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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 3cc2



3CC2 (2.4Å) -- RIBOSOME : The refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution with rrna sequence for the 23s rrna and genome-derived sequences for r-proteins
List of all 67 Mg2+ binding sites in the PDB structure 3cc2 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
3cc2 08110 Nb G:02609(N7) 03250, 03274, 05175, 05321, 09844 G:02609 G:02606, U:02610
3cc2 08011 2Nb G:0824(N7), G:0854(N7) 03514, 03852, 03986, 04093 G:0854, G:0824, U:0823, C:0853
3cc2 08084 Oph·Pout A:01742(OP2) 03188, 07408, 08778, 08906, 09290 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
3cc2 08039 Oph·Pout U:0115(OP2) 03520, 04667, 07376, 07377, 09453 G:0112 A:0114 A:0119, G:0118, A:0117
3cc2 08068 Oph·2Pout A:02568(OP2) 03305, 04386, 05794, 07454, 09272 A:02569, G:02567 A:02569, A:02568
3cc2 08019 Oph·2Pout A:02011(OP2) 03710, 06808, 07345, 07346, 07347 A:01941, G:01891 U:01890 G:01891, C:01892
3cc2 08020 Oph·2Pout C:01830(OP1) 07329, 07348, 08645, 08648, 08721 U:01831, A:01842 G:01828 G:01828, G:01832
3cc2 08083 Oph·2Pout A:01754(OP2) 03260, 03711, 05928, 07407, 07459 C:01753, A:01755 A:01755, A:01754
3cc2 08037 Oph·3Pout A:02553(OP2) 03202, 07427, 08600, 09681, 09755 A:02576, U:02554, C:02575 C:02552 A:02576
3cc2 08040 Oph·3Pout U:0392(OP2) 03343, 04208, 07429, 07430, 09228 U:0391, C:0171, U:0172
3cc2 08017 Oph·3Pout G:0456(OP2) 03499, 06965, 07326, 08948, C8356 G:0458, A:0455, U:0457
3cc2 08036 Oph·3Pout G:0956(OP2) 03223, 07371, 07372, 07373, 08899 A:01006, A:0955, A:0957 A:0957, G:0956
3cc2 08032 Oph·3Pout U:02115(OP1) 03342, 03749, 09533, A8546, A8622 U:02116, G:02272, C:02273
3cc2 08072 Oph·3Pout U:0954(OP1) 03552, 06989, 07397, 07455, 09777 G:02299, A:02301, C:02298
3cc2 08021 Oph·3Pout G:02304(OP2) 03191, 03192, 07332, 07333, 09507 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
3cc2 08035 Oph·4Pout G:01484(OP2) 03269, 07369, 07370, 07425, 07426 C:01456, C:01483, A:01485, C:01455 G:01484, U:01457
3cc2 08012 Oph·4Pout G:028(OP1) 03201, 07418, 08560, 09173, 09772 C:01305, U:01304, C:01343, G:01344
3cc2 08060 Oph·5Pout G:0175(OP2) 07386, 07387, 07388, 08694 C:0173, G:0225, U:0172, G:0393, U:0392
3cc2 08091 Oph·5Pout G:0918(OP1) 06058, 07412, 08614, 09082, 09869 C:02294, C:02391, A:02465, U:0919, G:02293 A:02465
3cc2 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03427, 03571, 03715, 07423 G:0267, U:0268

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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