Cobalt in the structure of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus (pdb 1xgn)

The binding sites of Cobalt atom in the structure of Methionine Aminopeptidase From Hyperthermophile Pyrococcus Furiosus (pdb code 1xgn). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1xgn structure was solved by T.H.TAHIROV, T.TSUKIHARA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.9 Space group P64 a (A) 110.980 b (A) 110.980 c (A) 124.960 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 15.6 Rfree (%) 22.6 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 1xgn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1xgn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp82, A: Asp93, A: His153, A: Ala185, A: Glu187, A: Glu280, A: Co297, conact list: Atom Atom Distance (A) Co OD2 A:Asp82 4.92 Co OD1 A:Asp82 4.36 Co CB A:Asp93 4.30 Co OD2 A:Asp93 2.00 Co OD1 A:Asp93 3.45 Co CG A:Asp93 3.04 Co NE2 A:His153 2.00 Co ND1 A:His153 4.09 Co CD2 A:His153 3.14 Co CE1 A:His153 2.88 Co CG A:His153 4.23 Co CB A:Ala185 4.20 Co OE1 A:Glu187 3.38 Co CB A:Glu187 4.86 Co OE2 A:Glu187 2.00 Co CD A:Glu187 2.98 Co CG A:Glu187 4.24 Co OE1 A:Glu280 3.43 Co OE2 A:Glu280 1.97 Co CD A:Glu280 3.03 Co CG A:Glu280 4.37 Co CO A:Co297 2.90 interactive model: Cobalt binding site 2 out of 4 in 1xgn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1xgn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe50, A: Asp82, A: Val83, A: Asp93, A: Thr94, A: Ala95, A: His153, A: Glu187, A: Gln278, A: Glu280, A: Co296, conact list: Atom Atom Distance (A) Co CE2 A:Phe50 4.83 Co CZ A:Phe50 4.02 Co CE1 A:Phe50 4.70 Co CB A:Asp82 3.87 Co OD2 A:Asp82 2.03 Co OD1 A:Asp82 2.03 Co CG A:Asp82 2.33 Co CA A:Asp82 4.76 Co O A:Val83 4.73 Co CB A:Asp93 4.26 Co OD2 A:Asp93 2.97 Co C A:Asp93 4.66 Co OD1 A:Asp93 2.01 Co CG A:Asp93 2.81 Co CA A:Asp93 4.76 Co O A:Thr94 4.67 Co N A:Thr94 4.67 Co C A:Thr94 4.81 Co CB A:Ala95 4.41 Co NE2 A:His153 4.76 Co OE1 A:Glu187 4.15 Co OE2 A:Glu187 4.24 Co CD A:Glu187 4.54 Co NE2 A:Gln278 4.67 Co OE1 A:Glu280 1.96 Co CB A:Glu280 4.99 Co OE2 A:Glu280 2.90 Co CD A:Glu280 2.75 Co CG A:Glu280 4.20 Co CO A:Co296 2.90 interactive model: Cobalt binding site 3 out of 4 in 1xgn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1xgn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp82, B: Asp93, B: His153, B: Ala185, B: Glu187, B: Glu280, B: Co297, conact list: Atom Atom Distance (A) Co OD1 B:Asp82 4.49 Co CB B:Asp93 4.32 Co OD2 B:Asp93 1.98 Co OD1 B:Asp93 3.75 Co CG B:Asp93 3.17 Co NE2 B:His153 2.01 Co ND1 B:His153 4.10 Co CD2 B:His153 3.02 Co CE1 B:His153 2.97 Co CG B:His153 4.14 Co CB B:Ala185 4.29 Co OE1 B:Glu187 2.96 Co CB B:Glu187 4.78 Co OE2 B:Glu187 2.01 Co CD B:Glu187 2.81 Co CG B:Glu187 4.23 Co OE1 B:Glu280 3.62 Co OE2 B:Glu280 1.97 Co CD B:Glu280 3.09 Co CG B:Glu280 4.29 Co CO B:Co297 2.99 interactive model: Cobalt binding site 4 out of 4 in 1xgn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1xgn. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Phe50, B: Asp82, B: Asp93, B: Thr94, B: Ala95, B: His153, B: Glu187, B: Glu280, B: Co296, conact list: Atom Atom Distance (A) Co CE2 B:Phe50 4.49 Co CZ B:Phe50 3.73 Co CE1 B:Phe50 4.36 Co CB B:Asp82 3.89 Co OD2 B:Asp82 2.03 Co OD1 B:Asp82 2.05 Co CG B:Asp82 2.35 Co CA B:Asp82 4.80 Co CB B:Asp93 4.10 Co OD2 B:Asp93 2.57 Co C B:Asp93 4.81 Co OD1 B:Asp93 1.99 Co CG B:Asp93 2.60 Co CA B:Asp93 4.78 Co O B:Thr94 4.58 Co N B:Thr94 4.76 Co C B:Thr94 4.89 Co CB B:Ala95 4.69 Co NE2 B:His153 4.86 Co OE1 B:Glu187 3.84 Co OE2 B:Glu187 4.38 Co CD B:Glu187 4.42 Co OE1 B:Glu280 2.00 Co CB B:Glu280 4.74 Co OE2 B:Glu280 2.69 Co CD B:Glu280 2.66 Co CG B:Glu280 4.13 Co CO B:Co296 2.99 interactive model: