Tom Sandbox: Difference between revisions

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These two main domains are labled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/1'>acidic leucine zipper dimerization domain and the basic DNA-binding domain</scene>. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> Here the acidic region is represented as Orange and the basic region in purple. The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The basic region at the N-terminal of the two chains clamps in on the DNA like a pair of tweezers and makes contact with both <scene name='Tom_Sandbox/Binding_with_dna/1'>~~the~~ bases and phosphate oxygens</scene> of DNA. In this example, Arginine residues of one of the helices are highlighted. The yellow Arginine binds to the oxygen of the phosphate backbone, while the light green Arginine binds to the inner nucleotide base.

These two main domains are labled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/1'>acidic leucine zipper dimerization domain and the basic DNA-binding domain</scene>. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> Here the acidic region is represented as Orange and the basic region in purple. The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The basic region at the N-terminal of the two chains clamps in on the DNA like a pair of tweezers and makes contact with both the <scene name='Tom_Sandbox/Binding_with_dna/2'>bases and phosphate oxygens</scene> of DNA. In this example, Arginine residues of one of the helices are highlighted. The yellow Arginine binds to the oxygen of the phosphate backbone, while the light green Arginine binds to the inner nucleotide base.

===Binding with DNA===

Tom Sandbox: Difference between revisions

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 {{STRUCTURE_1ysa|  PDB=1ysa  |  SCENE=  }}
-These two main domains are labled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/1'>acidic leucine zipper dimerization domain and the basic DNA-binding domain</scene>. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> Here the acidic region is represented as Orange and the basic region in purple. The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The basic region at the N-terminal of the two chains clamps in on the DNA like a pair of tweezers and makes contact with both <scene name='Tom_Sandbox/Binding_with_dna/1'>the bases and phosphate oxygens</scene> of DNA. In this example, Arginine residues of one of the helices are highlighted. The yellow Arginine binds to the oxygen of the phosphate backbone, while the light green Arginine binds to the inner nucleotide base.
+These two main domains are labled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/1'>acidic leucine zipper dimerization domain and the basic DNA-binding domain</scene>. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> Here the acidic region is represented as Orange and the basic region in purple. The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The basic region at the N-terminal of the two chains clamps in on the DNA like a pair of tweezers and makes contact with both the <scene name='Tom_Sandbox/Binding_with_dna/2'>bases and phosphate oxygens</scene>  of DNA. In this example, Arginine residues of one of the helices are highlighted. The yellow Arginine binds to the oxygen of the phosphate backbone, while the light green Arginine binds to the inner nucleotide base.
 ===Binding with DNA===