MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3382, See in JSmolClick on the image to toggle views Site type: 4Pout·Bout Schematic drawing for 4Pout·Bout List of all 125 Mg2+ binding sites with the site type 4Pout·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 3 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ofq A2949 4Pout·Bout A3249, A3250, A3251, A3252, A3253, A3254 C:A1351, C:A1376, U:A1352, G:A1377 G:A1377 3ofq A2956 4Pout·Bout A3281, A3282, A3283, A3284, A3285, A3286 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3ofr A2954 4Pout·Bout A3269, A3270, A3271, A3272, A3273, A3274 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3ofz A2945 4Pout·Bout A3230, A3231, A3232, A3233, A3234, A3235 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377 3ofz A2952 4Pout·Bout A3262, A3263, A3264, A3265, A3266, A3267 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3og0 A2947 4Pout·Bout A3246, A3247, A3248, A3249, A3250, A3251 C:A1351, C:A1376, U:A1352, G:A1377 G:A1377 3og0 A2954 4Pout·Bout A3278, A3279, A3280, A3281, A3282, A3283 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3orb A2953 4Pout·Bout A3269, A3270, A3271, A3272, A3273, A3274 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3orb A2946 4Pout·Bout A3237, A3238, A3239, A3240, A3241, A3242 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377 3r8s A2954 4Pout·Bout A3328, A3329, A3330, A3331, A3332, A3333 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3r8t A2946 4Pout·Bout A3269, A3270, A3271, A3272, A3273, A3274 U:A1352, C:A1376, G:A1377, C:A1351 G:A1377 3r8t A2953 4Pout·Bout A3301, A3302, A3303, A3304, A3305, A3306 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3ucz R670 4Pout·Bout R687, R688, R689, R690, R691, R692 U:R53, C:R52, U:R81, C:R44 A:R82 3v23 A3579 4Pout·Bout A4889, A4890, A4891, A4892, A4893 A:A1986, C:A2551, A:A1669, G:A1987 G:A1954 3v28 A1749 4Pout·Bout A2007, A2008, A2009, A2010, A2011 A:A16, U:A13, U:A14, G:A15 U:A14 3v29 A3571 4Pout·Bout A4655, A4656, A4657, A4658, A4659, A4660 G:A1987, A:A1669, A:A1986, C:A2551 G:A1954 3v2d A3223 4Pout·Bout A4312, A4313, A4314, A4315 C:A2745, U:A2746, U:A2754, C:A2755 G:A2747 3v2f A3599 4Pout·Bout A5065, A5066, A5067, A5068, A5069, A5070 G:A1987, A:A1669, A:A1986, C:A2551 G:A1954 4bpe A5002 4Pout·Bout A2164, A2165, A2188, A2241, A2343, A2344 A:A919, G:A920, A:A1005, A:A1743 A:A1003 4bpn A5012 4Pout·Bout A6317, A6319, A6326, A6333, A6340, A6347 A:A969, G:A989, C:A988, C:A968 G:A989 4bpo A5012 4Pout·Bout A2178, A2179, A2180, A2186, A2187, A2341 C:A968, G:A989, A:A969, C:A988 G:A989 4dr6 A1840 4Pout·Bout A2505, A2506, A2507, A2508, A2509, A2510 A:A151, C:A150, G:A168, G:A167 G:A168 4dr6 A1608 4Pout·Bout A2019, A2020, A2021, A2022 U:A751, U:A652, G:A752, C:A651 G:A752 4dr7 A1818 4Pout·Bout A2474, A2475, A2476, A2477, A2478, A2479 C:A150, G:A168, A:A151, G:A167 G:A168 4duy A1793 4Pout·Bout A2143, A2144, A2145, A2146, A2147, A2148 A:A151, G:A167, G:A168, C:A150 G:A168

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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