Cobalt in the structure of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target (pdb 3g5p)

The binding sites of Cobalt atom in the structure of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target (pdb code 3g5p). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 3g5p 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) 37.5-1.7 Space group C121 a (A) 116.332 b (A) 77.825 c (A) 111.041 alpha (°) 90.00 beta (°) 107.93 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 18.7 Cobalt Binding Sites: Cobalt binding site 1 out of 4 in 3g5p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 3g5p. 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: Po42, A: Hoh190, A: Hoh193, A: Hoh342, conact list: Atom Atom Distance (A) Co NE2 A:Gln57 3.47 Co OE1 A:Gln57 4.33 Co CD A:Gln57 4.13 Co O A:Gly113 4.67 Co N A:Cys114 4.95 Co CB A:Cys114 3.34 Co SG A:Cys114 4.64 Co C A:Cys114 4.24 Co CA A:Cys114 3.57 Co N A:Glu115 4.10 Co N A:Ser116 4.80 Co NE2 A:His156 2.08 Co ND1 A:His156 4.22 Co CD2 A:His156 3.02 Co CE1 A:His156 3.12 Co CG A:His156 4.18 Co OE1 A:Glu157 4.67 Co NE2 A:His160 2.02 Co ND1 A:His160 4.14 Co CD2 A:His160 3.05 Co CE1 A:His160 3.01 Co CG A:His160 4.20 Co O1 A:Po42 3.67 Co O2 A:Po42 1.93 Co P A:Po42 3.19 Co O4 A:Po42 4.40 Co O3 A:Po42 3.78 Co O A:Hoh190 4.52 Co O A:Hoh193 3.49 Co O A:Hoh342 4.70 interactive model: Cobalt binding site 2 out of 4 in 3g5p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 3g5p. 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: Po4188, B: Hoh191, B: Hoh194, B: Hoh317, conact list: Atom Atom Distance (A) Co NE2 B:Gln57 3.57 Co OE1 B:Gln57 4.37 Co CD B:Gln57 4.19 Co O B:Gly113 4.70 Co N B:Cys114 4.93 Co CB B:Cys114 3.26 Co SG B:Cys114 2.30 Co C B:Cys114 4.27 Co CA B:Cys114 3.63 Co N B:Glu115 4.12 Co N B:Ser116 4.77 Co NE2 B:His156 2.01 Co ND1 B:His156 4.14 Co CD2 B:His156 2.99 Co CE1 B:His156 3.03 Co CG B:His156 4.14 Co OE1 B:Glu157 4.65 Co NE2 B:His160 2.04 Co ND1 B:His160 4.14 Co CD2 B:His160 3.11 Co CE1 B:His160 2.98 Co CG B:His160 4.22 Co O1 B:Po4188 3.66 Co O2 B:Po4188 1.87 Co P B:Po4188 3.17 Co O4 B:Po4188 4.29 Co O3 B:Po4188 3.75 Co O B:Hoh191 4.47 Co O B:Hoh194 3.51 Co O B:Hoh317 4.67 interactive model: Cobalt binding site 3 out of 4 in 3g5p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 3g5p. 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: Po4187, C: Hoh194, C: Hoh195, C: Hoh328, conact list: Atom Atom Distance (A) Co NE2 C:Gln57 3.50 Co OE1 C:Gln57 4.30 Co CD C:Gln57 4.11 Co O C:Gly113 4.68 Co N C:Cys114 4.97 Co CB C:Cys114 3.59 Co SG C:Cys114 3.34 Co C C:Cys114 4.29 Co CA C:Cys114 3.62 Co N C:Glu115 4.18 Co N C:Ser116 4.83 Co NE2 C:His156 2.09 Co ND1 C:His156 4.20 Co CD2 C:His156 3.06 Co CE1 C:His156 3.08 Co CG C:His156 4.18 Co OE2 C:Glu157 4.66 Co NE2 C:His160 2.08 Co ND1 C:His160 4.18 Co CD2 C:His160 3.11 Co CE1 C:His160 3.04 Co CG C:His160 4.24 Co O1 C:Po4187 3.67 Co O2 C:Po4187 1.75 Co P C:Po4187 3.11 Co O4 C:Po4187 4.33 Co O3 C:Po4187 3.70 Co O C:Hoh194 3.49 Co O C:Hoh195 4.50 Co O C:Hoh328 4.60 interactive model: Cobalt binding site 4 out of 4 in 3g5p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 3g5p. 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: Po4187, D: Hoh191, D: Hoh197, D: Hoh321, conact list: Atom Atom Distance (A) Co NE2 D:Gln57 3.49 Co OE1 D:Gln57 4.26 Co CD D:Gln57 4.12 Co O D:Gly113 4.69 Co N D:Cys114 4.95 Co CB D:Cys114 3.34 Co SG D:Cys114 2.32 Co C D:Cys114 4.31 Co CA D:Cys114 3.65 Co N D:Glu115 4.13 Co N D:Ser116 4.82 Co NE2 D:His156 2.05 Co ND1 D:His156 4.21 Co CD2 D:His156 2.96 Co CE1 D:His156 3.12 Co CG D:His156 4.15 Co OE1 D:Glu157 4.69 Co NE2 D:His160 2.04 Co ND1 D:His160 4.10 Co CD2 D:His160 3.14 Co CE1 D:His160 2.91 Co CG D:His160 4.21 Co O1 D:Po4187 3.67 Co O2 D:Po4187 1.90 Co P D:Po4187 3.15 Co O4 D:Po4187 4.30 Co O3 D:Po4187 3.75 Co O D:Hoh191 4.44 Co O D:Hoh197 3.51 Co O D:Hoh321 4.63 interactive model: