Sodium in the structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States (pdb 1tkp)

The binding sites of Sodium atom in the structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States (pdb code 1tkp). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1tkp structure was solved by K.ZETH, S.OFFERMANN, L.O.ESSEN, D.OESTERHELT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 141.4-2.2 Space group P321 a (A) 91.110 b (A) 91.110 c (A) 150.040 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.5 Rfree (%) 23.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1tkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1tkp. 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: Ala58, A: Glu59, A: Thr174, A: Val176, D: Ala58, D: Glu59, D: Val176, conact list: Atom Atom Distance (A) Na C A:Ala58 4.92 Na CB A:Ala58 4.25 Na OE1 A:Glu59 2.62 Na CB A:Glu59 4.92 Na OE2 A:Glu59 4.70 Na CD A:Glu59 3.47 Na CG A:Glu59 3.49 Na OG1 A:Thr174 4.72 Na CG2 A:Val176 4.02 Na O D:Ala58 4.79 Na C D:Ala58 4.80 Na CB D:Ala58 4.07 Na OE1 D:Glu59 2.74 Na OE2 D:Glu59 4.83 Na CD D:Glu59 3.61 Na CG D:Glu59 3.62 Na CG2 D:Val176 3.87 interactive model: Sodium binding site 2 out of 2 in 1tkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1tkp. 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: Ala58, C: Glu59, C: Thr174, C: Val176, conact list: Atom Atom Distance (A) Na CB C:Ala58 4.16 Na OE1 C:Glu59 2.50 Na OE2 C:Glu59 4.64 Na CD C:Glu59 3.50 Na CG C:Glu59 3.74 Na OG1 C:Thr174 4.48 Na CG2 C:Val176 4.10 interactive model: