Sodium in the structure of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. (pdb 3ic9)

The binding sites of Sodium atom in the structure of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. (pdb code 3ic9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ic9 structure was solved by K.TAN, E.RAKOWSKI, S.CLANCY, A.JOACHIMIAK, MIDWEST CENTER FOR STRUCTURALGENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 43.9-2.1 Space group P1211 a (A) 73.497 b (A) 246.353 c (A) 73.664 alpha (°) 90.00 beta (°) 90.20 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 23.3 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3ic9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ic9. 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: Ala308, A: Gly309, A: Asp310, A: Asn312, A: Thr314, A: Leu315, A: Asp324, A: Hoh633, conact list: Atom Atom Distance (A) Na C A:Ala308 4.82 Na O A:Gly309 2.46 Na N A:Gly309 3.80 Na C A:Gly309 3.33 Na CA A:Gly309 3.79 Na N A:Asp310 4.38 Na CA A:Asp310 4.76 Na N A:Asn312 4.86 Na CB A:Asn312 4.55 Na ND2 A:Asn312 3.16 Na C A:Asn312 4.97 Na OD1 A:Asn312 2.49 Na CG A:Asn312 3.13 Na CA A:Asn312 5.00 Na O A:Thr314 2.39 Na N A:Thr314 4.14 Na CB A:Thr314 4.42 Na C A:Thr314 3.53 Na CA A:Thr314 4.27 Na O A:Leu315 4.04 Na N A:Leu315 4.53 Na CB A:Leu315 4.76 Na C A:Leu315 4.43 Na CA A:Leu315 4.81 Na CB A:Asp324 4.71 Na OD2 A:Asp324 2.49 Na OD1 A:Asp324 3.90 Na CG A:Asp324 3.51 Na O A:Hoh633 2.68 interactive model: Sodium binding site 2 out of 4 in 3ic9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ic9. 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: Ala308, B: Gly309, B: Asp310, B: Asn312, B: Asn313, B: Thr314, B: Leu315, B: Asp324, B: Hoh610, B: Hoh821, conact list: Atom Atom Distance (A) Na C B:Ala308 4.81 Na O B:Gly309 2.48 Na N B:Gly309 3.81 Na C B:Gly309 3.33 Na CA B:Gly309 3.87 Na N B:Asp310 4.33 Na CA B:Asp310 4.79 Na N B:Asn312 4.76 Na CB B:Asn312 4.45 Na ND2 B:Asn312 3.16 Na C B:Asn312 4.86 Na OD1 B:Asn312 2.30 Na CG B:Asn312 3.04 Na CA B:Asn312 4.87 Na N B:Asn313 4.86 Na O B:Thr314 2.31 Na N B:Thr314 3.95 Na CB B:Thr314 4.30 Na C B:Thr314 3.45 Na CA B:Thr314 4.11 Na O B:Leu315 4.01 Na N B:Leu315 4.50 Na CB B:Leu315 4.51 Na C B:Leu315 4.37 Na CA B:Leu315 4.72 Na CB B:Asp324 4.78 Na OD2 B:Asp324 2.49 Na OD1 B:Asp324 4.02 Na CG B:Asp324 3.58 Na O B:Hoh610 2.60 Na O B:Hoh821 2.43 interactive model: Sodium binding site 3 out of 4 in 3ic9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3ic9. 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: Ala308, C: Gly309, C: Asp310, C: Asn312, C: Asn313, C: Thr314, C: Leu315, C: Asp324, C: Hoh662, C: Hoh848, conact list: Atom Atom Distance (A) Na C C:Ala308 4.89 Na O C:Gly309 2.76 Na N C:Gly309 3.88 Na C C:Gly309 3.53 Na CA C:Gly309 3.96 Na N C:Asp310 4.54 Na CA C:Asp310 4.98 Na N C:Asn312 4.90 Na CB C:Asn312 4.49 Na ND2 C:Asn312 3.09 Na C C:Asn312 4.93 Na OD1 C:Asn312 2.37 Na CG C:Asn312 3.05 Na CA C:Asn312 4.96 Na N C:Asn313 4.98 Na O C:Thr314 2.38 Na N C:Thr314 4.04 Na CB C:Thr314 4.32 Na C C:Thr314 3.48 Na CA C:Thr314 4.17 Na O C:Leu315 4.10 Na N C:Leu315 4.49 Na CB C:Leu315 4.63 Na C C:Leu315 4.43 Na CA C:Leu315 4.75 Na CB C:Asp324 4.76 Na OD2 C:Asp324 2.52 Na OD1 C:Asp324 4.00 Na CG C:Asp324 3.57 Na O C:Hoh662 4.72 Na O C:Hoh848 2.35 interactive model: Sodium binding site 4 out of 4 in 3ic9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3ic9. 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: Ala308, D: Gly309, D: Asp310, D: Asn312, D: Asn313, D: Thr314, D: Leu315, D: Asp324, D: Hoh677, D: Hoh697, D: Hoh925, conact list: Atom Atom Distance (A) Na C D:Ala308 4.90 Na O D:Gly309 2.54 Na N D:Gly309 3.87 Na C D:Gly309 3.36 Na CA D:Gly309 3.87 Na N D:Asp310 4.34 Na CA D:Asp310 4.74 Na N D:Asn312 4.85 Na CB D:Asn312 4.52 Na ND2 D:Asn312 3.22 Na C D:Asn312 4.94 Na OD1 D:Asn312 2.43 Na CG D:Asn312 3.13 Na CA D:Asn312 4.92 Na N D:Asn313 4.94 Na O D:Thr314 2.34 Na N D:Thr314 4.09 Na CB D:Thr314 4.44 Na C D:Thr314 3.45 Na CA D:Thr314 4.20 Na O D:Leu315 3.88 Na N D:Leu315 4.44 Na CB D:Leu315 4.54 Na C D:Leu315 4.32 Na CA D:Leu315 4.66 Na CB D:Asp324 4.79 Na OD2 D:Asp324 2.48 Na OD1 D:Asp324 4.05 Na CG D:Asp324 3.59 Na O D:Hoh677 4.18 Na O D:Hoh697 2.45 Na O D:Hoh925 2.29 interactive model: