MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1yhq:08001, See in JSmolClick on the image to toggle views Site type: fac-3Oph Schematic drawing for fac-3Oph List of all 392 Mg2+ binding sites with the site type fac-3Oph 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 7 of 16 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1yjw 78001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 09077, 09083, 09181 U:02484 G:02482, A:02532 1yjw 78016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 07336, 07578, 07579 1yjw 78003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 09435, A4079, A4080 2avy A1589 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1826, A1827, A1828 G:A1504, U:A1498 2avy A1553 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A1651, A1652, A1653 A:A1196 2aw4 B2989 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B3409, B3410, B3411 U:B762, G:B763 2aw4 B2941 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3189, B3190, B3191 C:B1306 2aw4 B2986 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3400, B3401, B3402 A:B2497, G:B2447 2aw4 B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3427, B3428, B3429 C:B2507 2aw7 A1593 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1852, A1853, A1854 U:A1498, G:A1504 A:A1500 2awb B2996 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3439, B3440, B3441 C:B2507 2awb B2987 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3412, B3413, B3414 U:B2449 G:B2447, A:B2497 2awb B2972 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3345, B3346, C454 2awb B2977 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3366, B3367, B3368 C:B1306 2awb B3008 fac-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3485, B3486, B3487 2i2p A1590 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1835, A1836, A1837 G:A1504, U:A1498 A:A1500 2i2t B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3437, B3438, B3439 C:B2507, G:B2508 2i2t B2909 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3046, B3047, C273 2i2t B2928 fac-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3137, B3138, B3139 2i2t B2941 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3199, B3200, B3201 C:B1306 2i2t B2989 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B3419, B3420, B3421 U:B762, G:B763 2i2t B2986 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3410, B3411, B3412 U:B2449 A:B2497, G:B2447 G:B2447 2i2u A1567 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1714, A1715, A1716 U:A1498, G:A1504 A:A1500 2i2v B2972 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3353, B3354, B3355 2i2v B2987 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3420, B3421, B3422 U:B2449 G:B2447, A:B2497

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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