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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qam:B3090, See in JSmolMgRNA representative site for type OP-2PO Click on the image to toggle views


Site type: Oph·2Pout

Schematic drawing for
Oph·2Pout
MgRNA type OP-2PO
List of all 1607 Mg2+ binding sites with the site type Oph·2Pout 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"
Page 4 of 65 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1s72 08036 Oph·2Pout G:0956(OP2) 03192, 07313, 07314, 07315, 08886 A:01006, A:0955 A:0957, G:0956
1s72 08068 Oph·2Pout A:02568(OP2) 03274, 04347, 05748, 07396, 09257 A:02569, G:02567 A:02569, A:02568
1s72 08045 Oph·2Pout G:01979(OP2) 07321, 07374, 07375, 07376 G:01998, C:01999
1s72 08020 Oph·2Pout C:01830(OP1) 07271, 07290, 08641, 08644, 08714 U:01831, A:01842 G:01828 G:01828, G:01832
1s72 08083 Oph·2Pout A:01754(OP2) 03229, 03676, 05881, 07349, 07403 C:01753, A:01755 A:01755, A:01754
1vq4 08020 Oph·2Pout C:01830(OP1) 07935, 07954, 09440, 09443, 09516 U:01831, A:01842 G:01828 G:01828, G:01832
1vq4 08019 Oph·2Pout A:02011(OP2) 04461, 07442, 07951, 07952, 07953 A:01941, G:01891 U:01890 G:01891, C:01892
1vq4 08083 Oph·2Pout A:01754(OP2) 04011, 04462, 06613, 08120, 08170 C:01753, A:01755 A:01755, A:01754
1vq5 08083 Oph·2Pout A:01754(OP2) 04021, 04465, 06622, 08164, 08215 C:01753, A:01755 A:01755, A:01754
1vq5 08051 Oph·2Pout G:0641(OP2) 04418, 08137, 08138 A:01355, G:0640 G:0642, A:01355
1vq5 08068 Oph·2Pout A:02568(OP2) 04066, 05128, 06501, 08209, E920 A:02569, G:02567 A:02569, A:02568
1vq5 08045 Oph·2Pout G:01979(OP2) 08136, 08189, 08190, 08191 G:01998, C:01999 C:01826
1vq5 08020 Oph·2Pout C:01830(OP1) 07980, 07999, 09445, 09448, 09520 U:01831, A:01842 G:01828 G:01828, A:01845, G:01832
1vq6 08068 Oph·2Pout A:02568(OP2) 04060, 05109, 06467, 08171, E920 A:02569, G:02567 A:02569, A:02568
1vq6 08040 Oph·2Pout U:0392(OP2) 03010, 04096, 04934, 08150, 08151 U:0172, C:0171
1vq6 08020 Oph·2Pout C:01830(OP1) 07944, 07963, 09446, 09449, 09522 U:01831, A:01842 G:01828 G:01828, G:01832
1vq7 08068 Oph·2Pout A:02568(OP2) 04076, 05138, 06496, 08205, E920 A:02569, G:02567 A:02569, A:02568
1vq7 08019 Oph·2Pout A:02011(OP2) 04477, 07474, 07991, 07992, 07993 A:01941, G:01891 U:01890 G:01891, C:01892
1vq7 08083 Oph·2Pout A:01754(OP2) 04031, 04478, 06621, 08159, 08210 C:01753, A:01755 A:01755, A:01754
1vq7 08039 Oph·2Pout U:0115(OP2) 03231, 04289, 05407, 08129, 08130 G:0112, G:0116 A:0114 G:0118, A:0119, G:0116
1vq7 08020 Oph·2Pout C:01830(OP1) 07975, 07994, 09448, 09451, 09525 U:01831, A:01842 G:01828 G:01828, G:01832
1vq8 08020 Oph·2Pout C:01830(OP1) 08293, 08312, 09747, 09750, 09821 U:01831, A:01842 G:01828 G:01828, G:01832
1vq8 08032 Oph·2Pout U:02115(OP1) 03600, 04774, A9540, A9614 G:02272, C:02273
1vq8 08019 Oph·2Pout A:02011(OP2) 04737, 07715, 08309, 08310, 08311 A:01941, G:01891 U:01890 G:01891, C:01892
1vq9 08032 Oph·2Pout U:02115(OP1) 03575, 04750, A9586, A9666 G:02272, C:02273 G:02271

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>