MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 341 Mg2+ binding sites with the site type Pout·3Bout in RNA crystal structures in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID" Page 1 of 14 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1egk C9 Pout·3Bout B64, C64, C65, C67, C68, D63 G:C103 DG:B36, DA:B45, DG:D132 1hr2 A16 Pout·3Bout A353, A354, A355, A356, A357, A358 A:A114 G:A116, U:A205, A:A115 1egk A25 Pout·3Bout A46, A47, A48, B65, B66, D70 G:A3 DG:B32, DG:D136, DA:D135 4a1a 079 Pout·3Bout 05603, 05604, 05605, 05606, 05607, 05608 A:23 A:24, A:25, A:26 4oji A101 Pout·3Bout A245, A246, A247, A248, A249, A250 A:A29 G:A22, G:A23, U:A24 3ivk M132 Pout·3Bout M176, M177, M178, M179, M180, M181 A:M-4 A:M-4, G:M-3, U:M-2 4a1e 0204 Pout·3Bout 06803, 06804, 06805, 06806, 06807, 06808 A:374 U:376, A:3101, A:3100 4a17 0204 Pout·3Bout 07059, 07060, 07061, 07062, 07063, 07064 A:374 U:376, A:3101, A:3100 3v27 B220 Pout·3Bout A4908, B339, B340, B341, B342, B343 C:A951 G:B85, G:B86, C:B92 2z75 B304 Pout·3Bout B411, B492, B493, B494, B544 A:B129 U:B100, G:B101, G:B102 4a1a 0345 Pout·3Bout 07955, 07956, 07957, 07958, 07959, 07960 A:289 U:270, G:271, G:290 2gcs B505 Pout·3Bout B211, B300, B330, B331, B332, B333 A:B129 U:B100, G:B102, G:B101 2h0x B505 Pout·3Bout B211, B300, B330, B331, B332, B333 A:B129 U:B100, G:B102, G:B101 1ffy T1202 Pout·3Bout T1298, T1299, T1300, T1301, T1302, T1303 A:T58 G:T53, U:T54, U:T55 1qu2 T1202 Pout·3Bout T1298, T1299, T1300, T1301, T1302, T1303 A:T58 G:T53, U:T54, U:T55 3i1s A1540 Pout·3Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A645 G:A645, G:A592, U:A593 3ofp A1543 Pout·3Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A645 G:A592, G:A646, G:A645 3ora A1543 Pout·3Bout A1621, A1622, A1623, A1624, A1625, A1626 G:A645 G:A646, G:A645, G:A592 3or9 A1544 Pout·3Bout A1627, A1628, A1629, A1630, A1631, A1632 G:A803 G:A771, U:A772, G:A773 3oaq A1544 Pout·3Bout A1627, A1628, A1629, A1630, A1631, A1632 G:A803 G:A771, U:A772, G:A773 2qou A1545 Pout·3Bout A1908, A1909, A1910, A1911, A1912, A1913 G:A803 U:A772, G:A773, G:A771 2i2u A1546 Pout·3Bout A1611, A1612, A1613, A1614, A1615, A1616 G:A803 U:A772, G:A773, G:A771 3i1o A1546 Pout·3Bout A1647, A1648, A1649, A1650, A1651, N122 A:A1360 C:A980, G:A1361, A:A1360 3or9 A1549 Pout·3Bout A1653, A1654, N101, N102, N103, N104 A:A1360 G:A1361, C:A980, A:A1360 3ora A1549 Pout·3Bout A1652, A1653, A1654, A1655, N101, N102 A:A1360 C:A980, G:A1361, A:A1360

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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