Sodium in the structure of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex With Amicyanin. (pdb 2j56)

The binding sites of Sodium atom in the structure of X-Ray Reduced Paraccocus Denitrificans Methylamine Dehydrogenase N-Semiquinone in Complex With Amicyanin. (pdb code 2j56). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2j56 structure was solved by A.R.PEARSON, R.PAHL, V.L.DAVIDSON, C.M.WILMOT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 43.5-2.1 Space group P41212 a (A) 123.029 b (A) 123.029 c (A) 245.303 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.9 Rfree (%) 20.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2j56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2j56. 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: H: Phe55, L: Asp32, L: Tqq57, L: Asp76, L: Asn104, L: Asp105, L: Ile106, L: Ile107, L: Trp108, L: Hoh2055, conact list: Atom Atom Distance (A) Na CE2 H:Phe55 3.95 Na CD2 H:Phe55 4.94 Na CZ H:Phe55 3.97 Na CE1 H:Phe55 4.95 Na O L:Asp32 3.30 Na CB L:Asp32 4.03 Na OD2 L:Asp32 4.10 Na C L:Asp32 4.31 Na OD1 L:Asp32 4.54 Na CG L:Asp32 4.02 Na CA L:Asp32 4.76 Na N2 L:Tqq57 3.00 Na CE3 L:Tqq57 4.35 Na CZ3 L:Tqq57 3.37 Na CZ2 L:Tqq57 4.14 Na O2 L:Tqq57 4.63 Na CH2 L:Tqq57 3.21 Na OD2 L:Asp76 4.56 Na O L:Asn104 2.77 Na C L:Asn104 3.81 Na CA L:Asn104 4.74 Na O L:Asp105 3.97 Na N L:Asp105 4.55 Na C L:Asp105 3.95 Na CA L:Asp105 4.36 Na O L:Ile106 2.72 Na N L:Ile106 4.25 Na C L:Ile106 3.79 Na CA L:Ile106 4.69 Na N L:Ile107 4.57 Na CD1 L:Ile107 4.41 Na CA L:Ile107 4.53 Na N L:Trp108 4.97 Na O L:Hoh2055 2.20 interactive model: Sodium binding site 2 out of 2 in 2j56 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2j56. 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: J: Phe55, M: Asp32, M: Tqq57, M: Asp76, M: Asn104, M: Asp105, M: Ile106, M: Ile107, M: Hoh2072, conact list: Atom Atom Distance (A) Na CE2 J:Phe55 3.84 Na CD2 J:Phe55 4.90 Na CZ J:Phe55 3.94 Na O M:Asp32 3.31 Na CB M:Asp32 4.03 Na OD2 M:Asp32 3.47 Na C M:Asp32 4.34 Na OD1 M:Asp32 4.65 Na CG M:Asp32 3.87 Na CA M:Asp32 4.77 Na N2 M:Tqq57 2.90 Na CE3 M:Tqq57 4.48 Na CZ3 M:Tqq57 3.45 Na CZ2 M:Tqq57 4.20 Na O2 M:Tqq57 4.63 Na CH2 M:Tqq57 3.24 Na OD2 M:Asp76 4.36 Na O M:Asn104 2.70 Na C M:Asn104 3.82 Na CA M:Asn104 4.82 Na O M:Asp105 4.06 Na N M:Asp105 4.52 Na C M:Asp105 3.93 Na CA M:Asp105 4.27 Na O M:Ile106 2.71 Na N M:Ile106 4.24 Na C M:Ile106 3.75 Na CA M:Ile106 4.69 Na N M:Ile107 4.49 Na CD1 M:Ile107 4.53 Na CA M:Ile107 4.59 Na O M:Hoh2072 2.42 interactive model: