Crystallographic waters

The complex of protein, crystallographic water and the counter ions are treated as a fully solvated system. Two key developments were made to treat the system in a more realistic manner during molecular dynamics (i) water molecules were placed as a spherical shell with a radius 34 A from the center of the protein. The outer boundary of the spherical shell was defined by means of an artificial wall with a potential of the type W defined as ... 

Three types of interaction between ligand and protein heavy atoms arising from different atom types. Primary and secondary amines are defined to be donors while oxygen and nitrogen atoms with no bound hydrogens are defined to be acceptors. Crystallographic water molecules and hydroxyl groups are defined to be both donor and acceptor. Carbon and sulfur atoms are defined to be nonpolar... 

It is interesting to compare the hydration structure obtained by the 3D-RISM theory with crystallographic water sites of X-ray structure [30]. The crystallographic water molecules in the cavity are depicted in the right of Fig. 10.3, showing four water sites in the cavity, much as the 3D-RISM theory has detected. Moreover, the water distributions obtained from the theory and experiment are quite similar to each other. Thus the 3D-RISM theory can predict the water-binding sites with great success. 

The next-most constraining part of the volume is a low-energy channel with a cross section that is narrow in one direction and somewhat wider in the other. This channel is filled with five crystallographic water molecules, so arranged that they can form five hydrogen bonds with each other. (Figure lb and c, right of center.)... 

Thermal parameters, B, of the 47 crystallographic waters of BPTI range from 7 to 60 all but 7 values are between 12 and 44... 

Figure 7.3 ACHE X-ray crystallography structures (pdb lamn). (a) Ribbon display structure depiction with X-ray crystallographic water molecules illustrated and bound substrate depicted in the CPK display mode. Colour coding is as follows Hydrogen White Oxygen Red Nitrogen Blue Carbon Grey. In this structure, sulphate (Sulphur Yellow) is also included, (b) Close-up of active site to show dense hydrogenbonding network (bright yellow). Bound substrates and water molecules are shown in the stick display mode. The protein polypeptide is also shown in CA display mode.

Figure 8.10 Acetylcholine Esterase, (a) Hydrolysis reaction catalyzed by acetyl choline esterase (AChE) (b) ribbon display structure of AChE Torpedo californica) (pdb lamn) illustrating crystallographic water molecules (oxygen red hydrogen white) plus sulphate ion and substrate analogue bound in catalytic site. Both these are rendered as CPK structures (red oxygen yellow sulphur grey carbon blue nitrogen).

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