A detailed computational analysis employing density functional theory (DFT), atoms in molecules, and quantum mechanics/molecular mechanics (QM/MM) tools has been performed to investigate the primary coordination environment of cob(I)alamin (Co+Cbx), which is a ubiquitous B12 intermediate in methyltransferases and ATP:corrinoid adenosyltransferases. The DFT calculations suggest that the simplified (Co+Cbl) as well as the complete (Co+Cbi) complexes can adapt to the square pyramidal or octahedral coordination geometry owing to the unconventional H-bonding between the Co+ ion and its axial ligands. These Co+–H bonds contain appreciable amounts of electrostatic, charge transfer, long-range correlation, and dispersion components. The computed reduction potentials of the Co2+/Co+ couple imply that the Co+–H(H2O) interaction causes a greater anodic shift [5–98 mV vs. the normal hydrogen electrode (NHE) in chloroform solvent] than the analogous Co+–H(imidazole) interaction (1 mV vs. NHE) in the reduction potential of the Co2+/Co+ couple. This may explain why a β-axial H2O ligand has specifically been found in the active sites of certain methyltransferases. The QM/MM analysis of methionine synthase bound Co+Cbx (Protein Data Bank ID 1BMT, resolution 3.0 Å) indicates that the enzyme-bound Co+Cbx can also form a Co+–H bond, but can only exist in square pyramidal form because of the steric constraints imposed by the cellular environment. The present calculations thus support a recently proposed alternate mechanism for the enzyme-bound Co2+/Co+ reduction that involves the conversion of square pyramidal Co2+Cbx into square pyramidal Co+Cbx (Kumar and Kozlowski in Angew. Chem. Int. Ed. 50:8702–8705, 2011).