MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1545, See in JSmolClick on the image to toggle views Site type: Pout·Bout Schematic drawing for Pout·Bout List of all 223 Mg2+ binding sites with the site type Pout·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 5 of 9 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4ji7 A2002 Pout·Bout A3517, A3518, A3519, A3520, A3521, A3522 G:A1079 G:A1077 3df1 A2007 Pout·Bout A4008, A4009, A4010, A4011, A4012, A4013 G:A1079 G:A1077 2qal A2007 Pout·Bout A2008, A2009, A2010, A2011, A2012, A2013 G:A1079 G:A1077 3df3 A2049 Pout·Bout A4050, A4051, A4052, A4053, A4054, A4055 A:A172 G:A148 2qan A2049 Pout·Bout A2050, A2051, A2052, A2053, A2054, A2055 A:A172 G:A148 3df3 A2062 Pout·Bout A4063, A4064, A4065, A4066, E4067 C:A1195 A:A1398 3df1 A2077 Pout·Bout A4078, A4079, A4080, A4081, A4082, A4083 A:A1046 G:A1047 2qan N2091 Pout·Bout A2093, A2094, A2096, N2092, N2095 A:A1360 C:A980 2qbb A2107 Pout·Bout A2455, A2456, A2457, A2458, A2459, A2460 G:A1079 G:A1077 2qb9 A2136 Pout·Bout A2466, A2467, A2468, A2469, A2470, A2471 G:A727 G:A727 2qbb A2155 Pout·Bout A2496, A2497, A2498, A2499, A2500 U:A20 G:A21 3df3 A2161 Pout·Bout A4162, A4163, A4164, A4165, A4166, A4167 G:A727 G:A727 2qb9 A2335 Pout·Bout A2630, A2631, A2632, A2633, A2634, A2635 C:A1400 G:A926 3og0 A2910 Pout·Bout A3068, A3069, A3070, A3071, A3072 U:A419 G:A230 3ofd A2911 Pout·Bout A3070, A3071, A3072, A3073, A3074 U:A419 G:A230 3og0 A2913 Pout·Bout A3081, A3082, A3083, A3084, A3085 G:A536 G:A537 2z4l B2938 Pout·Bout B3170, B3171, B3172, B3173, B3174, B3175 G:B649 C:B650 2z4n B2965 Pout·Bout B3304, B3305, B3306, B3307, B3308 C:B2310 G:B2303 3og0 A2965 Pout·Bout A3333, A3334, A3335, A3336, A3337, A3338 G:A2027 G:A2027 3i1t A2967 Pout·Bout A3337, A3338, A3339, A3340, A3341, A3342 G:A2027 G:A2027 3r8s A2973 Pout·Bout A3420, A3421, A3422, A3423, A3424 C:A2310 G:A2304 3og0 A2975 Pout·Bout A3380, A3381, A3382, A3383, A3384 C:A2310 U:A2302 3oas A2976 Pout·Bout A3382, A3383, A3384, A3385, A3386 C:A2310 U:A2302 1vt2 A2977 Pout·Bout A3385, A3386, A3387, A3388, A3389 C:A2310 U:A2302 3i1p A2977 Pout·Bout A3381, A3382, A3383, A3384, A3385 C:A2310 G:A2303

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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