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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 1yj9



1YJ9 (2.9Å) -- RIBOSOME : Crystal structure of the mutant 50s ribosomal subunit of haloarcula marismortui containing a three residue deletion in l22
List of all 50 Mg2+ binding sites in the PDB structure 1yj9 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1yj9 08110 Nb G:02609(N7) 03115, 03512, 03535, 05424, 05565 G:02609 U:02610, G:02606
1yj9 08011 2Nb G:0824(N7), G:0854(N7) 03776, 04115, 04247, 04355 G:0854, G:0824, U:0823, C:0853
1yj9 08083 Oph·Pout A:01754(OP2) 03522, 03973, 06164, 07627, 07675 C:01753 A:01755, A:01754
1yj9 08084 Oph·Pout A:01742(OP2) 03449, 07628, 09070, 09193, 09569 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yj9 08036 Oph·2Pout G:0956(OP2) 03486, 07591, 07592, 07593, 09187 A:01006, A:0955 A:0957, G:0956
1yj9 08068 Oph·2Pout A:02568(OP2) 03566, 04646, 06032, 07670, 09553 A:02569, G:02567 A:02569, A:02568
1yj9 08020 Oph·2Pout C:01830(OP1) 07551, 07570, 08942, 08945, 09018 U:01831, A:01842 G:01828 G:01828, G:01832
1yj9 08021 Oph·3Pout G:02304(OP2) 03453, 03454, 07554, 07555, 09778 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1yj9 08058 Oph·3Pout G:02013(OP2) 07604, 07605, 09205, A8925, A8927 U:01883, C:02626, G:01884
1yj9 08040 Oph·3Pout U:0392(OP2) 03605, 04468, 07648, 07649, 09514 U:0391, C:0171, U:0172
1yj9 08032 Oph·3Pout U:02115(OP1) 03604, 09804, A8846, A8854, A8924 U:02116, G:02272, C:02273
1yj9 08035 Oph·4Pout G:01484(OP2) 03530, 07589, 07590, 07644 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
1yj9 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03447, 03775, 09215 A:01487 G:01489, G:01490
1yj9 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03493, 03514, 03525, S8545 G:01676
1yj9 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03690, 03830, 03977, M8946 G:0267, U:0268
1yj9 08109 Oph·Nb U:0903(OP1) A:01357(N7) 03743, 05224, 05841, 09329 U:0904 G:0622, A:01356
1yj9 08023 cis-2Oph G:02617(OP2), G:02618(OP2) 03442, 03636, 07575, 07576 G:02616 G:02618
1yj9 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03687, 07559, 08932, 09277 A:02095 A:02096 G:02097
1yj9 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03037, 03428, 07256, 07639 C:0910 G:0911, G:01292
1yj9 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03457, 03470, 07571, 08842 C:02475, A:02624 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>