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Visualisation of Xanthomonas citri pv. citri carboxylesterase protein
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- 13 hydrophobic cores were detected. The biggest one contains of 2593 atoms, other ones comprise less than 8 atoms.
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Packing density of atoms in a hydrophobic core
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- For investigation i have taken phenylalanine 289:B. Atoms barely able to cover residues surface are located on the distance of 5 angstrom. Specific distance between neighboring not-linked atoms in protein was calculated as an average of 11 measures, with a value 3,7 A. Van der Waals radius for O is 1,4 A, for S and C - 1,85 A, for N - 1,54 A. Free distance between atoms is 3,7-2*1,4=0,9, so that means that a water molecule is unable to locate between them, because it's radius is close to oxygen's one (2,8).
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- Human DNA polymerase eta is presented on this applet. It's function is to catalyze DNA replication.[1]
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Few more examples of protein-DNA interaction:
- RNA-polymerase - takes part in DNA transcription and replication
- Histones - create chromatine
- Transcriptions factors
- Topoisomerases - change DNA's swirl's degree
- Helicases disrupt hydrogenic bonds and untwist the DNA
- Nucleases cut the DNA
- Lygases sew the DNA together
- DNA-methyltransferase regulate DNA reading process, by addition of methyl groups
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