2spt
DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1
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| , resolution 2.5Å | |||||||
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| Ligands: | , , | ||||||
| Activity: | Thrombin, with EC number 3.4.21.5 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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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