MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2qov:B2933, See in JSmolMgRNA representative site for type OP-3PO         Click on the image to toggle views

Site type: Oph·3Pout

Schematic drawing for

MgRNA type OP-3PO
List of all 867 Mg2+ binding sites with the site type Oph·3Pout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" 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
1hr2 B8 Oph·3Pout A:B171(OP2) B336, B337, B338, B339, B340 C:B170, C:B165, U:B168 U:B167 A:B171, U:B167
1hr2 A7 Oph·3Pout A:A171(OP2) A332, A333, A334, A335, A336 C:A165, C:A170, U:A168 U:A167 A:A171, U:A167
1jj2 08072 Oph·3Pout U:0954(OP1) 03524, 06966, 07384, 07442, 09756 G:02299, A:02301, C:02298
1jj2 08037 Oph·3Pout A:02553(OP2) 03175, 07413, 08598, 09659, 09734 A:02576, U:02554, C:02575 C:02552 A:02576
1jj2 08021 Oph·3Pout G:02304(OP2) 03164, 03165, 07319, 07320, 09489 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
1jj2 08017 Oph·3Pout G:0456(OP2) 03471, 07313, 08933, C8358, C8466 G:0458, A:0455, U:0457
1jj2 08032 Oph·3Pout U:02115(OP1) 03315, 03717, 09515, A8551, A8631 U:02116, G:02272, C:02273 G:02271
1jj2 08040 Oph·3Pout U:0392(OP2) 03316, 04178, 07415, 07416, 09216 U:0391, C:0171, U:0172
1k73 A8040 Oph·3Pout U:A392(OP2) A3783, A4640, A7879, A7880, A9691 U:A391, C:A171, U:A172
1k73 A8021 Oph·3Pout G:A2304(OP2) A3633, A3634, A7783, A7784, A9963 A:A2301, A:A2303, A:A2305 A:A2305, G:A2304, U:A2306
1k73 A8035 Oph·3Pout G:A1484(OP2) A3711, A7820, A7821, A7875, A7876 C:A1456, A:A1485, C:A1455 G:A1484, U:A1457
1k73 A8032 Oph·3Pout U:A2115(OP1) A3782, A4186, A9990, C8550, C8632 U:A2116, G:A2272, C:A2273
1k73 A8037 Oph·3Pout A:A2553(OP2) A3134, A3209, A3643, A7877, A9077 C:A2575, A:A2576, U:A2554 C:A2552 A:A2576
1k73 A8072 Oph·3Pout U:A954(OP1) A3231, A3993, A7431, A7848, A7906 C:A2298, G:A2299, A:A2301
1k8a A8017 Oph·3Pout G:A456(OP2) A3212, A3532, A7315, A9003, E8471 A:A455, G:A458, U:A457
1k8a A8032 Oph·3Pout U:A2115(OP1) A3312, A3377, A3777, A9576, C8644 U:A2116, G:A2272, C:A2273
1k8a A8035 Oph·3Pout G:A1484(OP2) A3303, A7357, A7358, A7413, A7414 C:A1456, A:A1485, C:A1455
1k8a A8037 Oph·3Pout A:A2553(OP2) A3238, A7415, A8679, A9718, A9797 A:A2576, U:A2554, C:A2575 C:A2552 A:A2576
1k9m A8035 Oph·3Pout G:A1484(OP2) A3706, A7818, A7819, A7873, A7874 C:A1456, A:A1485, C:A1455 G:A1484, U:A1457
1k9m A8037 Oph·3Pout A:A2553(OP2) A3124, A3203, A3639, A7875, A9081 C:A2575, A:A2576, U:A2554 C:A2552 A:A2576
1k9m A8021 Oph·3Pout G:A2304(OP2) A3629, A3630, A7780, A7781, A9951 A:A2301, A:A2303, A:A2305 A:A2305, G:A2304, U:A2306
1k9m A8032 Oph·3Pout U:A2115(OP1) A3716, A3780, A4182, A9979, C8631 U:A2116, G:A2272, C:A2273
1k9m A8040 Oph·3Pout U:A392(OP2) A3781, A4640, A7877, A7878, A9682 U:A391, C:A171, U:A172
1kc8 A8021 Oph·3Pout G:A2304(OP2) A3643, A3644, A7769, A7770, A9959 A:A2301, A:A2305, A:A2303 A:A2305, G:A2304, U:A2306
1kc8 A8058 Oph·3Pout G:A2013(OP2) A3768, A7823, A7824, C8633, C8635 G:A1884, U:A1883, C:A2626

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>