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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"
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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
1yi2 08052 Oph·2Pout U:01125(OP1) 03621, 07849, 98590, 98616 C:01126, G:992 C:01129, G:990
1yi2 08019 Oph·2Pout A:02011(OP2) 04146, 07211, 07742, 07743, 07744 A:01941, G:01891 U:01890 G:01891, C:01892
1yi2 08083 Oph·2Pout A:01754(OP2) 03704, 04147, 06340, 07804, 07857 C:01753, A:01755 A:01755, A:01754
1yi2 08068 Oph·2Pout A:02568(OP2) 03749, 04811, 06208, 07851, 09736 A:02569, G:02567 A:02569, A:02568
1yi2 08020 Oph·2Pout C:01830(OP1) 07726, 07745, 09121, 09124, 09195 U:01831, A:01842 G:01828 G:01828, G:01832
1yij 08068 Oph·2Pout A:02568(OP2) 03761, 04834, 06222, 07864, 09737 A:02569, G:02567 A:02569, A:02568
1yij 08020 Oph·2Pout C:01830(OP1) 07738, 07757, 09123, 09126, 09198 U:01831, A:01842 G:01828 G:01828, G:01832
1yij 08019 Oph·2Pout A:02011(OP2) 04166, 07225, 07754, 07755, 07756 A:01941, G:01891 U:01890 G:01891, C:01892
1yij 08083 Oph·2Pout A:01754(OP2) 03716, 04167, 06354, 07817, 07869 C:01753, A:01755 A:01755, A:01754
1yj9 08020 Oph·2Pout C:01830(OP1) 07551, 07570, 08942, 08945, 09018 U:01831, A:01842 G:01828 G:01828, G:01832
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
1yjn 08020 Oph·2Pout C:01830(OP1) 07750, 07769, 09121, 09124, 09198 U:01831, A:01842 G:01828 G:01828, G:01832
1yjn 08019 Oph·2Pout A:02011(OP2) 04167, 07233, 07766, 07767, 07768 A:01941, G:01891 U:01890 G:01891, C:01892
1yjn 08037 Oph·2Pout A:02553(OP2) 03143, 03217, 03661, 07850, 09077 C:02575, U:02554 C:02552 A:02576
1yjw 78083 Oph·2Pout A:01754(OP2) 07792, 07794, 07797, 07800, 07803 C:01753, A:01755 A:01754, A:01755
1yjw 78019 Oph·2Pout A:02011(OP2) 08084, 08085, 08123, 08234 G:01891, A:01941 U:01890 G:01891
1yjw 78020 Oph·2Pout C:01830(OP1) 07913, 07918, 07919, 07921, 07953 A:01842, U:01831 G:01828 G:01828, G:01832
1yjw 78072 Oph·2Pout U:0954(OP1) 06233, 08673, 08675, 08681, 08684 C:02298, A:02301
1yjw 78068 Oph·2Pout A:02568(OP2) 09263, 09265, 09268, 09269, E4036 G:02567, A:02569 A:02568, A:02569
1yls D341 Oph·2Pout C:D233(OP2) D394, D395, D396, D397, D398 G:D208, U:D234 G:D211, C:D210
2avy A1582 Oph·2Pout A:A608(OP2) A1791, A1792, A1793, A1794, A1795 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
2avy A1593 Oph·2Pout C:A536(OP1) A1844, A1845, A1846, A1847, A1848 C:A504, G:A537 C:A522
2avy A1568 Oph·2Pout A:A768(OP2) A1727, A1728, A1729, A1730, A1731 A:A767, U:A804 G:A769
2avy A1583 Oph·2Pout A:A1110(OP2) A1796, A1797, A1798, A1799, A1800 C:A1109, A:A1111 U:A1189, C:A1112

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>