Cobalt in the structure of Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain (pdb 1c0w)

The binding sites of Cobalt atom in the structure of Crystal Structure of the Cobalt-Activated Diphtheria Toxin Repressor-Dna Complex Reveals A Metal Binding Sh-Like Domain (pdb code 1c0w). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1c0w structure was solved by E.POHL, R.K.HOLMES, W.G.HOL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.2 Space group P4222 a (A) 180.200 b (A) 180.200 c (A) 151.000 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.9 Rfree (%) 27.9 Cobalt Binding Sites: Cobalt binding site 1 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1c0w. 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: His79, A: Glu83, A: His98, A: Phe128, A: Asn130, A: Glu170, A: Gln173, conact list: Atom Atom Distance (A) Co NE2 A:His79 2.19 Co ND1 A:His79 4.37 Co CD2 A:His79 3.04 Co CE1 A:His79 3.30 Co CG A:His79 4.27 Co OE1 A:Glu83 2.22 Co OE2 A:Glu83 3.07 Co CD A:Glu83 2.84 Co CG A:Glu83 4.06 Co O A:His98 4.95 Co NE2 A:His98 4.34 Co CB A:His98 3.91 Co ND1 A:His98 2.32 Co CD2 A:His98 4.53 Co CE1 A:His98 3.10 Co CG A:His98 3.47 Co CA A:His98 4.37 Co CE2 A:Phe128 4.43 Co CD2 A:Phe128 4.34 Co OD1 A:Asn130 4.96 Co OE1 A:Glu170 2.23 Co CB A:Glu170 4.83 Co OE2 A:Glu170 2.40 Co CD A:Glu170 2.62 Co CG A:Glu170 4.12 Co CA A:Glu170 4.87 Co NE2 A:Gln173 3.50 Co OE1 A:Gln173 1.97 Co CB A:Gln173 4.59 Co CD A:Gln173 3.03 Co CG A:Gln173 4.35 interactive model: Cobalt binding site 2 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1c0w. 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: His79, B: Glu83, B: His98, B: Glu170, B: Gln173, conact list: Atom Atom Distance (A) Co NE2 B:His79 2.09 Co ND1 B:His79 4.22 Co CD2 B:His79 3.15 Co CE1 B:His79 3.05 Co CG B:His79 4.28 Co OE1 B:Glu83 1.80 Co OE2 B:Glu83 3.42 Co CD B:Glu83 2.86 Co CG B:Glu83 4.02 Co O B:His98 4.52 Co NE2 B:His98 3.95 Co CB B:His98 3.50 Co ND1 B:His98 1.87 Co CD2 B:His98 4.07 Co C B:His98 4.70 Co CE1 B:His98 2.75 Co CG B:His98 3.00 Co CA B:His98 3.94 Co OE1 B:Glu170 1.90 Co CB B:Glu170 4.64 Co OE2 B:Glu170 3.09 Co CD B:Glu170 2.81 Co CG B:Glu170 4.18 Co CA B:Glu170 4.80 Co NE2 B:Gln173 4.28 Co OE1 B:Gln173 2.37 Co CB B:Gln173 4.58 Co CD B:Gln173 3.54 Co CG B:Gln173 4.61 interactive model: Cobalt binding site 3 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1c0w. 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: His79, C: Glu83, C: His98, C: Glu170, C: Gln173, conact list: Atom Atom Distance (A) Co NE2 C:His79 2.17 Co ND1 C:His79 4.30 Co CD2 C:His79 3.22 Co CE1 C:His79 3.13 Co CG C:His79 4.36 Co OE1 C:Glu83 2.22 Co OE2 C:Glu83 3.55 Co CD C:Glu83 3.14 Co CG C:Glu83 4.33 Co O C:His98 4.58 Co NE2 C:His98 3.79 Co CB C:His98 3.70 Co ND1 C:His98 1.81 Co CD2 C:His98 4.04 Co C C:His98 4.76 Co CE1 C:His98 2.53 Co CG C:His98 3.06 Co CA C:His98 4.07 Co O C:Glu170 5.00 Co OE1 C:Glu170 1.99 Co CB C:Glu170 4.62 Co OE2 C:Glu170 2.96 Co CD C:Glu170 2.79 Co CG C:Glu170 4.22 Co CA C:Glu170 4.79 Co NE2 C:Gln173 3.90 Co OE1 C:Gln173 2.03 Co CB C:Gln173 4.31 Co CD C:Gln173 3.20 Co CG C:Gln173 4.33 interactive model: Cobalt binding site 4 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1c0w. 