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An introduction to stereochemical restraints.

Evans PR - Acta Crystallogr. D Biol. Crystallogr. (2006)

Bottom Line: A dictionary entry contains information about the atom types, their connectivity and all the appropriate restraints.Torsion angles are not usually restrained, but they do have optimum values.In the special case of flexible five- and six-membered rings, including pentose and hexose sugars, the ring pucker is defined by combinations of torsion angles and the pucker affects the position of substituents.

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Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England. pre@mrc-lmb.cam.ac.uk

ABSTRACT
At the resolution available from most macromolecular crystals, the X-ray data alone are insufficient to lead to a chemically reasonable structure, so stereochemical restraints are essential. These usually restrain bond lengths, bond angles, planes and chiral volumes. The definition of these restraints and where the values come from are described. A dictionary entry contains information about the atom types, their connectivity and all the appropriate restraints. Torsion angles are not usually restrained, but they do have optimum values. In the special case of flexible five- and six-membered rings, including pentose and hexose sugars, the ring pucker is defined by combinations of torsion angles and the pucker affects the position of substituents.

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Axial and equatorial substituents on six-membered rings. (a) β-d-Glucose is most stable in the all-equatorial conformer. (b) d-myo-Inositol hexakisphosphate is largely axial in its crystal structure (CCSD code NAMIHP10), but when bound to a protein it is in the more stable largely equatorial form (bound to AP2; PDB code 1gw5).
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fig2: Axial and equatorial substituents on six-membered rings. (a) β-d-Glucose is most stable in the all-equatorial conformer. (b) d-myo-Inositol hexakisphosphate is largely axial in its crystal structure (CCSD code NAMIHP10), but when bound to a protein it is in the more stable largely equatorial form (bound to AP2; PDB code 1gw5).

Mentions: Flexible six-membered rings include cyclohexane derivatives, but most importantly pyran­ose sugars such as glucose and inositol derivatives. These rings can cycle through a series of conformations including the stable chair forms, through boat and twist-boat conformations that are less stable. In the chair forms, the substituents on each tetrahedral carbon can be divided into ‘equatorial’ substituents, in the approximate plane of the C atoms, and ‘axial’ substituents perpendicular to this plane. The ring can flip between two alternative chair forms, which interchanges axial and equatorial substituents. The molecule is most stable if the majority of bulky substituents are equatorial rather than axial, as this places them farther apart. For example, β-d-glucose, the most stable hexose sugar, has all its hydroxyl substituents equatorial. The ring-flipped form would have all hydroxyl substituents axial and is less stable (Fig. 2 ▶ a). The pathway for the ring-flipping operation takes the molecule through higher energy boat conformations, so it is unlikely that a refinement procedure would flip an incorrectly puckered ring: this would probably have to be performed manually. This is not relevant to the construction of the dictionary, but it should be borne in mind during rebuilding.


An introduction to stereochemical restraints.

Evans PR - Acta Crystallogr. D Biol. Crystallogr. (2006)

Axial and equatorial substituents on six-membered rings. (a) β-d-Glucose is most stable in the all-equatorial conformer. (b) d-myo-Inositol hexakisphosphate is largely axial in its crystal structure (CCSD code NAMIHP10), but when bound to a protein it is in the more stable largely equatorial form (bound to AP2; PDB code 1gw5).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483478&req=5

fig2: Axial and equatorial substituents on six-membered rings. (a) β-d-Glucose is most stable in the all-equatorial conformer. (b) d-myo-Inositol hexakisphosphate is largely axial in its crystal structure (CCSD code NAMIHP10), but when bound to a protein it is in the more stable largely equatorial form (bound to AP2; PDB code 1gw5).
Mentions: Flexible six-membered rings include cyclohexane derivatives, but most importantly pyran­ose sugars such as glucose and inositol derivatives. These rings can cycle through a series of conformations including the stable chair forms, through boat and twist-boat conformations that are less stable. In the chair forms, the substituents on each tetrahedral carbon can be divided into ‘equatorial’ substituents, in the approximate plane of the C atoms, and ‘axial’ substituents perpendicular to this plane. The ring can flip between two alternative chair forms, which interchanges axial and equatorial substituents. The molecule is most stable if the majority of bulky substituents are equatorial rather than axial, as this places them farther apart. For example, β-d-glucose, the most stable hexose sugar, has all its hydroxyl substituents equatorial. The ring-flipped form would have all hydroxyl substituents axial and is less stable (Fig. 2 ▶ a). The pathway for the ring-flipping operation takes the molecule through higher energy boat conformations, so it is unlikely that a refinement procedure would flip an incorrectly puckered ring: this would probably have to be performed manually. This is not relevant to the construction of the dictionary, but it should be borne in mind during rebuilding.

Bottom Line: A dictionary entry contains information about the atom types, their connectivity and all the appropriate restraints.Torsion angles are not usually restrained, but they do have optimum values.In the special case of flexible five- and six-membered rings, including pentose and hexose sugars, the ring pucker is defined by combinations of torsion angles and the pucker affects the position of substituents.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England. pre@mrc-lmb.cam.ac.uk

ABSTRACT
At the resolution available from most macromolecular crystals, the X-ray data alone are insufficient to lead to a chemically reasonable structure, so stereochemical restraints are essential. These usually restrain bond lengths, bond angles, planes and chiral volumes. The definition of these restraints and where the values come from are described. A dictionary entry contains information about the atom types, their connectivity and all the appropriate restraints. Torsion angles are not usually restrained, but they do have optimum values. In the special case of flexible five- and six-membered rings, including pentose and hexose sugars, the ring pucker is defined by combinations of torsion angles and the pucker affects the position of substituents.

Show MeSH
Related in: MedlinePlus