MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1545, See in JSmolClick on the image to toggle views Site type: Pout·Bout Schematic drawing for Pout·Bout List of all 223 Mg2+ binding sites with the site type Pout·Bout 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 4 of 9 | « 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 3i1z A1 Pout·Bout A1577, A1578, A1579, A1580, A1581, A1582 G:A259 G:A259 3i1z A1549 Pout·Bout A1653, A1654, N121, N123, N124, N125 A:A1360 C:A980 3i21 A1546 Pout·Bout A1647, A1648, A1649, A1650, A1651, N122 A:A1360 C:A980 3i21 A1549 Pout·Bout A1661, A1662, A1663, A1664, A1665, A1666 U:A1076 G:A1077 3i21 A1554 Pout·Bout A1687, A1688, A1689, A1690, A1691, A1692 U:A20 G:A21 3i22 A3001 Pout·Bout A3501, A3502, A3503, A3504, A3505, A3506 C:A2616 G:A2048 3oas A3001 Pout·Bout A3500, A3501, A3502, A3503, A3504, A3505 C:A2616 G:A2048 3oas A2976 Pout·Bout A3382, A3383, A3384, A3385, A3386 C:A2310 U:A2302 3oas A3033 Pout·Bout A3621, A3622, A3623, A3624, 4757, 4760 A:A2741 G:A2742 3ofb A1552 Pout·Bout A1660, A1661, A1662, A1663, A1664, A1665 G:A1079 G:A1077 3ofd A2911 Pout·Bout A3070, A3071, A3072, A3073, A3074 U:A419 G:A230 3ofd A3001 Pout·Bout A3499, A3500, A3501, A3502, A3503, A3504 C:A2616 G:A2049 3ofp A1552 Pout·Bout A1661, A1662, A1663, E159, E160, E161 G:A1079 G:A1077 3ofp A1549 Pout·Bout A1648, A1649, A1650, A1651, N101, N102 A:A1360 C:A980 3ofx A1549 Pout·Bout A1652, A1653, N102, N103, N104, N105 A:A1360 C:A980 3ofy A1555 Pout·Bout A1675, A1676, A1677, A1678, A1679, A1680 G:A266 G:A257 3ofy A1552 Pout·Bout A1661, A1662, A1663, A1664, A1665, A1666 G:A1079 G:A1077 3og0 A2910 Pout·Bout A3068, A3069, A3070, A3071, A3072 U:A419 G:A230 3og0 A2975 Pout·Bout A3380, A3381, A3382, A3383, A3384 C:A2310 U:A2302 3og0 A3032 Pout·Bout A3623, A3624, A3625, A3626, 4757, 4760 A:A2740 G:A2742 3og0 A2965 Pout·Bout A3333, A3334, A3335, A3336, A3337, A3338 G:A2027 G:A2027 3og0 A2913 Pout·Bout A3081, A3082, A3083, A3084, A3085 G:A536 G:A537 3og0 A2989 Pout·Bout A3447, A3448, A3449, A3450, A3451, A3452 A:A933 U:A842 3ora A1555 Pout·Bout A1679, A1680, A1681, A1682, A1683, A1684 G:A266 G:A257 3ora A1557 Pout·Bout A1691, A1692, A1693, A1694, A1695, A1696 U:A20 G:A21

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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