Structure of ribonuclease T1 complexed with zinc(II) at 1.8 A resolution: a Zn2+.6H2O.carboxylate clathrate.
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.
Ding
J
J
Institut für Kristallographie, Freie Universität Berlin, Germany.
Choe
H W
HW
Granzin
J
J
Saenger
W
W
D000595:Amino Acid Sequence; D001236:Aspergillus oryzae / Q000201:enzymology; D001665:Binding Sites; D003460:Crystallization; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D006163:Ribonuclease T1 / Q000037:antagonists & inhibitors / Q000737:chemistry*; D013816:Thermodynamics; D014961:X-Ray Diffraction / Q000379:methods; D015032:Zinc / Q000494:pharmacology
D006163:Ribonuclease T1; D015032:Zinc