MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4k:A1546, See in JSmolClick on the image to toggle views Site type: Pout·2Bout Schematic drawing for Pout·2Bout List of all 343 Mg2+ binding sites with the site type Pout·2Bout 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 8 of 14 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v29 A3463 Pout·2Bout A4266, A4267, A4268, A4269, A4270 G:A520 G:A521, G:A520 3v2c A1653 Pout·2Bout A1963, A1964, A1965, A1966 U:A871 G:A853, G:A854 3v2c A1717 Pout·2Bout A2118, A2119, A2120, A2121 G:A803 G:A774, G:A773 3v2c A1655 Pout·2Bout A1971, A1972, A1973, A1974, A1975 U:A793 G:A785, G:A786 3v2d A3435 Pout·2Bout A4953, A4954, A4955, A4956 C:A1607 G:A1624, G:A1623 3v2d A3321 Pout·2Bout A4591, A4592, A4593, A4594, A4595 G:A1624 A:A1634, G:A1626 3v2d A3668 Pout·2Bout A5569, A5570, A5571, A5572, A5573 A:A2860 G:A2861, G:A2862 3v2d A3629 Pout·2Bout A5450, A5451, A5452, A5453, A5454, A5455 A:A2352 G:A2353, G:A2354 3v2e A1796 Pout·2Bout A2281, A2282, A2283, A2284 A:A781 G:A800, G:A799 3v2e A1756 Pout·2Bout A2180, A2181, A2182, A2183 G:A610 G:A627, G:A628 3v2f A3236 Pout·2Bout A4052, A4053, A4054, A4055 C:A1607 G:A1622, G:A1623 4a17 0324 Pout·2Bout 08355, 08356, 08357, 08358, 08359, 08360 A:316 A:316, A:317 4a17 01 Pout·2Bout 05011, 05012, 05013, 05014, 05015, 05016 U:2148 G:2147, G:2149 4a17 0345 Pout·2Bout 08643, 08644, 08645, 08646, 08647, 08648 A:269 U:270, G:290 4a1c 0345 Pout·2Bout 07411, 07412, 07413, 07414, 07415, 07416 A:289 G:271, G:290 4bpe A5017 Pout·2Bout A2008, A2009, A2130, A2131, A2267, A2349 C:A18 U:A602, A:A600 4bpe A5010 Pout·2Bout A2171, A2172, A2173, A2184, A2185, A2254 G:A992 G:A963, G:A962 4bpe A5041 Pout·2Bout A2198, A2199, A2200, A2205, A2306, A2342 A:A1063 G:A1051, U:A1052 4bpe A5071 Pout·2Bout A2381, A2382, A2408, A2411, A2456, A2457 C:A1418 C:A1185, U:A1420 4bpe A5022 Pout·2Bout A2088, A2089, A2090, A2123, A2271, A2272 G:A589 A:A463, G:A464 4bpn A5022 Pout·2Bout A6414, A6416, A6417, A6418, A6419, A6420 G:A589 A:A463, G:A464 4bpn A5017 Pout·2Bout A6384, A6385, A6386, A6387, A6388, A6389 C:A18 A:A600, U:A602 4bpn A5078 Pout·2Bout A6613, A6614, A6615, A6616, A6617, A6618 U:A1277 G:A1296, A:A1297 4bpn A5041 Pout·2Bout A6096, A6097, A6098, A6099, A6100, A6101 A:A1063 G:A1051, U:A1052 4bpn A5010 Pout·2Bout A6228, A6240, A6248, A6255, A6261, A6269 G:A992 G:A962, G:A963

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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