MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 4tp7 4TP7 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 50s subunit of the second 70s ribosome with virginiamycin m1 bound. List of all 126 Mg2+ binding sites in the PDB structure 4tp7 in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 5 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4tp7 A3022 4Bout A3296, A3297, A3298, A3299, A3300, A3301 G:A757, A:A756, A:A739, U:A755 4tp7 A3096 4Bout A3630, A3631, A3632, A3633, A3634, A3635 G:A1464, G:A1445, C:A1446, G:A1465 4tp7 A3067 7Bout A3495, A3496, A3497, A3498, A3499, A3500 A:A2077, G:A2238, G:A2242, U:A2074, U:A2075, U:A2243, A:A2241 4tp7 A3031 Pout A3332, A3333, A3334, A3335, A3336, A3337 C:A965 4tp7 A3071 Pout·2Bout A3514, A3515, A3516, A3517, A3518 C:A2310 G:A2304, G:A2303 4tp7 2101 Pout·2Bout A3713, A3714, A3715, A3716, A3717, 2201 U:A686 G:A770, G:A771 4tp7 A3062 Pout·2Bout A3472, A3473, A3474, A3475 A:A2033 U:A2028, G:A2029 4tp7 A3136 Pout·3Bout A3794, A3795, A3796, A3797, A3798, N201 G:A2004 G:A1651, G:A1649, A:A1650 4tp7 A3019 Pout·3Bout A3284, A3285, A3286, A3287, A3288, E306 A:A616 G:A617, G:A618, G:A619 4tp7 A3104 Pout·3Bout A3668, A3669, A3670, A3671, A3672, A3673 C:A2616 G:A2048, G:A2049, G:A2618 4tp7 A3094 Pout·4Bout A3620, A3621, A3622, A3623, A3624, A3625 A:A1572 G:A1423, G:A1424, C:A1574, G:A1425 4tp7 A3085 Pout·4Bout A3576, A3577, A3578, A3579, A3580, A3581 A:A933 U:A842, G:A843, U:A934, G:A841 4tp7 A3020 2Pout A3289, A3290, A3291, L202 A:A621, G:A622 4tp7 A3134 2Pout·Bout A3786, A3787, A3788, A3789, A3790, 4201 A:A2740, A:A2741 G:A2742 4tp7 A3016 2Pout·Rout·Bout A3269, A3270, A3271, A3272, E303, E304 U:A2016, G:A1256 U:A1255 U:A1255 4tp7 A3083 2Pout·2Bout A3566, A3567, A3568, A3569, A3570, A3571 A:A574, C:A2055 G:A2035, U:A2034 4tp7 A3125 2Pout·2Bout A3750, A3751, A3752, A3753 C:A787, U:A790 U:A1781, A:A1780 4tp7 A3086 2Pout·2Bout A3582, A3583, A3584, A3585, A3586, A3587 G:A977, G:A976 G:A977, G:A978 4tp7 A3120 2Pout·2Bout A3730, A3731, A3732, A3733, A3734, A3735 A:A1000, A:A1001 G:A1003, G:A1002 4tp7 A3028 2Pout·2Rout·Bout A3318, A3319, A3320, A3321, A3322 A:A204, A:A800 G:A799, A:A203 A:A191

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>