Cobalt in the structure of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target (pdb 3g5k)

The binding sites of Cobalt atom in the structure of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target (pdb code 3g5k). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3g5k structure was solved by S.ESCOBAR-ALVAREZ, Y.GOLDGUR, G.YANG, O.OUERFELLI, Y.LI, D.A.SCHEINBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 35.0-1.7 Space group C121 a (A) 116.144 b (A) 77.830 c (A) 110.532 alpha (°) 90.00 beta (°) 107.46 gamma (°) 90.00 Rfactor (%) 16.4 Rfree (%) 19.3 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 3g5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3g5k. 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: Gln57, A: Gly113, A: Cys114, A: Glu115, A: Ser116, A: His156, A: Glu157, A: His160, A: Bb21001, A: Hoh1006, A: Hoh1009, conact list: Atom Atom Distance (A) Co NE2 A:Gln57 3.33 Co OE1 A:Gln57 4.31 Co CD A:Gln57 4.09 Co O A:Gly113 4.85 Co N A:Cys114 4.98 Co CB A:Cys114 3.32 Co SG A:Cys114 2.28 Co C A:Cys114 4.36 Co CA A:Cys114 3.66 Co N A:Glu115 4.10 Co N A:Ser116 4.84 Co NE2 A:His156 2.02 Co ND1 A:His156 4.17 Co CD2 A:His156 3.02 Co CE1 A:His156 3.05 Co CG A:His156 4.15 Co OE1 A:Glu157 4.60 Co OE2 A:Glu157 4.85 Co NE2 A:His160 2.06 Co ND1 A:His160 4.20 Co CD2 A:His160 3.12 Co CE1 A:His160 3.04 Co CG A:His160 4.25 Co N1 A:Bb21001 3.13 Co C6 A:Bb21001 4.80 Co C5 A:Bb21001 4.41 Co O2 A:Bb21001 2.33 Co C3 A:Bb21001 3.08 Co O4 A:Bb21001 2.08 Co O A:Hoh1006 4.60 Co O A:Hoh1009 3.56 interactive model: Cobalt binding site 2 out of 4 in 3g5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3g5k. 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: Gln57, B: Gly113, B: Cys114, B: Glu115, B: Ser116, B: His156, B: Glu157, B: His160, B: Bb21002, B: Hoh1006, B: Hoh1009, conact list: Atom Atom Distance (A) Co NE2 B:Gln57 3.41 Co OE1 B:Gln57 4.31 Co CD B:Gln57 4.12 Co O B:Gly113 4.92 Co CB B:Cys114 3.36 Co SG B:Cys114 2.31 Co C B:Cys114 4.36 Co CA B:Cys114 3.68 Co N B:Glu115 4.13 Co N B:Ser116 4.83 Co NE2 B:His156 2.00 Co ND1 B:His156 4.15 Co CD2 B:His156 3.00 Co CE1 B:His156 3.04 Co CG B:His156 4.14 Co OE1 B:Glu157 4.69 Co OE2 B:Glu157 4.88 Co NE2 B:His160 2.04 Co ND1 B:His160 4.17 Co CD2 B:His160 3.10 Co CE1 B:His160 3.00 Co CG B:His160 4.21 Co N1 B:Bb21002 3.13 Co C6 B:Bb21002 4.87 Co C5 B:Bb21002 4.46 Co O2 B:Bb21002 2.39 Co C3 B:Bb21002 3.10 Co O4 B:Bb21002 2.09 Co O B:Hoh1006 4.53 Co O B:Hoh1009 3.50 interactive model: Cobalt binding site 3 out of 4 in 3g5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 3g5k. 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: C: Gln57, C: Gly113, C: Cys114, C: Glu115, C: Ser116, C: His156, C: Glu157, C: His160, C: Bb21003, C: Hoh1010, C: Hoh1011, conact list: Atom Atom Distance (A) Co NE2 C:Gln57 3.32 Co OE1 C:Gln57 4.23 Co CD C:Gln57 4.03 Co O C:Gly113 4.91 Co CB C:Cys114 3.41 Co SG C:Cys114 2.36 Co C C:Cys114 4.44 Co CA C:Cys114 3.74 Co N C:Glu115 4.19 Co N C:Ser116 4.90 Co NE2 C:His156 2.02 Co ND1 C:His156 4.18 Co CD2 C:His156 3.01 Co CE1 C:His156 3.09 Co CG C:His156 4.16 Co OE1 C:Glu157 4.81 Co OE2 C:Glu157 4.60 Co CD C:Glu157 5.00 Co NE2 C:His160 2.04 Co ND1 C:His160 4.19 Co CD2 C:His160 3.10 Co CE1 C:His160 3.03 Co CG C:His160 4.23 Co N1 C:Bb21003 3.02 Co C6 C:Bb21003 4.71 Co C5 C:Bb21003 4.37 Co O2 C:Bb21003 2.08 Co C3 C:Bb21003 3.01 Co O4 C:Bb21003 2.20 Co O C:Hoh1010 3.63 Co O C:Hoh1011 4.58 interactive model: Cobalt binding site 4 out of 4 in 3g5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 3g5k. 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: D: Gln57, D: Gly113, D: Cys114, D: Glu115, D: Ser116, D: His156, D: Glu157, D: His160, D: Bb21004, D: Hoh1008, D: Hoh1014, conact list: Atom Atom Distance (A) Co NE2 D:Gln57 3.34 Co OE1 D:Gln57 4.25 Co CD D:Gln57 4.09 Co O D:Gly113 4.92 Co CB D:Cys114 3.38 Co SG D:Cys114 2.33 Co C D:Cys114 4.42 Co CA D:Cys114 3.77 Co N D:Glu115 4.15 Co N D:Ser116 4.93 Co NE2 D:His156 2.08 Co ND1 D:His156 4.24 Co CD2 D:His156 3.04 Co CE1 D:His156 3.14 Co CG D:His156 4.21 Co OE1 D:Glu157 4.69 Co OE2 D:Glu157 4.79 Co NE2 D:His160 2.04 Co ND1 D:His160 4.18 Co CD2 D:His160 3.11 Co CE1 D:His160 3.03 Co CG D:His160 4.23 Co N1 D:Bb21004 3.06 Co C6 D:Bb21004 4.69 Co C5 D:Bb21004 4.37 Co O2 D:Bb21004 2.13 Co C3 D:Bb21004 3.01 Co O4 D:Bb21004 2.17 Co O D:Hoh1008 4.59 Co O D:Hoh1014 3.56 interactive model: