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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 3ccq



3CCQ (2.9Å) -- RIBOSOME : Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation a2488u
List of all 19 Mg2+ binding sites in the PDB structure 3ccq 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ccq 08065 Oph·Pout A:01742(OP2) 03656, 07896, 09266, 09390, 09771 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
3ccq 08014 Oph·2Pout C:01830(OP1) 07817, 07836, 09134, 09137, 09209 U:01831, A:01842 G:01828 G:01832, G:01828
3ccq 08025 Oph·3Pout U:02115(OP1) 03013, 03748, 03812, A9021, A9087 G:02272, C:02273, U:02116 G:02271
3ccq 08045 Oph·3Pout G:02013(OP2) 03789, 07871, 07872, 07873, A9089 G:01884, U:01883, C:02626 U:02012
3ccq 08012 Oph·3Pout G:0456(OP2) 03972, 07455, 07814, 09433, C8557 G:0458, A:0455, U:0457
3ccq 08026 Oph·3Pout G:0956(OP2) 03692, 07858, 07859, 07860, 09383 A:01006, A:0955, A:0957 A:0957, G:0956
3ccq 08008 Oph·4Pout G:028(OP1) 03250, 03669, 07906, 09049, 09653 G:01344, C:01305, U:01304, C:01343
3ccq 08021 Oph·Ob A:01448(OP2) U:01677(O4) 03700, 03721, 03733, S8994 G:01676
3ccq 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03807, 07813, 09057, 09798 A:0455, A:0460, A:0477 A:0455
3ccq 08041 cis-2Oph C:0162(OP1), U:02276(OP1) 07819, 07869, 07870, 09450 U:0163, A:0169
3ccq 08009 cis-2Oph G:0877(OP1), G:02623(OP1) 03663, 03676, 07837, 09029 C:02475 G:0885
3ccq 08023 cis-2Oph U:01748(OP1), U:01749(OP2) 03661, 07815, 07826, 09692 G:02585, G:02584
3ccq 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03643, 07838, 09013, 09032 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccq 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04356, 07806, 07807 U:02535 C:02533, U:0625 U:0626
3ccq 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03637, 07828, 09189 U:02484 A:02532, G:02482
3ccq 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03687, 09847, A8979
3ccq 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03632, 07829, 07830 G:01837 U:01835 A:01839
3ccq 08028 6Bout 03647, 03671, 03693, 03695, 07862, 09298 G:02271, G:02275, U:02116, A:02274, U:02115, U:02276
3ccq 08061 poly-nuclear Mg2+ site A:0167(OP1), C:0168(OP2) A:0165(N7) 03631, 03638, 03650 G:0164, A:0165 G:0164

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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