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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 3ccr



3CCR (3Å) -- RIBOSOME : Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation a2488c. density for anisomycin is visible but not included in the model.
List of all 12 Mg2+ binding sites in the PDB structure 3ccr 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
3ccr 08012 Oph·3Pout G:0456(OP2) 03629, 03951, 07759, 09435, C8661 A:0455, G:0458, U:0457
3ccr 08025 Oph·3Pout U:02115(OP1) 03733, 03798, 04197, 09999, A9110 U:02116, G:02272, C:02273
3ccr 08008 Oph·4Pout G:028(OP1) 03131, 03657, 07849, 09047, 09654 C:01305, U:01304, G:01344, C:01343
3ccr 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03792, 07758, 09055, 09787 A:0455, A:0460, A:0477 A:0455
3ccr 08021 Oph·Ob A:01448(OP2) U:01677(O4) 03708, 03718, 07793, S8972 G:01676
3ccr 08009 cis-2Oph G:0877(OP1), G:02623(OP1) 03651, 03664, 07782, 09028 C:02475, G:02634, A:02624 G:0885
3ccr 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03628, 07783, 09012, 09032 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccr 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04327, 07751, 07752 U:0625 U:0626
3ccr 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03618, 07774, 07775 G:01837 U:01835 A:01839
3ccr 08006 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03637, 07767, 07848 G:02466, C:0920, G:02293
3ccr 08028 Pout·5Bout 03113, 03633, 03659, 03682, 07809, 09297 G:02275 G:02271, A:02274, G:02275, U:02276, U:02115
3ccr 08007 poly-nuclear Mg2+ site G:02611(OP1), A:02612(OP1) 03749, 07434, 07768, 07769 G:02094, G:02093

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>