Sandbox Reserved 717: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 69: | Line 69: | ||
The exact position of the lipo-polysaccharide(LPS)-binding site is not known. Proteolysis experiments showed, that it contains to the domain with the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. Compared with the homologous bacteriophage T4-like strain AR1 sequence, which also binds to the same LPS core molecule like gp12, there can be some possible binding residues be assumed. | The exact position of the lipo-polysaccharide(LPS)-binding site is not known. Proteolysis experiments showed, that it contains to the domain with the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. Compared with the homologous bacteriophage T4-like strain AR1 sequence, which also binds to the same LPS core molecule like gp12, there can be some possible binding residues be assumed. | ||
Basic putative binding residues: | <scene name='Sandbox_Reserved_717/Mynewscene/16'>Basic putative binding residues</scene>: | ||
<scene name='Sandbox_Reserved_717/Myscene/2'>Lys446</scene>, <scene name='Sandbox_Reserved_717/Myscene/3'>Lys422</scene> ,<scene name='Sandbox_Reserved_717/Myscene/4'>Arg504</scene> ,<scene name='Sandbox_Reserved_717/Myscene/6'>Arg424</scene> , <scene name='Sandbox_Reserved_717/Myscene/7'>Arg513</scene> | <scene name='Sandbox_Reserved_717/Myscene/2'>Lys446</scene>, <scene name='Sandbox_Reserved_717/Myscene/3'>Lys422</scene> ,<scene name='Sandbox_Reserved_717/Myscene/4'>Arg504</scene> ,<scene name='Sandbox_Reserved_717/Myscene/6'>Arg424</scene> , <scene name='Sandbox_Reserved_717/Myscene/7'>Arg513</scene> | ||
Aromatic putative binding residues: | <scene name='Sandbox_Reserved_717/Mynewscene/17'>Aromatic putative binding residues</scene>: | ||
<scene name='Sandbox_Reserved_717/Myscene/8'>Tyr454</scene> ,<scene name='Sandbox_Reserved_717/Myscene/9'>Phe451</scene>, <scene name='Sandbox_Reserved_717/Myscene/10'>Trp477</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/8'>Phe468</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/9'>Phe460</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/10'>Phe420</scene> , Tyr488, Tyr444, His408, Tyr433 | <scene name='Sandbox_Reserved_717/Myscene/8'>Tyr454</scene> ,<scene name='Sandbox_Reserved_717/Myscene/9'>Phe451</scene>, <scene name='Sandbox_Reserved_717/Myscene/10'>Trp477</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/8'>Phe468</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/9'>Phe460</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/10'>Phe420</scene> ,<scene name='Sandbox_Reserved_717/Mynewscene/11'>Tyr488</scene>,<scene name='Sandbox_Reserved_717/Mynewscene/13'>Tyr444</scene> , <scene name='Sandbox_Reserved_717/Mynewscene/14'>His408</scene>, <scene name='Sandbox_Reserved_717/Mynewscene/15'>Tyr433</scene> | ||
'''It can not be ruled out that also other amino acids are important for binding! Further it can not be ruled out that not all of these named amino acids are important for binding''' | '''It can not be ruled out that also other amino acids are important for binding! Further it can not be ruled out that not all of these named amino acids are important for binding''' | ||
| Line 84: | Line 84: | ||
The other SO4 molecule (1530) interacts with Ser387. It builds two hydrogen bounds to Ser287 with the distances 2.66 and 3.20. | The other SO4 molecule (1530) interacts with Ser387. It builds two hydrogen bounds to Ser287 with the distances 2.66 and 3.20. | ||
==2.) | ==2.)Citric Acid== | ||
The citric acid interacts with following amino acids: Arg465 (distance 3.01) and Asp455(distance 2.42). These interactions are caused by hydrogen bounds. | The citric acid interacts with following amino acids: Arg465 (distance 3.01) and Asp455(distance 2.42). These interactions are caused by hydrogen bounds. | ||
==3.) | ==3.)Zinc== | ||
The zinc is located in the centre of the receptor-binding domain. The zinc-binding site lies on the border between the head and the bonnet of the 45kDa domain. It interacts with the amino acids His445 and His447 of each monomer. The distances of the zinc ion to the NE2 of His445 and His447 ara 2.22 Å and 2.25 Å. The normally found distances between His and zinc are shorter. The explaination that these distances are longer than normally found is the octahedral coordination of the zinc in this structure. | The zinc is located in the centre of the receptor-binding domain. The zinc-binding site lies on the border between the head and the bonnet of the 45kDa domain. It interacts with the amino acids His445 and His447 of each monomer. The distances of the zinc ion to the NE2 of His445 and His447 ara 2.22 Å and 2.25 Å. The normally found distances between His and zinc are shorter. The explaination that these distances are longer than normally found is the octahedral coordination of the zinc in this structure. | ||
The role of the zinc ion is probably absolute of structural nature. It increases the stability of the C-terminus of gp12 against proteases, but it also raises the stability of the C-terminus in general. | The role of the zinc ion is probably absolute of structural nature. It increases the stability of the C-terminus of gp12 against proteases, but it also raises the stability of the C-terminus in general. | ||
