8RNT

STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH ZINC(II) AT 1.8 ANGSTROMS RESOLUTION: A ZN2+.6H2O.CARBOXYLATE CLATHRATE

Summary for 8RNT

• Entry DOI: 10.2210/pdb8rnt/pdb
• Descriptor: RIBONUCLEASE T1, ZINC ION (3 entities in total)
• Functional Keywords: hydrolase(endoribonuclease)
• Biological source: Aspergillus oryzae
• Total number of polymer chains: 1
• Total formula weight: 11160.10

Authors

Ding, J.,Choe, H.-W.,Granzin, J.,Saenger, W. (deposition date: 1991-09-23, release date: 1993-01-15, Last modification date: 2017-11-29)

Primary citation

Ding, J.,Choe, H.W.,Granzin, J.,Saenger, W.
Structure of ribonuclease T1 complexed with zinc(II) at 1.8 A resolution: a Zn2+.6H2O.carboxylate clathrate.
Acta Crystallogr.,Sect.B, 48:185-191, 1992

PubMed Abstract: In order to study the inhibitory effect of Zn2+ on ribonuclease T1 [RNase T1; Itaya & Inoue (1982). Biochem. J. 207, 357-362], the enzyme was cocrystallized with 2 mM Zn2+, pH 5.2, from a solution containing 55% (v/v) 2-methyl-2,4-pentanediol. The crystals are orthorhombic, P2(1)2(1)2(1), a = 48.71 (1), b = 46.51 (1), c = 41.14 (1) A, Z = 4, V = 93203 A3. The crystal structure was determined by molecular replacement and refined by restrained least-squares methods based on Fhkl for 8291 unique reflections with Fo greater than or equal to 1 sigma (Fo) in the resolution range 10 to 1.8 A and converged at a crystallographic R factor of 0.140. The Zn2+ is not bonded to the active site of RNase T1, probably because the His40 and His92 side chains are protonated. Zn2+ occupies the same site as Ca2+ in a series of crystal structures of free and nucleotide-complexed RNase T1. It is coordinated to Asp15 carboxylate and to six water molecules forming a dodecahedron of square antiprismatic form. The Zn2+...O distances are approximately 2.5 A, suggesting that Zn2+ is clathrated and not coordinated, which would require distances of 2.0 A.

PubMed: 1515106
DOI: 10.1107/S0108768191013058

Experimental method

X-RAY DIFFRACTION (1.8 Å)