MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 341 Mg2+ binding sites with the site type Pout·3Bout 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 14 | « 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 4tp7 A3104 Pout·3Bout A3668, A3669, A3670, A3671, A3672, A3673 C:A2616 G:A2048, G:A2049, G:A2618 4tpf A3104 Pout·3Bout A3670, A3671, A3672, A3673, A3674, A3675 C:A2616 G:A2048, G:A2049, G:A2618 4tpb A3103 Pout·3Bout A3669, A3670, A3671, A3672, A3673, A3674 C:A2616 G:A2049, C:A2047, G:A2048 4qd0 A3096 Pout·3Bout A4016, A4017, A4018, A4019, A4020 A:A781 G:A799, G:A798, G:A800 4tpb A3094 Pout·3Bout A3626, A3627, A3628, A3629 A:A1439 A:A1551, U:A1440, G:A1441 4tp9 A3094 Pout·3Bout A3627, A3628, A3629, A3630, A3631, A3632 G:A1422 G:A1423, G:A1424, G:A1425 4too A3093 Pout·3Bout A3619, A3620, A3621, A3622, A3623, A3624 A:A1572 G:A1423, G:A1424, G:A1425 4tp5 A3093 Pout·3Bout A3629, A3630, A3631, A3632, A3633, A3634 A:A1572 G:A1423, G:A1424, G:A1425 4tpb A3093 Pout·3Bout A3620, A3621, A3622, A3623, A3624, A3625 A:A1572 G:A1424, C:A1574, G:A1425 4tp3 A3093 Pout·3Bout A3620, A3621, A3622, A3623, A3624, A3625 A:A1572 G:A1424, C:A1574, G:A1425 4peb A3092 Pout·3Bout A3630, A3631, A3632, A3633, A3634, A3635 A:A1572 G:A1423, G:A1424, G:A1425 4qcs A3088 Pout·3Bout A4036, A4037, A4038, A4039, A4040 A:A781 G:A799, G:A800, G:A798 4qco A3087 Pout·3Bout A3219, A3220, A3221, A3222, A3223 A:A781 G:A800, G:A798, G:A799 4tp9 A3086 Pout·3Bout A3589, A3590, A3591, A3592, A3593, A3594 G:A976 G:A978, A:A979, G:A977 4tpf A3086 Pout·3Bout A3585, A3586, A3587, A3588, A3589, A3590 G:A976 G:A976, G:A977, G:A978 4tox A3085 Pout·3Bout A3580, A3581, A3582, A3583, A3584, A3585 A:A933 U:A842, G:A843, G:A841 4tp1 A3085 Pout·3Bout A3584, A3585, A3586, A3587, A3588, A3589 A:A933 G:A841, U:A842, A:A936 4tp5 A3084 Pout·3Bout A3585, A3586, A3587, A3588, A3589, A3590 A:A933 G:A841, U:A842, A:A936 4gau A3080 Pout·3Bout A3582, A3583, A3584, A3585, A3586, A3587 A:A933 G:A841, U:A842, G:A843 2qao B3074 Pout·3Bout B3679, B3680, B3681, B3682, B3683, B3684 A:B2033 G:B2027, U:B2028, G:B2029 2qbc B3074 Pout·3Bout B3680, B3681, B3682, B3683, B3684, B3685 A:B2033 G:B2027, U:B2028, G:B2029 4tpf A3071 Pout·3Bout A3517, A3518, A3519, A3520, A3521 C:A2310 G:A2304, G:A2303, U:A2302 4tox A3071 Pout·3Bout A3517, A3518, A3519, A3520, A3521 C:A2310 G:A2304, U:A2302, G:A2303 4too A3070 Pout·3Bout A3514, A3515, A3516, A3517, A3518 C:A2310 G:A2304, U:A2302, G:A2303 4tpb A3070 Pout·3Bout A3516, A3517, A3518, A3519, A3520 C:A2310 G:A2304, U:A2302, 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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