Hydrogen in macromolecular models: Difference between revisions
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Eric Martz (talk | contribs) |
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*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens. | *'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens. | ||
*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only 22% (639/2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: | *'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor. | ||
*'''Example: All hydrogens from theory''': (an example is needed here) | *'''Example: All hydrogens from theory''': (an example is needed here) | ||