Cobalt in the structure of How A Protein Binds B12: A 3.O Angstrom X-Ray Structure Of the B12-Binding Domains of Methionine Synthase (pdb 1bmt)

The binding sites of Cobalt atom in the structure of How A Protein Binds B12: A 3.O Angstrom X-Ray Structure Of the B12-Binding Domains of Methionine Synthase (pdb code 1bmt). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1bmt structure was solved by C.L.DRENNAN, S.HUANG, J.T.DRUMMOND, R.G.MATTHEWS, M.L.LUDWIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-3.0 Space group P212121 a (A) 96.700 b (A) 55.300 c (A) 103.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) n/a Cobalt Binding Sites: Cobalt binding site 1 out of 2 in 1bmt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1bmt. 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: His759, A: Cob122, conact list: Atom Atom Distance (A) Co NE2 A:His759 2.24 Co ND1 A:His759 4.42 Co CD2 A:His759 3.27 Co CE1 A:His759 3.25 Co CG A:His759 4.45 Co C18 A:Cob122 3.88 Co C11 A:Cob122 2.95 Co C1 A:Cob122 2.69 Co C8 A:Cob122 4.18 Co C2 A:Cob122 4.06 Co C46 A:Cob122 4.84 Co N22 A:Cob122 2.02 Co C35 A:Cob122 4.73 Co C17 A:Cob122 4.09 Co N21 A:Cob122 1.93 Co C12 A:Cob122 4.30 Co C19 A:Cob122 2.65 Co C41 A:Cob122 4.87 Co CO A:Cob122 0.00 Co C15 A:Cob122 3.34 Co C37 A:Cob122 4.66 Co C16 A:Cob122 2.89 Co C6 A:Cob122 2.92 Co C5 A:Cob122 3.30 Co C4 A:Cob122 2.86 Co C10 A:Cob122 3.32 Co C13 A:Cob122 4.22 Co C20 A:Cob122 3.33 Co C48 A:Cob122 4.81 Co C9 A:Cob122 2.94 Co C54 A:Cob122 4.94 Co C14 A:Cob122 2.95 Co N24 A:Cob122 1.91 Co N23 A:Cob122 2.02 Co C7 A:Cob122 4.13 Co C3 A:Cob122 4.16 Co C26 A:Cob122 4.72 Co C1A A:Cob122 1.96 interactive model: Cobalt binding site 2 out of 2 in 1bmt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1bmt. 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: His759, B: Cob122, conact list: Atom Atom Distance (A) Co NE2 B:His759 2.14 Co ND1 B:His759 4.28 Co CD2 B:His759 3.31 Co CE1 B:His759 3.06 Co CG B:His759 4.42 Co C18 B:Cob122 3.92 Co C11 B:Cob122 3.03 Co C1 B:Cob122 2.70 Co C8 B:Cob122 4.18 Co C2 B:Cob122 4.07 Co N22 B:Cob122 1.85 Co C35 B:Cob122 4.66 Co C17 B:Cob122 4.15 Co N21 B:Cob122 1.84 Co C12 B:Cob122 4.38 Co C19 B:Cob122 2.73 Co C41 B:Cob122 4.75 Co CO B:Cob122 0.00 Co C15 B:Cob122 3.40 Co C30 B:Cob122 4.95 Co C37 B:Cob122 4.73 Co C16 B:Cob122 2.96 Co C6 B:Cob122 2.82 Co C5 B:Cob122 3.20 Co C4 B:Cob122 2.78 Co C10 B:Cob122 3.40 Co C13 B:Cob122 4.29 Co C20 B:Cob122 3.32 Co C48 B:Cob122 4.79 Co C9 B:Cob122 2.95 Co C14 B:Cob122 2.98 Co N24 B:Cob122 1.91 Co N23 B:Cob122 1.98 Co C7 B:Cob122 4.11 Co C53 B:Cob122 4.95 Co C3 B:Cob122 4.12 Co C26 B:Cob122 4.65 Co C1A B:Cob122 2.08 interactive model: