala224 3.21 Na CB B:Ala224 4.29 Na CA B:Ala224 4.35 Na O B:Val225 3.22 Na N B:Val225 3.56 Na CB B:Val225 4.94 Na C B:Val225 3.21 Na CA B:Val225 3.42 Na O B:Gly226 4.97 Na N B:Gly226 3.81 Na C B:Gly226 4.14 Na CA B:Gly226 4.49 Na O B:Gly227 2.47 Na N B:Gly227 3.42 Na C B:Gly227 3.47 Na CA B:Gly227 3.81 Na N B:Asp228 4.66 Na OE1 B:Glu234 4.54 Na OE2 B:Glu258 4.44 Na CG B:Glu258 4.90 Na C B:Asp292 4.77 Na OD1 B:Asp292 4.37 Na O B:Ser293 2.40 Na N B:Ser293 4.00 Na CB B:Ser293 4.65 Na C B:Ser293 3.49 Na CA B:Ser293 4.17 Na N B:Val294 4.53 Na CG1 B:Val294 4.59 Na CA B:Val294 4.73 Na N7N B:Nad801 4.80 Na O B:Hoh1104 2.53 Na O B:Hoh1105 2.43 Na O B:Hoh1106 4.67 interactive model: