2spt: Difference between revisions
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'''DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1''' | {{Structure | ||
|PDB= 2spt |SIZE=350|CAPTION= <scene name='initialview01'>2spt</scene>, resolution 2.5Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> and <scene name='pdbligand=SR:STRONTIUM ION'>SR</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] | |||
|GENE= | |||
}} | |||
'''DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2SPT is a [ | 2SPT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SPT OCA]. | ||
==Reference== | ==Reference== | ||
Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1., Seshadri TP, Skrzypczak-Jankun E, Yin M, Tulinsky A, Biochemistry. 1994 Feb 8;33(5):1087-92. PMID:[http:// | Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1., Seshadri TP, Skrzypczak-Jankun E, Yin M, Tulinsky A, Biochemistry. 1994 Feb 8;33(5):1087-92. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8110739 8110739] | ||
[[Category: Bos taurus]] | [[Category: Bos taurus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: hydrolase(serine proteinase)]] | [[Category: hydrolase(serine proteinase)]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:38:42 2008'' | ||
Revision as of 19:38, 20 March 2008
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| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Thrombin, with EC number 3.4.21.5 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1
OverviewOverview
The structure of Sr-prothrombin fragment 1 has been solved and refined by restrained least-squares methods at 2.5-A resolution to a crystallographic R value of 0.167. The protein structure is very similar to that of Ca-fragment 1. A polymeric array of five Sr2+ ions separated by about 4.0 A is buried among six gamma-carboxyglutamic acid (Gla) residues; three other Sr2+ ions interact with other Gla residues and are located further apart. One of these was not found in the Ca-fragment 1 structure. The coordination of the Sr2+ ions resembles that of Ca2+, but there are some significant differences between them. The most notable is the lack of water coordination with Sr2+ ions and two conformations for Gla 8, which change the coordination of Sr-2 and Sr-3. A hexose moiety of an oligosaccharide was located in the vicinity of Asn101 that was flexibly disordered in Ca-fragment 1. The new Sr2+ ion found may be involved in metal ion phospholipid binding interactions along with Sr-1, and Sr-7, Sr-8.
About this StructureAbout this Structure
2SPT is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
ReferenceReference
Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1., Seshadri TP, Skrzypczak-Jankun E, Yin M, Tulinsky A, Biochemistry. 1994 Feb 8;33(5):1087-92. PMID:8110739
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