Factor Xa: Difference between revisions

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<scene name='Factor_Xa/Transparent_-_no_inhib_s4/1'>S4 pocket</scene> is formed between the 90s and 170s loops and binds an Ile. This region contains 3 ligand binding domains. The <scene name='Factor_Xa/Transparent_-_no_inhib_phob_bo/3'>hydrophobic box</scene> is located at the entrance to S4 and contains Phe174, Tyr99 and Trp215, which form a deep aryl-binding pocket. The <scene name='Factor_Xa/Transparent_-_no_inhib_oxianio/2'>cationic hole</scene> is formed by the backbone carbonyl and side chain of Glu97 and the backbone carbonyl of Lys96. The <scene name='Factor_Xa/Transparent_-_no_inhib-_h2o_si/2'>water site</scene> is composed of the hydrophobic side chains of Thr98, Ile175 and Thr177 and traps a water molecule. <ref name="Inhib" />

===Helix capping ===

Helices have exposed hydrogen bond donors from the first 4 residues at the N-terminus. Helix capping refers to H-bonding to these groups, primarily by nearby side chains, to "seal" the helix. Factor Xa forms a helix from residue 165-171 that is capped at the N-terminus by an aspartate residue number 164. The aspartate side chain is twisted to follow the helix and provide capping. The backbone carbonyl is hydrogen bonded to the backbone nitrogen groups of serine 167 and cysteine 168. One of the side chain oxygen groups of aspartate forms hydrogen bonds with the backbone nitrogen groups of asparagine 166 and serine 167. Arginine 165 is the first residue in the helix and it provides capping hydrogen bonds for lysine 169. The backbone nitrogen group of arginine 165 appears to form a hydrogen bond with the solvent. The aspartate and asparagine residues 164 and 165 provide capping hydrogen bonds for the hydrogen bond donors of the first 4 N-terminal helix residues.

==Enzyme Mechanism==

Factor Xa: Difference between revisions

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@@ Line 28: / Line 28: @@
 <scene name='Factor_Xa/Transparent_-_no_inhib_s4/1'>S4 pocket</scene> is formed between the 90s and 170s loops and binds an Ile. This region contains 3 ligand binding domains. The <scene name='Factor_Xa/Transparent_-_no_inhib_phob_bo/3'>hydrophobic box</scene> is located at the entrance to S4 and contains Phe174, Tyr99 and Trp215, which form a deep aryl-binding pocket. The <scene name='Factor_Xa/Transparent_-_no_inhib_oxianio/2'>cationic hole</scene>  is formed by the backbone carbonyl and side chain of Glu97 and the backbone carbonyl of Lys96. The <scene name='Factor_Xa/Transparent_-_no_inhib-_h2o_si/2'>water site</scene> is composed of  the hydrophobic side chains of Thr98, Ile175 and Thr177 and traps a water molecule. <ref name="Inhib" />
+===Helix capping ===
+Helices have exposed hydrogen bond donors from the first 4 residues at the N-terminus. Helix capping refers to H-bonding to these groups, primarily by nearby side chains, to "seal" the helix. Factor Xa forms a helix from residue 165-171 that is capped at the N-terminus by an aspartate residue number 164. The aspartate side chain is twisted to follow the helix and provide capping. The backbone carbonyl is hydrogen bonded to the backbone nitrogen groups of serine 167 and cysteine 168.  One of the side chain oxygen groups of aspartate forms hydrogen bonds with the backbone nitrogen groups of asparagine 166 and serine 167. Arginine 165 is the first residue in the helix and it provides capping hydrogen bonds for lysine 169. The backbone nitrogen group of arginine 165 appears to form a hydrogen bond with the solvent. The aspartate and asparagine residues 164 and 165 provide capping hydrogen bonds for the hydrogen bond donors of the first 4 N-terminal helix residues.
 ==Enzyme Mechanism==