. Author manuscript; available in PMC: 2009 May 30.

Published in final edited form as: J Mol Biol. 2008 Mar 28;379(2):299–316. doi: 10.1016/j.jmb.2008.03.043

Table 4. Different structures, similar dinucleotide binding sites.

Clusters comprised of similar dinucleotide binding sites of proteins with different overall folds. The columns are the same as in Table 2 except the column which indicates whether the proteins belong to the same Pfam family. It was removed since none of the clusters was comprised of proteins with more than 25% sequence identity or similar Pfam annotation.

Num.	π type	Cl. size	Nts pairs	Cl. center (pdb:chains:nts)	Location	Cluster members annotation

103	2	2	CU, AA	1qtq:AB:C32U33	-2,-3 AA at the PAP binding site of 2q66	Glutaminyl-tRNA synthetase (1qtq) and tRNA-guanine transglycosylase (2q66)
55	3	3	UC, AG	1n78:AC:U34C35	UC of anticodon loop, A11-G12 of 2gzt	Glutamyl-tRNA synthetase (1n78) and Hut operon regulatory protein (1wpu, 2gzt)
354	2	2	CU, CA	1q2r:AE:C8U9	3′ CCA	tRNA-guanine transglycosylase (1q2r) and Aminoacyl-tRNA synthetases (1u0b)
59	2	2	AG, AU	1jbr:AC:A16G17	A700-U701 of 1m90	Restrictocin (1jbr) and Ribosomal proteins L18e (1m90P)
12	2	3	UA, GA	2gzt:AD:U10A11	U641-A-642 of 1j02	Hut operon regulatory protein (2gzt, 1wpu), Ribosomal protein S8 (2j02:H)
235	2	2	GG	2j01:7A:G116G117	G147-G148 of 1jid	Ribosomal protein L34 (2j01), SRP19 (1jid)
61	1	2	UC, AC	2bh2:AC:U8C9	5′ loop U1940-C1941 stack⁶³, A11-C12 of 1hq1	rRNA methyltransferase (2bh2), Signal sequence binding protein (1hq1)
67	2	2	GU, AG	2bh2:AC:G22U23	hairpin recognition G1954-U1955⁶³, A35-G36 of 2du3	rRNA methyltransferase (2bh2), O-phosphoseryl-tRNA synthetase (2du3)
76	2	2	CG, CA	1yvp:AC:C7G8	3′ CCA of t-RNA	60-kda SS-aARo ribonucleoprotein (1yvp), Aspartyl-tRNA synthetases (1il2)
52	3	3	CG, AA	1r3e:AC:C7G8	part of a UCG flipped out triplet⁶⁷	Pseudouridine synthase II TruB (1r3e,1k8w) and Ribonuclease II (2ix1)