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 4 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 4duz A1829 4Pout·Bout A2198, A2199, A2200, A2201, A2202, A2203 A:A509, A:A510, G:A506, C:A507 A:A510 4dv1 A1812 4Pout·Bout A2217, A2218, A2219, A2220, A2221 A:A509, A:A510, G:A506, C:A507 A:A510 4dv3 A1837 4Pout·Bout A2201, A2202, A2203, A2204, A2205, A2206 A:A509, A:A510, C:A507, G:A506 A:A510 4dv6 A1804 4Pout·Bout A2155, A2156, A2157, A2158, A2159, A2160 A:A151, G:A168, G:A167, C:A150 G:A168 4dv7 A1829 4Pout·Bout A2115, A2116, A2117, A2118, A2119, A2120 C:A150, A:A151, G:A168, G:A167 G:A168 4gar A3008 4Pout·Bout A3243, A3244, A3245, A3246 A:A471, A:A472, A:A449, A:A453 G:A450 4gar C301 4Pout·Bout A3747, A3748, A3749, C406, C407 G:A1828, U:A1827, A:A1789, C:A1788 G:A1828 4gar A3055 4Pout·Bout A3459, A3460, A3461, A3462, A3463, A3464 A:A1936, A:A1937, C:A1958, G:A1959 G:A1959 4gau A3048 4Pout·Bout A3427, A3428, A3429, A3430, A3431, A3432 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 4gau A3117 4Pout·Bout A3745, A3746, A3747, A3748 C:A192, U:A2243, C:A198, A:A199 A:A195 4ji1 A1797 4Pout·Bout A2473, A2474, A2475, A2476, A2477, A2478 C:A150, G:A168, G:A167, A:A151 G:A168 4ji1 A1730 4Pout·Bout A2070, A2071, A2072, A2073, A2074, A2075 U:A751, G:A752, U:A652, C:A651 G:A752 4ji8 A1951 4Pout·Bout A3211, A3212, A3213, A3214, A3215, A3216 C:A150, G:A167, G:A168, A:A151 G:A168 4nvw A3083 4Pout·Bout A4021, A4022, A4023, A4024 A:A768, U:A804, C:A805, A:A767 A:A768 4nvx A3553 4Pout·Bout A4700, A4701, A4702, A4703, A4704, A4705 A:A2051, A:A2614, C:A2050, G:A2578 A:A2051 4nvz A3449 4Pout·Bout A4471, A4472, A4473, A4474 A:A2008, C:A2563, A:A1716, G:A2009 G:A1976 4nw0 A3083 4Pout·Bout A4021, A4022, A4023, A4024 A:A768, U:A804, C:A805, A:A767 A:A768 4nw1 A3547 4Pout·Bout A4699, A4700, A4701, A4702, A4703, A4704 A:A2051, A:A2614, C:A2050, G:A2578 A:A2051 4peb A3050 4Pout·Bout A3430, A3431, A3432, A3433, A3434, A3435 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 4peb A3043 4Pout·Bout A3398, A3399, A3400, A3401, A3402, A3403 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377 4pec A3043 4Pout·Bout A3390, A3391, A3392, A3393, A3394, A3395 U:A1352, G:A1377, C:A1376, C:A1351 G:A1377 4pec A3050 4Pout·Bout A3422, A3423, A3424, A3425, A3426, A3427 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 4pec A3039 4Pout·Bout A3378, A3379, A3380, A3381 A:A2005, C:A2006, A:A1268, A:A1269 A:A1269 4qcz A3432 4Pout·Bout A4446, A4447, A4448, A4449 A:A2008, C:A2563, A:A1716, G:A2009 G:A1976 4tom A3043 4Pout·Bout A3395, A3396, A3397, A3398, A3399, A3400 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377

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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