MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs7:A1593, See in JSmolClick on the image to toggle views Site type: 2Pout Schematic drawing for 2Pout List of all 191 Mg2+ binding sites with the site type 2Pout 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 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qbg B2917 2Pout B3077, B3078, B3079, B3080, B3081, B3082 A:B2033, U:B2026 2qbg B2962 2Pout B3294, B3295, B3296, B3297, B3298, B3299 G:B1653, G:B2819 2qbh A1598 2Pout A1865, A1866, A1867, A1868, A1869, A1870 U:A1393, A:A919 2qbi B3004 2Pout B3464, B3465, B3466, B3467, B3468, B3469 G:B205, C:B385 2qbi B2908 2Pout B3033, B3034, B3035, B3036, B3037, B3038 C:B560, A:B1008 2qbj A1591 2Pout A1841, A1842, A1843, A1844, A1845, A1846 A:A553, U:A552 2qbk B2962 2Pout B3289, B3290, B3291, B3292, B3293, B3294 G:B1653, G:B2819 2qbk B2932 2Pout B3152, B3153, B3154, B3155, B3156, B3157 G:B822, C:B965 2qex B8055 2Pout 03584, 06267, 07552, B8853, B8954, B8955 U:02721, C:02720 2qou A1589 2Pout A2122, A2123, A2124, A2125, A2126, L281 C:A25, A:A553 2qow A1571 2Pout A2025, A2026, A2027, A2028, A2029, A2030 U:A552, A:A553 2qox N337 2Pout B3290, B3291, B3292, B3293, N339, N340 U:B2818, A:B1652 2qox B2932 2Pout B3150, B3151, B3152, B3153, B3154, B3155 G:B822, C:B965 2qoy A1589 2Pout A2124, A2125, A2126, A2127, A2128, L1831 A:A553, U:A552 2qoy A1559 2Pout A1977, A1978, A1979, A1980, A1981, A1982 U:A13, U:A14 2qoz B2908 2Pout B3528, B3529, B3530, B3531, B3532, B3533 C:B560, A:B1008 2qp0 A1571 2Pout A2028, A2029, A2030, A2031, A2032, A2033 U:A552, A:A553 2z4k A1590 2Pout A1827, A1828, A1829, A1830, A1831, A1832 C:A25, A:A553 2z4n B2933 2Pout B3152, B3153, B3154, B3155, B3156, B3157 G:B822, C:B965 3cc2 B8055 2Pout 03311, 05993, 07283, B8551, B8663 U:02721, C:02720 3cxc B8055 2Pout 04707, 07321, 08614, B8560, B8677, B8678 U:02721, C:02720 3df1 A2328 2Pout A4329, A4330, A4331, A4332, A4333, A4334 A:A1394, A:A918 3df2 B3096 2Pout B4097, B4098, B4099, B4100, B4101, B4102 C:B965, G:B822 3df3 A2295 2Pout A4296, A4297, A4298, A4299, A4300, A4301 U:A552, A:A553 3df4 B3165 2Pout B4166, B4167, B4168, B4169, B4170, B4171 G:B822, C:B965

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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>