Nickel in the structure of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase With Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla (pdb 1iid)

The binding sites of Nickel atom in the structure of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase With Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla (pdb code 1iid). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1iid structure was solved by T.A.FARAZI, J.I.GORDON, G.WAKSMAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.7-2.5 Space group C2221 a (A) 75.129 b (A) 97.060 c (A) 141.809 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.2 Rfree (%) 28.8 Nickel Binding Sites: Nickel binding site 1 out of 2 in 1iid Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1iid. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala34, A: Met35, A: Asp37, A: His38, A: Phe49, A: Val209, conact list: Atom Atom Distance (A) Ni O A:Ala34 2.32 Ni N A:Ala34 3.32 Ni C A:Ala34 2.66 Ni CB A:Ala34 3.80 Ni CA A:Ala34 2.55 Ni N A:Met35 3.86 Ni CA A:Met35 4.75 Ni O A:Asp37 4.71 Ni N A:Asp37 4.58 Ni CB A:Asp37 4.18 Ni OD2 A:Asp37 2.61 Ni C A:Asp37 4.78 Ni OD1 A:Asp37 2.15 Ni CG A:Asp37 2.70 Ni CA A:Asp37 4.76 Ni NE2 A:His38 2.47 Ni ND1 A:His38 3.94 Ni CD2 A:His38 3.50 Ni CE1 A:His38 2.89 Ni CG A:His38 4.27 Ni CE1 A:Phe49 4.91 Ni O A:Val209 4.49 interactive model: Nickel binding site 2 out of 2 in 1iid Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1iid. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys125, A: His296, A: Hoh534, A: Hoh535, A: Hoh552, conact list: Atom Atom Distance (A) Ni O A:Lys125 4.18 Ni O A:His296 4.97 Ni NE2 A:His296 4.45 Ni CB A:His296 3.55 Ni ND1 A:His296 2.43 Ni CD2 A:His296 4.45 Ni C A:His296 4.98 Ni CE1 A:His296 3.38 Ni CG A:His296 3.32 Ni CA A:His296 4.07 Ni O A:Hoh534 2.43 Ni O A:Hoh535 4.06 Ni O A:Hoh552 2.68 interactive model: