1evv
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1evv |SIZE=350|CAPTION= <scene name='initialview01'>1evv</scene>, resolution 2.00Å | |PDB= 1evv |SIZE=350|CAPTION= <scene name='initialview01'>1evv</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5'-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5'-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5'-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5'-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=T:THYMIDINE-5'-MONOPHOSPHATE'>T</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[4tna|4TNA]], [[1tra|1TRA]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1evv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evv OCA], [http://www.ebi.ac.uk/pdbsum/1evv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1evv RCSB]</span> | ||
}} | }} | ||
| Line 25: | Line 28: | ||
[[Category: Jovine, L.]] | [[Category: Jovine, L.]] | ||
[[Category: Rhodes, D.]] | [[Category: Rhodes, D.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: SPM]] | ||
[[Category: amino-acid transport]] | [[Category: amino-acid transport]] | ||
[[Category: phe-trna]] | [[Category: phe-trna]] | ||
| Line 33: | Line 34: | ||
[[Category: yeast]] | [[Category: yeast]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:10:40 2008'' |
Revision as of 17:10, 30 March 2008
| |||||||
| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , , , , , , , , , , | ||||||
| Related: | 4TNA, 1TRA
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION
Overview
We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg(2+) is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg(2+).
About this Structure
1EVV is a Single protein structure of sequence from Saccharomyces. Full crystallographic information is available from OCA.
Reference
The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals., Jovine L, Djordjevic S, Rhodes D, J Mol Biol. 2000 Aug 11;301(2):401-14. PMID:10926517
Page seeded by OCA on Sun Mar 30 20:10:40 2008
