Sodium in the structure of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase (pdb 3pm8)

The binding sites of Sodium atom in the structure of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase (pdb code 3pm8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3pm8 structure was solved by A.K.WERNIMONT, A.HUTCHINSON, J.LEW, CHAMBERLAIN K., F.MACKENZIE, P.LOPPNAU, D.COSSAR, L.CROMBET, C.H.ARROWSMITH, A.M.EDWARDS, C.BOUNTRA, J.WEIGELT, R.HUI, M.AMANI, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 26.6-2.0 Space group P1 a (A) 47.019 b (A) 51.378 c (A) 51.639 alpha (°) 68.53 beta (°) 65.75 gamma (°) 64.49 Rfactor (%) 19.9 Rfree (%) 22.5 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3pm8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3pm8. 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: Asp501, A: Phe502, A: His503, B: Asn386, B: Cl518, A: Hoh108, A: Hoh125, A: Hoh207, conact list: Atom Atom Distance (A) Na CB A:Asp501 3.84 Na OD2 A:Asp501 4.18 Na C A:Asp501 4.42 Na OD1 A:Asp501 3.93 Na CG A:Asp501 3.77 Na CA A:Asp501 4.74 Na N A:Phe502 3.64 Na CB A:Phe502 4.10 Na C A:Phe502 4.03 Na CA A:Phe502 4.06 Na N A:His503 3.15 Na CB A:His503 3.50 Na CG A:His503 4.88 Na CA A:His503 3.91 Na ND2 B:Asn386 4.12 Na CL B:Cl518 4.14 Na O A:Hoh108 3.53 Na O A:Hoh125 4.58 Na O A:Hoh207 4.82 interactive model: Sodium binding site 2 out of 3 in 3pm8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3pm8. 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: Asn353, B: Glu354, B: Leu355, B: Leu488, B: Hoh90, B: Hoh142, B: Hoh145, conact list: Atom Atom Distance (A) Na CB B:Asn353 3.68 Na C B:Asn353 4.00 Na OD1 B:Asn353 4.87 Na CG B:Asn353 4.70 Na CA B:Asn353 3.85 Na N B:Glu354 3.16 Na CB B:Glu354 3.72 Na OE2 B:Glu354 4.98 Na CD B:Glu354 4.84 Na CG B:Glu354 3.61 Na CA B:Glu354 4.02 Na N B:Leu355 5.00 Na CB B:Leu488 4.44 Na CD1 B:Leu488 3.75 Na CD2 B:Leu488 4.93 Na CG B:Leu488 4.58 Na CA B:Leu488 4.92 Na O B:Hoh90 4.58 Na O B:Hoh142 2.91 Na O B:Hoh145 2.86 interactive model: Sodium binding site 3 out of 3 in 3pm8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3pm8. 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: Lys512, B: Cys368, B: Asp369, B: Val370, conact list: Atom Atom Distance (A) Na O A:Lys512 4.83 Na C A:Lys512 4.88 Na CB B:Cys368 3.93 Na CB B:Cys368 4.00 Na SG B:Cys368 4.06 Na C B:Cys368 4.47 Na C B:Cys368 4.43 Na CA B:Cys368 4.75 Na CA B:Cys368 4.81 Na N B:Asp369 3.79 Na CB B:Asp369 4.13 Na C B:Asp369 4.16 Na CA B:Asp369 4.14 Na N B:Val370 3.37 Na CB B:Val370 3.85 Na CG2 B:Val370 3.43 Na CA B:Val370 4.19 interactive model: