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. Author manuscript; available in PMC: 2013 Aug 14.

Published in final edited form as: Biochemistry. 2007 Dec 4;46(51):14878–14888. doi: 10.1021/bi701532r

Fits of electron density. a) Fit of the electron density at the center of the pore for the binary complex, revealing the nicotinamide rings for two of the four symmetry-related NADP⁺ positions. Electron density represents 2F_obs-F_calc, contoured at 0.5σ in order to illustrate density for ligands at 25% occupancy. Each color (red, blue, green, and magenta) identifies a unique set of NADP⁺ or water ligands among the four symmetry-related groups which are averaged in the crystal. Two symmetry-related nicotinamide rings are shown. Since only one NADP⁺ binds per tetramer (9), the ligand is present at 25% occupancy at each position. Symmetry-related water molecules bind to each of the sites not occupied by NADP⁺, resulting in 75% occupancy. For example, the green, magenta and blue water molecules describe water seen in three symmetry related sites when the red colored cofactor is bound. The protein side chains at the top and bottom of the figure correspond to the NH and O backbone atoms from symmetry related Ile68 residues, which interact with the amide of the nicotinamide. b) Electron density for one side of the pore in the ternary complex (contoured the same as a), showing overlapping nicotinamide and pteridine groups. Color-coding is as in panel a, however in this case, the two ligands exclude several water molecules from two of the four sites. Electron density for the pyridine ring of the nicotinamide overlaps closely with that arising from the pyrazine ring of DHF. Note that these figures illustrate electron density for symmetry-related molecules, rather than for an interacting substrate-cofactor pair, which is discussed below. WAT114, positioned near the pteridine O4, has only 25 % occupancy and appears to be associated with the pteridine ring. c) Electron density corresponding to the phospho-adenosine pyrophosphate group of NADP⁺. The bracketed P_N5′ and P_A5′ from a symmetry-related NADP⁺ molecule, shown in lighter shades of magenta and red, are also included. The density was taken from data for the ternary complex. Symmetry-related water molecules are also indicated by faded coloring.

Fits of electron density. a) Fit of the electron density at the center of the pore for the binary complex, revealing the nicotinamide rings for two of the four symmetry-related NADP⁺ positions. Electron density represents 2F_obs-F_calc, contoured at 0.5σ in order to illustrate density for ligands at 25% occupancy. Each color (red, blue, green, and magenta) identifies a unique set of NADP⁺ or water ligands among the four symmetry-related groups which are averaged in the crystal. Two symmetry-related nicotinamide rings are shown. Since only one NADP⁺ binds per tetramer (9), the ligand is present at 25% occupancy at each position. Symmetry-related water molecules bind to each of the sites not occupied by NADP⁺, resulting in 75% occupancy. For example, the green, magenta and blue water molecules describe water seen in three symmetry related sites when the red colored cofactor is bound. The protein side chains at the top and bottom of the figure correspond to the NH and O backbone atoms from symmetry related Ile68 residues, which interact with the amide of the nicotinamide. b) Electron density for one side of the pore in the ternary complex (contoured the same as a), showing overlapping nicotinamide and pteridine groups. Color-coding is as in panel a, however in this case, the two ligands exclude several water molecules from two of the four sites. Electron density for the pyridine ring of the nicotinamide overlaps closely with that arising from the pyrazine ring of DHF. Note that these figures illustrate electron density for symmetry-related molecules, rather than for an interacting substrate-cofactor pair, which is discussed below. WAT114, positioned near the pteridine O4, has only 25 % occupancy and appears to be associated with the pteridine ring. c) Electron density corresponding to the phospho-adenosine pyrophosphate group of NADP⁺. The bracketed P_N5′ and P_A5′ from a symmetry-related NADP⁺ molecule, shown in lighter shades of magenta and red, are also included. The density was taken from data for the ternary complex. Symmetry-related water molecules are also indicated by faded coloring.