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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 3cxc



3CXC (3Å) -- RIBOSOME : The structure of an enhanced oxazolidinone inhibitor bound to the 50s ribosomal subunit of h. marismortui
List of all 64 Mg2+ binding sites in the PDB structure 3cxc 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 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3cxc 08112 Nb A:0187(N1) 03120, 03319, 03549, 04675, 04718 C:0155, U:0207 G:0206 C:0188, C:0438
3cxc 08011 2Nb G:0824(N7), G:0854(N7) 04906, 05231, 05359, 05460 G:0854, U:0823, G:0824, C:0853
3cxc 08084 Oph·Pout A:01742(OP2) 03236, 03361, 03727, 04583, 08740 G:02033 G:01743, G:01744, G:01745, G:02033, A:01742
3cxc 08083 Oph·2Pout A:01754(OP2) 04655, 05095, 07263, 08739, 08791 C:01753, A:01755 A:01755, A:01754
3cxc 08068 Oph·2Pout A:02568(OP2) 04701, 05752, 07134, 08785, E920 A:02569, G:02567 A:02569, A:02568
3cxc 08020 Oph·2Pout C:01830(OP1) 03114, 03117, 03186, 08662, 08681 A:01842, U:01831 G:01828 G:01832, G:01828
3cxc 08019 Oph·2Pout A:02011(OP2) 05094, 08132, 08678, 08679, 08680 A:01941, G:01891 U:01890 G:01891, C:01892
3cxc 08017 Oph·3Pout G:0456(OP2) 03401, 04891, 08659, C8362, C8475 U:0457, G:0458, A:0455
3cxc 08040 Oph·3Pout U:0392(OP2) 03670, 04739, 05575, 08760, 08761 U:0172, U:0391, C:0171
3cxc 08037 Oph·3Pout A:02553(OP2) 03076, 04102, 04174, 04597, 08758 U:02554, C:02575, A:02576 C:02552 A:02576
3cxc 08036 Oph·3Pout G:0956(OP2) 03355, 04618, 08704, 08705, 08706 A:0957, A:01006, A:0955 A:0957, G:0956
3cxc 08032 Oph·3Pout U:02115(OP1) 03960, 04738, 05133, A8553, A8641 C:02273, U:02116, G:02272
3cxc 08021 Oph·3Pout G:02304(OP2) 03934, 04587, 04588, 08665, 08666 A:02301, A:02303, A:02305 U:02306, A:02305, G:02304
3cxc 08035 Oph·4Pout G:01484(OP2) 04664, 08702, 08703, 08756, 08757 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
3cxc 08012 Oph·4Pout G:028(OP1) 03037, 03617, 04190, 04596, 08750 U:01304, C:01305, C:01343, G:01344
3cxc 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04822, 04959, 05099, 08754 G:0267, U:0268
3cxc 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03382, 04581, 04905, 07083 G:01490, A:01487, U:01488 G:01489, G:01490
3cxc 08028 Oph·Ob A:01448(OP2) U:01677(O4) 04626, 04648, 04659, R8352 G:01676
3cxc 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03045, 03753, 04732, 08658 A:0460, A:0477, A:0455 A:0455
3cxc 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03018, 04591, 04603, A8640 A:02624, C:02475 G:0885

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>