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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 2qoz



2QOZ (3.5Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin and neomycin. this file contains the 50s subunit of the first 70s ribosome, with neomycin bound. the entire crystal structure contains two 70s ribosomes.
List of all 101 Mg2+ binding sites in the PDB structure 2qoz 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 1 of 6 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qoz B2936 Ob U:B746(O4) B3660, B3661, B3662, B3663, D3170 U:B744, C:B2610, C:B2611, U:B2580
2qoz B2939 Ob C:B2499(O2) B3674, B3675, B3676, B3677, B3678 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qoz B2932 2Nb G:B1358(N7), G:B1371(N7) B3642, B3643, B3644, B3645 G:B1358, G:B1371, C:B1357, C:B1370
2qoz B2959 2Nb G:B733(N7), A:B761(N7) B3766, B3767, B3768, B3769 A:B761, G:B733, G:B760, C:B732
2qoz B2934 Oph U:B419(OP1) B3649, B3650, B3651, B3652, B3653 C:B418 G:B230
2qoz B2972 Oph A:B1678(OP2) B3826, B3827, B3828, B3829, B3830 A:B1679
2qoz B2962 Oph A:B800(OP1) B3780, B3781, B3782, B3783, B3784 G:B799 C:B192, A:B800
2qoz B2930 Oph A:B945(OP1) B3631, B3632, B3633, B3634, B3635 G:B831
2qoz B2948 Oph·Pout U:B120(OP2) B3712, B3713, B3714, B3715, B3716 G:B121 G:B122, G:B123, G:B121
2qoz B3010 Oph·Pout A:B1676(OP2) B3982, B3983, B3984, B3985, B3986 C:B1675 A:B1677, A:B1676
2qoz B2969 Oph·Pout A:B1664(OP2) B3811, B3812, B3813, B3814, B3815 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2qoz B2965 Oph·Pout A:B1156(OP2) B3792, B3793, B3794, B3795, B3796 A:B1155 U:B999, G:B1157, G:B997
2qoz B2951 Oph·Pout G:B536(OP2) B3726, B3727, B3728, B3729, B3730 G:B535 G:B536, G:B537
2qoz B2913 Oph·2Pout G:B297(OP2) B3549, B3550, B3551, B3552, B3553 U:B296, G:B338 G:B298, G:B297
2qoz B2911 Oph·2Pout U:B1647(OP2) B3539, B3540, B3541, B3542, B3543 U:B1325, A:B1272 C:B1646, A:B1616 A:B1616
2qoz B2942 Oph·2Pout G:B1455(OP2) B3686, B3687, B3688, B3689, B3690 A:B1453, C:B1454 C:B1454 G:B1456, U:B1457
2qoz B2929 Oph·2Pout U:B1313(OP1) B3626, B3627, B3628, B3629, B3630 G:B1333, G:B1334
2qoz B2927 Oph·2Pout A:B1970(OP2) B3618, B3619, B3620, B3621, B3622 G:B1835, A:B1900 U:B1834 G:B1835
2qoz B2925 Oph·2Pout G:B1187(OP2) B3609, B3610, B3611, B3612, B3613 C:B816, C:B817 G:B1185 G:B818, G:B1187
2qoz B2914 Oph·2Pout C:B1153(OP2) B3554, B3555, B3556, B3557 U:B999, C:B998 G:B1154

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/)
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