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: His79, D: Glu83, D: His98, D: Phe128, D: Glu170, D: Gln173, conact list: Atom Atom Distance (A) Co NE2 D:His79 2.24 Co ND1 D:His79 4.40 Co CD2 D:His79 3.20 Co CE1 D:His79 3.27 Co CG D:His79 4.38 Co OE1 D:Glu83 2.10 Co OE2 D:Glu83 3.04 Co CD D:Glu83 2.76 Co CG D:Glu83 3.99 Co O D:His98 4.81 Co NE2 D:His98 4.30 Co CB D:His98 3.73 Co ND1 D:His98 2.21 Co CD2 D:His98 4.42 Co C D:His98 4.96 Co CE1 D:His98 3.08 Co CG D:His98 3.32 Co CA D:His98 4.14 Co CE2 D:Phe128 4.46 Co CD2 D:Phe128 4.39 Co OE1 D:Glu170 2.26 Co CB D:Glu170 4.85 Co OE2 D:Glu170 2.88 Co CD D:Glu170 2.89 Co CG D:Glu170 4.34 Co CA D:Glu170 4.92 Co NE2 D:Gln173 3.52 Co OE1 D:Gln173 1.87 Co CB D:Gln173 4.41 Co CD D:Gln173 2.97 Co CG D:Gln173 4.24 interactive model: Cobalt binding site 5 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 1c0w. 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: Leu4, A: Met10, A: Arg13, A: Cys102, A: Arg103, A: Glu105, A: His106, conact list: Atom Atom Distance (A) Co O A:Leu4 4.30 Co CB A:Met10 4.78 Co CE A:Met10 3.39 Co CG A:Met10 3.43 Co SD A:Met10 2.23 Co CZ A:Arg13 4.83 Co NE A:Arg13 4.82 Co NH2 A:Arg13 4.04 Co O A:Cys102 1.92 Co N A:Cys102 4.83 Co CB A:Cys102 3.62 Co SG A:Cys102 2.74 Co C A:Cys102 2.93 Co CA A:Cys102 3.42 Co N A:Arg103 4.13 Co CA A:Arg103 4.68 Co OE1 A:Glu105 1.98 Co OE2 A:Glu105 4.18 Co CD A:Glu105 3.14 Co CG A:Glu105 3.74 Co NE2 A:His106 2.10 Co ND1 A:His106 4.22 Co CD2 A:His106 3.20 Co CE1 A:His106 3.03 Co CG A:His106 4.32 interactive model: Cobalt binding site 6 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 1c0w. 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: Leu4, B: Met10, B: Arg13, B: Cys102, B: Arg103, B: Glu105, B: His106, conact list: Atom Atom Distance (A) Co O B:Leu4 3.90 Co C B:Leu4 4.80 Co CB B:Met10 4.71 Co CE B:Met10 3.70 Co CG B:Met10 3.22 Co SD B:Met10 2.33 Co NH2 B:Arg13 4.27 Co O B:Cys102 1.94 Co N B:Cys102 4.90 Co CB B:Cys102 3.61 Co SG B:Cys102 2.86 Co C B:Cys102 2.97 Co CA B:Cys102 3.47 Co N B:Arg103 4.15 Co CA B:Arg103 4.64 Co OE1 B:Glu105 2.12 Co OE2 B:Glu105 4.33 Co CD B:Glu105 3.27 Co CG B:Glu105 3.86 Co NE2 B:His106 2.01 Co ND1 B:His106 4.10 Co CD2 B:His106 3.14 Co CE1 B:His106 2.90 Co CG B:His106 4.23 interactive model: Cobalt binding site 7 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 1c0w. 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: Leu4, C: Met10, C: Arg13, C: Cys102, C: Arg103, C: Glu105, C: His106, conact list: Atom Atom Distance (A) Co O C:Leu4 4.13 Co C C:Leu4 4.96 Co CB C:Met10 4.86 Co CE C:Met10 3.44 Co CG C:Met10 3.44 Co SD C:Met10 2.30 Co CZ C:Arg13 4.98 Co NE C:Arg13 4.98 Co NH2 C:Arg13 4.12 Co O C:Cys102 1.89 Co N C:Cys102 4.89 Co CB C:Cys102 3.63 Co SG C:Cys102 2.83 Co C C:Cys102 2.93 Co CA C:Cys102 3.46 Co N C:Arg103 4.10 Co CA C:Arg103 4.63 Co OE1 C:Glu105 2.02 Co OE2 C:Glu105 4.21 Co CD C:Glu105 3.20 Co CG C:Glu105 3.87 Co NE2 C:His106 2.18 Co ND1 C:His106 4.30 Co CD2 C:His106 3.22 Co CE1 C:His106 3.13 Co CG C:His106 4.36 interactive model: Cobalt binding site 8 out of 8 in 1c0w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 1c0w. 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: Leu4, D: Met10, D: Arg13, D: Cys102, D: Arg103, D: Glu105, D: His106, conact list: Atom Atom Distance (A) Co O D:Leu4 4.36 Co CB D:Met10 4.72 Co CE D:Met10 3.27 Co CG D:Met10 3.41 Co SD D:Met10 2.17 Co CZ D:Arg13 4.68 Co NE D:Arg13 4.74 Co NH2 D:Arg13 3.89 Co O D:Cys102 1.91 Co N D:Cys102 4.73 Co CB D:Cys102 3.50 Co SG D:Cys102 2.66 Co C D:Cys102 2.87 Co CA D:Cys102 3.30 Co N D:Arg103 4.10 Co CA D:Arg103 4.68 Co OE1 D:Glu105 1.96 Co OE2 D:Glu105 4.16 Co CD D:Glu105 3.16 Co CG D:Glu105 3.86 Co NE2 D:His106 2.26 Co ND1 D:His106 4.37 Co CD2 D:His106 3.38 Co CE1 D:His106 3.16 Co CG D:His106 4.49 interactive model: