2XRE: Detection Of Cobalt In Previously Unassigned Human Senp1 Structure

Metal ions often stabilize intermolecular contacts between macromolecules, thereby promoting crystallization. When interpreting a medium-resolution electron-density map of the catalytic domain of human sentrin-specific protease 1 (SENP1), a strong feature indicative of an ordered divalent cation was noted. This was assigned as Co(2+), an essential component of the crystallization mixture. The ion displays tetrahedral coordination by Glu430 and His640 from one molecule and the corresponding residues from a symmetry-related molecule. Analysis of the data derived from a previous structure of SENP1 suggested that Co(2+) had been overlooked and re-refinement supported this conclusion. High-throughput automated re-refinement protocols also failed to mark the Co(2+) position, supporting the requirement for the incorporation of as much information as possible to enhance the value of such protocols.
PDB ID: 2XREDownload
MMDB ID: 85290
PDB Deposition Date: 2010/9/14
Updated in MMDB: 2013/11
Experimental Method:
x-ray diffraction
Resolution: 2.45  Å
Source Organism:
Similar Structures:
Biological Unit for 2XRE: monomeric; determined by author
Molecular Components in 2XRE
Label Count Molecule
Protein (1 molecule)
Sentrin-specific Protease 1(Gene symbol: SENP1)
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB