Answers.Body: <p>It is a crystallisation artefact. Namely, the protein are placed in a condition where they fall out of solution without aggregating a gloop (as happens in most well in xstal trial) and to pack as a crystal they need to be placed nice and orderly. It is coordinated by water so is not relevant. A lot of structures have these —DMSO and ions are the most commonly.</p>
  
  <p>Two footnotes.</p>
  
  <ul>
  <li>1ZV7 is a crystal structure, <em>i.e.</em> solved by X-ray diffraction. A model is generally used to described an <em>in silico</em> model, such as those from Swissmodel, phyre, I-Tasser etc. These are generated <em>ab initio</em> (from scratch) or threaded (mapped on top of) against crystal/EM/NMR structures. For Covid I-Tasser has a <a href="https://zhanglab.ccmb.med.umich.edu/COVID-19/" rel="nofollow noreferrer">nice picture of its models</a>.</li>
  <li>The best source of info about structures is the PDB. <a href="https://www.rcsb.org/" rel="nofollow noreferrer">RCSB PDB</a> is more commonly used, while <a href="https://www.ebi.ac.uk/pdbe/" rel="nofollow noreferrer">PDBe</a> is more tricker to navigate (or used to be). Both have the same data, but are better for the extras than NCBI.</li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-05T12:05:49.070Z
Answers.LastActivityDate: 2020-06-05T12:05:49.070Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>Here we have a 3D model of a sequence that match with this sequence
  VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK
  in Blast</p>
  
  <p>the 3D structure is <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&amp;mmdbid=38995&amp;bu=1&amp;showanno=1" rel="nofollow noreferrer">here</a></p>
  
  <p>Why is there a chloride ion in <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&amp;mmdbid=38995&amp;bu=1&amp;showanno=1" rel="nofollow noreferrer">this</a> 3D model?</p>
  
  <p><a href="https://i.sstatic.net/HMNJn.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/HMNJn.png" alt="screenshot of the 3D structure"></a></p>
  
Tags: <protein-structure><covid-19><protein-protein-interaction><interactions><sars-cov-2>
Title: Why is there a chloride ion in this 3D model?
ThreadText: # Why is there a chloride ion in this 3D model?
  
  (Asked by: username_0 on 2020-06-05)
  
  Here we have a 3D model of a sequence that match with this sequence
  VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK
  in Blast
  
  the 3D structure is [here](https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&mmdbid=38995&bu=1&showanno=1)
  
  Why is there a chloride ion in [this](https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&mmdbid=38995&bu=1&showanno=1) 3D model?
  
  [![screenshot of the 3D structure](https://i.sstatic.net/HMNJn.png)](https://i.sstatic.net/HMNJn.png)
  
  **Tags:** protein-structure, covid-19, protein-protein-interaction, interactions, sars-cov-2
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-06-05. Score: 3
  
  It is a crystallisation artefact. Namely, the protein are placed in a condition where they fall out of solution without aggregating a gloop (as happens in most well in xstal trial) and to pack as a crystal they need to be placed nice and orderly. It is coordinated by water so is not relevant. A lot of structures have these —DMSO and ions are the most commonly.
  
  Two footnotes.
  
  * 1ZV7 is a crystal structure, *i.e.* solved by X-ray diffraction. A model is generally used to described an *in silico* model, such as those from Swissmodel, phyre, I-Tasser etc. These are generated *ab initio* (from scratch) or threaded (mapped on top of) against crystal/EM/NMR structures. For Covid I-Tasser has a [nice picture of its models](https://zhanglab.ccmb.med.umich.edu/COVID-19/).
  * The best source of info about structures is the PDB. [RCSB PDB](https://www.rcsb.org/) is more commonly used, while [PDBe](https://www.ebi.ac.uk/pdbe/) is more tricker to navigate (or used to be). Both have the same data, but are better for the extras than NCBI.
  
  
  ---
  
  