Sodium in the structure of Mutation Of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction With Amicyanin (pdb 1mg3)

The binding sites of Sodium atom in the structure of Mutation Of Alpha PHE55 of Methylamine Dehydrogenase Alters the Reorganization Energy and Electronic Coupling For Its Electron Transfer Reaction With Amicyanin (pdb code 1mg3). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1mg3 structure was solved by D.SUN, Z.W.CHEN, F.S.MATHEWS, V.L.DAVIDSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.4 Space group P1211 a (A) 79.520 b (A) 188.372 c (A) 127.366 alpha (°) 90.00 beta (°) 98.84 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 24.6 Sodium Binding Sites: Sodium binding site 1 out of 4 in 1mg3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1mg3. 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: Lys29, C: Glu31, D: Gly72, D: Leu73, D: Asn74, D: Asp75, D: Tyr77, D: Trp78, D: Hoh1177, conact list: Atom Atom Distance (A) Na NZ C:Lys29 4.83 Na OE1 C:Glu31 3.81 Na OE2 C:Glu31 3.40 Na CD C:Glu31 3.80 Na CG C:Glu31 4.93 Na O D:Gly72 2.62 Na N D:Gly72 4.61 Na C D:Gly72 3.33 Na CA D:Gly72 4.18 Na N D:Leu73 3.99 Na C D:Leu73 4.48 Na CA D:Leu73 4.09 Na N D:Asn74 4.51 Na O D:Asp75 4.15 Na N D:Asp75 4.28 Na CB D:Asp75 4.53 Na OD2 D:Asp75 2.62 Na C D:Asp75 4.62 Na OD1 D:Asp75 3.63 Na CG D:Asp75 3.34 Na CA D:Asp75 4.69 Na O D:Tyr77 2.73 Na N D:Tyr77 4.60 Na CB D:Tyr77 4.45 Na CD2 D:Tyr77 4.33 Na C D:Tyr77 3.84 Na CG D:Tyr77 4.86 Na CA D:Tyr77 4.52 Na N D:Trp78 4.85 Na O D:Hoh1177 2.74 interactive model: Sodium binding site 2 out of 4 in 1mg3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1mg3. 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: G: Glu31, H: Gly72, H: Leu73, H: Asn74, H: Asp75, H: Tyr77, H: Hoh1248, conact list: Atom Atom Distance (A) Na OE1 G:Glu31 3.80 Na CB G:Glu31 5.00 Na OE2 G:Glu31 3.02 Na CD G:Glu31 3.49 Na CG G:Glu31 4.42 Na O H:Gly72 2.69 Na N H:Gly72 4.38 Na C H:Gly72 3.37 Na CA H:Gly72 4.10 Na N H:Leu73 4.10 Na C H:Leu73 4.64 Na CA H:Leu73 4.34 Na N H:Asn74 4.55 Na O H:Asp75 4.41 Na N H:Asp75 4.19 Na CB H:Asp75 4.56 Na OD2 H:Asp75 2.26 Na C H:Asp75 4.67 Na OD1 H:Asp75 3.79 Na CG H:Asp75 3.32 Na CA H:Asp75 4.67 Na O H:Tyr77 2.80 Na N H:Tyr77 4.67 Na CB H:Tyr77 4.89 Na C H:Tyr77 4.00 Na CA H:Tyr77 4.73 Na O H:Hoh1248 3.10 interactive model: Sodium binding site 3 out of 4 in 1mg3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1mg3. 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: K: Glu31, L: Gly72, L: Leu73, L: Asn74, L: Asp75, L: Tyr77, L: Trp78, L: Hem200, L: Hoh1155, conact list: Atom Atom Distance (A) Na OE1 K:Glu31 4.00 Na CB K:Glu31 4.72 Na OE2 K:Glu31 3.12 Na CD K:Glu31 3.60 Na CG K:Glu31 4.40 Na O L:Gly72 2.40 Na N L:Gly72 4.34 Na C L:Gly72 3.33 Na CA L:Gly72 4.14 Na N L:Leu73 4.16 Na C L:Leu73 4.71 Na CA L:Leu73 4.30 Na N L:Asn74 4.73 Na O L:Asp75 4.65 Na N L:Asp75 4.57 Na CB L:Asp75 4.73 Na OD2 L:Asp75 2.39 Na OD1 L:Asp75 3.70 Na CG L:Asp75 3.39 Na O L:Tyr77 2.90 Na N L:Tyr77 4.93 Na CB L:Tyr77 4.73 Na CD2 L:Tyr77 4.55 Na C L:Tyr77 4.01 Na CA L:Tyr77 4.79 Na N L:Trp78 4.95 Na O2A L:Hem200 4.79 Na O L:Hoh1155 2.96 interactive model: Sodium binding site 4 out of 4 in 1mg3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1mg3. 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: O: Glu31, P: Gly72, P: Leu73, P: Asn74, P: Asp75, P: Tyr77, P: Trp78, P: Hem200, P: Hoh1132, P: Hoh1289, conact list: Atom Atom Distance (A) Na OE1 O:Glu31 3.88 Na OE2 O:Glu31 3.05 Na CD O:Glu31 3.60 Na CG O:Glu31 4.61 Na O P:Gly72 2.60 Na N P:Gly72 4.54 Na C P:Gly72 3.41 Na CA P:Gly72 4.25 Na N P:Leu73 4.13 Na C P:Leu73 4.73 Na CA P:Leu73 4.26 Na N P:Asn74 4.77 Na O P:Asp75 4.36 Na N P:Asp75 4.47 Na CB P:Asp75 4.84 Na OD2 P:Asp75 2.89 Na C P:Asp75 4.78 Na OD1 P:Asp75 3.94 Na CG P:Asp75 3.65 Na CA P:Asp75 4.90 Na O P:Tyr77 2.62 Na N P:Tyr77 4.52 Na CB P:Tyr77 4.38 Na CD2 P:Tyr77 4.28 Na C P:Tyr77 3.71 Na CG P:Tyr77 4.82 Na CA P:Tyr77 4.42 Na N P:Trp78 4.68 Na CE3 P:Trp78 4.78 Na CA P:Trp78 4.83 Na O2A P:Hem200 4.63 Na O P:Hoh1132 2.77 Na O P:Hoh1289 2.66 interactive model: