MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3i20:A2945, See in JSmolClick on the image to toggle views Site type: Oph·Pout Schematic drawing for Oph·Pout List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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 9 of 53 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qan A2239 Oph·Pout A:A1433(OP2) A2240, A2241, A2242, A2243, A2244 A:A1434 A:A1434, G:A1435 2qao B3245 Oph·Pout U:B120(OP2) B3820, B3821, B3822, B3823, B3824 G:B121 G:B121, G:B122, G:B123 2qao B3229 Oph·Pout G:B536(OP2) B3807, B3808, B3809, B3810, B3811 G:B535 G:B536, G:B537 2qao B3159 Oph·Pout A:B945(OP1) B3749, B3750, B3751, B3752, B3753 G:B831 G:B831, U:B832 2qao B3251 Oph·Pout A:B1678(OP2) B3825, B3826, B3827, B3828, B3829 A:B1679 A:B1678, A:B1679 2qao B3127 Oph·Pout A:B1156(OP2) B3722, B3723, B3724, B3725, B3726 A:B1155 G:B1157, C:B998 2qao B3058 Oph·Pout U:B567(OP1) B3666, B3667, B3668, B3669, B3670 G:B809 U:B810 2qao B3474 Oph·Pout G:B2588(OP2) B4007, B4008, B4009, C477, C479 A:B2589 A:B2589 2qao B3052 Oph·Pout A:B1664(OP2) B3661, B3662, B3663, B3664, B3665 G:B1992 G:B1667, A:B1665, G:B1992, G:B1666 2qb9 A2242 Oph·Pout A:A608(OP2) A2553, A2554, A2555, A2556, A2557 A:A609 A:A630, A:A609, U:A610 2qb9 A2322 Oph·Pout G:A111(OP2) A2619, A2620, A2621, A2622, A2623 C:A110 G:A112, G:A111 2qb9 A2316 Oph·Pout C:A352(OP2) A2614, A2615, A2616, A2617, A2618 G:A354 G:A331, C:A352, C:A330 C:A330, A:A59 2qb9 A2170 Oph·Pout A:A572(OP1) A2495, A2496, A2497, A2498, A2499 A:A573 2qb9 A2025 Oph·Pout C:A934(OP1) A2379, A2380, A2381, A2382, A2383 U:A1345 2qba B3353 Oph·Pout A:B1156(OP2) B3896, B3897, B3898, B3899, B3900 A:B1155 G:B1157, G:B997, C:B998 2qba B3590 Oph·Pout A:B1676(OP2) B4086, B4087, B4088, B4089, B4090 C:B1675 A:B1677, A:B1676 2qba B3151 Oph·Pout A:B945(OP1) B3734, B3735, B3736, B3737, B3738 G:B831 A:B829 G:B831 2qba B3276 Oph·Pout U:B567(OP1) B3837, B3838, B3839, B3840, B3841 G:B809 U:B810 2qba B3444 Oph·Pout A:B2270(OP2) B3971, B3972, B3973, B3974, B3975 A:B2267 A:B2268, A:B2266 G:B2271 2qba B3376 Oph·Pout A:B1664(OP2) B3915, B3916, B3917, B3918, B3919 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666 2qbb A2334 Oph·Pout C:A352(OP2) A2643, A2644, A2645, A2646, A2647 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59 2qbb A2261 Oph·Pout A:A608(OP2) A2583, A2584, A2585, A2586, A2587 A:A607 A:A630, A:A609, C:A631, U:A610 2qbb A2239 Oph·Pout A:A1433(OP2) A2566, A2567, A2568, A2569, A2570 A:A1434 G:A1432 A:A1434, G:A1435 2qbb A2128 Oph·Pout A:A937(OP2) A2473, A2474, A2475, A2476, A2477 A:A938 A:A937, A:A938, G:A939 2qbb A2340 Oph·Pout G:A111(OP2) A2648, A2649, A2650, A2651, A2652 C:A110 G:A112

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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