BioPHYSICAL chemistry

338 PART 2 QUANTUM MECHANICS AND SPECTROSCOPY

negative ripple that obscures the electron density of any light atom. In

the higher-resolution data, the truncation effects are less pronounced and

the calculated density no longer shows the ripple of negative density.

Unambiguous identification of the new atom based solely upon the elec-

tron density is problematic as all of the light atoms – carbon, nitrogen,

oxygen, and sulfur – are chemically plausible and consistent with the

density, although the interaction of nitrogenase with dinitrogen and

ammonia suggests the assignment of nitrogen. The need to insert an

interstitial nitrogen adds to the complexity of the cluster and questions

arise concerning the biosynthesis of the cofactor and assembly into the

protein.

The mechanism of this complex enzyme system is under active

investigation (Barney et al. 2005, 2006; Texcan et al. 2005; Peters &

Szilagyi 2006). As part of the dynamics of the overall process, the iron

protein docks to the molybdenum–iron protein, transfers an electron,

and dissociates in a repetitive process until the eight-electron transfer

is completed. Coupled to the docking-and-release gating process is the

hydrolysis of MgATP. Crystal structures have been determined in dif-

ferent nucleotide states that identify conformational changes in the

nitrogenase complex during ATP turnover (Figure 15.24). These struc-

tures show that the arrangement of the two proteins in the complex

is dependent upon the nucleotide state. For each conformational state,

different distances are observed between the redox cofactors involved in

the electron-transfer process implying differences in the electron-transfer

6  Fe

9  S

Fe1

Mo

Sum

0.5

0.0

0.5

1.0

1.5

2.0

1.0

3.5 3.0 2.5 2.0 1.5 1.0 0.5

ρ(

r) [e

/Å

3 ]

dmax [Å]

Figure 15.23The effect of a series of termination errors on the resolution-dependent electron-
density profile around the iron atom of the cofactor results in the calculation of negative density.
Contributions of individual atom types to the resolution-dependent profile show a pronounced
negative density at 1.8 Å. Modified from Einsle et al. (2002).