MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2u:A1552, See in JSmolClick on the image to toggle views Site type: 5Bout Schematic drawing for 5Bout List of all 45 Mg2+ binding sites with the site type 5Bout 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ivk M122 5Bout M138, M139, M140, M141, M142, M143 A:M97, G:M91, G:M92, U:M93, U:M94 3ivk C134 5Bout C183, C184, C185, C186, C187, C188 G:C77, U:C36, G:C37, C:C38, G:C78 3ivk M134 5Bout M182, M183, M184, M185, M186, M187 G:M77, U:M36, G:M37, C:M38, G:M78 2i2u A1552 5Bout A1640, A1641, A1642, A1643, A1644, A1645 U:A593, U:A594, G:A592, G:A645, G:A646 2qbj A1557 5Bout A1671, A1672, A1673, A1674, A1675, A1676 G:A1050, G:A1207, U:A1205, G:A1048, C:A1051 2z4m A1558 5Bout A1671, A1672, A1673, A1674, A1675, A1676 G:A1050, G:A1207, C:A1051, U:A1205, G:A1048 2aw7 A1562 5Bout A1696, A1697, A1698, A1699, A1700, A1701 U:A593, U:A594, G:A645, G:A592, G:A646 1vs7 A1563 5Bout A1695, A1696, A1697, A1698, A1699, A1700 U:A593, U:A594, G:A592, G:A645, G:A646 4tpc A1610 5Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, C:A647, U:A593, G:A592, G:A645 4pe9 A1610 5Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, U:A593, U:A594, U:A644, G:A645 4duz A1770 5Bout A2076, A2077, A2078, A2079, A2080, A2081 G:A664, G:A742, G:A741, G:A666, U:A740 4dr5 A1829 5Bout A2363, A2364, A2365, A2366, A2367, A2368 G:A21, G:A11, U:A12, G:A22, C:A23 4ji7 A1978 5Bout A3371, A3372, A3373, A3374, A3375, A3376 C:A43, G:A44, U:A45, G:A396, C:A395 2qbg B2905 5Bout B3016, B3017, B3018, B3019, B3020, B3021 G:B2238, G:B2242, A:B2241, U:B2074, U:B2243 2qoz B2906 5Bout B3516, B3517, B3518, B3519, B3520, B3521 U:B2074, U:B2243, G:B2242, U:B2075, G:B2238 1vs6 B2906 5Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, U:B2075, G:B2238, G:B2242 2aw4 B2906 5Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, U:B2075, G:B2238, G:B2242 3ofc A2967 5Bout A3339, A3340, A3341, A3342, A3343, A3344 A:A2241, G:A2242, U:A2075, U:A2074, U:A2243 3i22 A2971 5Bout A3361, A3362, A3363, A3364, A3365, A3366 A:A2077, G:A2238, G:A2242, U:A2243, A:A2241 3i1t A2972 5Bout A3362, A3363, A3364, A3365, A3366, A3367 A:A2077, G:A2238, G:A2242, U:A2243, A:A2241 1vt2 A2972 5Bout A3362, A3363, A3364, A3365, A3366, A3367 G:A2238, G:A2242, A:A2241, U:A2243, U:A2074 3r8s A2995 5Bout A3522, A3523, A3524, A3525, A3526, A3527 U:A1411, G:A1410, A:A1591, U:A1409, A:A1590 4too A3001 5Bout A3201, A3202, A3203, A3204, A3205, A3206 U:A521, C:A16, G:A17, U:A18, A:A522 4gau A3001 5Bout A3201, A3202, A3203, A3204, A3205, A3206 G:A17, U:A18, A:A19, U:A521, A:A522 3df4 B3001 5Bout B4002, B4003, B4004, B4005, B4006, B4007 G:B2238, G:B2242, A:B2241, U:B2243, U:B2075

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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