Nickel in the structure of Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans (pdb 1ru3)

The binding sites of Nickel atom in the structure of Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans (pdb code 1ru3). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1ru3 structure was solved by V.SVETLITCHNYI, H.DOBBEK, W.MEYER-KLAUCKE, T.MEINS, B.THIELE, P.RMER, R.HUBER, O.MEYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.2 Space group H32 a (A) 200.310 b (A) 200.310 c (A) 169.410 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.7 Rfree (%) 27.4 Nickel Binding Sites: Nickel binding site 1 out of 2 in 1ru3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1ru3. 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: Cys512, A: Phe515, A: Leu530, A: Cys531, A: Cys598, A: Gly599, A: Cys600, A: Ni735, A: Sf4733, A: Hoh736, conact list: Atom Atom Distance (A) Ni CB A:Cys512 3.43 Ni SG A:Cys512 2.20 Ni CA A:Cys512 4.76 Ni CE2 A:Phe515 4.90 Ni CZ A:Phe515 3.77 Ni CE1 A:Phe515 4.20 Ni CD1 A:Leu530 4.92 Ni CB A:Cys531 4.56 Ni CB A:Cys598 3.52 Ni SG A:Cys598 2.30 Ni CA A:Cys598 4.83 Ni N A:Gly599 4.59 Ni N A:Cys600 4.25 Ni CB A:Cys600 3.35 Ni SG A:Cys600 2.19 Ni CA A:Cys600 4.45 Ni NI A:Ni735 2.98 Ni S1 A:Sf4733 2.93 Ni FE3 A:Sf4733 4.47 Ni FE2 A:Sf4733 4.74 Ni S2 A:Sf4733 4.37 Ni FE4 A:Sf4733 2.68 Ni S3 A:Sf4733 4.62 Ni O A:Hoh736 2.74 interactive model: Nickel binding site 2 out of 2 in 1ru3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1ru3. 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: Cys512, A: Phe515, A: Leu530, A: Ser597, A: Cys598, A: Gly599, A: Cys600, A: Phe601, A: Ni734, A: Sf4733, conact list: Atom Atom Distance (A) Ni SG A:Cys512 4.80 Ni CE2 A:Phe515 4.19 Ni CZ A:Phe515 3.82 Ni CD1 A:Leu530 3.82 Ni C A:Ser597 4.77 Ni O A:Cys598 4.09 Ni N A:Cys598 3.52 Ni CB A:Cys598 2.88 Ni SG A:Cys598 2.13 Ni C A:Cys598 2.94 Ni CA A:Cys598 3.24 Ni O A:Gly599 3.93 Ni N A:Gly599 1.91 Ni C A:Gly599 2.74 Ni CA A:Gly599 2.81 Ni O A:Cys600 4.65 Ni N A:Cys600 1.88 Ni CB A:Cys600 2.94 Ni SG A:Cys600 2.09 Ni C A:Cys600 3.61 Ni CA A:Cys600 2.90 Ni N A:Phe601 3.59 Ni CD2 A:Phe601 4.82 Ni CA A:Phe601 4.85 Ni NI A:Ni734 2.98 Ni S1 A:Sf4733 4.64 interactive model: