User:Michael Roberts/BIOL115 CaM: Difference between revisions

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'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'.

'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/5'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'.

The α-helical region is now clearly defined, and there are also regions of β-structure.

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In each EF hand loop, the Ca2+ ions are bound by amino acid residues in and near the loops.

The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.

The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/4'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.

'''CO-ORDINATING RESIDUES''':

To illustrate how Ca2+ is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca2+ ions.

To illustrate how Ca2+ is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/5'>residues that take part in binding</scene> one of the Ca2+ ions.

<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly.

<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/6'>Zoom in</scene> to see this more clearly.

'''CO-ORDINATING ATOMS''':

To highlight the atoms that co-ordinate the Ca2+ ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule.

To highlight the atoms that co-ordinate the Ca2+ ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/4'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule.

@@ Line 21: / Line 21: @@
-'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'.
+'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/5'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style 'ribbons'.
 The α-helical region is now clearly defined, and there are also regions of β-structure.
@@ Line 35: / Line 35: @@
 In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.
-The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.
+The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/4'>calcium ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.
 '''CO-ORDINATING RESIDUES''':
-To illustrate how Ca<sup>2+</sup>  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.
+To illustrate how Ca<sup>2+</sup>  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/5'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.
-<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly.
+<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/6'>Zoom in</scene> to see this more clearly.
 '''CO-ORDINATING ATOMS''':
-To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule.
+To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/4'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule.