MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3i20:A2925, See in JSmolClick on the image to toggle views Site type: Ob Schematic drawing for Ob List of all 468 Mg2+ binding sites with the site type Ob 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 2 of 19 | « Previous | Next » | 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 4tom B202 Ob U:B95(O4) B305, B306, B307, B308, B309 U:B80, G:B96 4tpf B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94 354d B204 Ob G:B98(O6) A319, A323, B320, B321, B322 G:A76, G:A76, C:B97 G:A75 3v25 D301 Ob U:A2593(O4) A3594, A3595, A3596, A3597 C:A2591 G:A2592, C:A2594, G:A2599 1dfu M501 Ob U:M95(O4) M518, M525, M529, N520, P131 A:M94, G:M96, U:N80 3oas B590 Ob U:B95(O4) B591, B592, B593, B594, B595 U:B80 3ofd B590 Ob U:B95(O4) B591, B592, B593, B595, V594 U:B80 3ofq B590 Ob U:B95(O4) B591, B592, B593, V594, V595 U:B80 3og0 B590 Ob U:B95(O4) B591, B592, B593, B595, V594 U:B80 3oat B602 Ob U:B95(O4) B603, B604, B605, B606, B607 U:B80, G:B96 3ofr B609 Ob U:B95(O4) B610, B611, B612, B613, V614 U:B80, G:B96 3orb B609 Ob U:B95(O4) B610, B611, B612, B613, B614 U:B80, G:B96 3ofz B609 Ob U:B95(O4) B610, B611, B612, B613, B614 U:B80, G:B96 3ofc B614 Ob U:B95(O4) B615, B616, B617, V618, V619 U:B80, G:B96 3r8t B615 Ob U:B95(O4) B616, B617, B618, B619, B620 U:B80, A:B94 2r8s R1003 Ob G:R188(O6) R1010, R1011, R1012, R1013, R1014 U:R182, U:R168, A:R183, C:R166, C:R165 A:R183 1ffy T1204 Ob G:T43(O6) T1218, T1308, T1309, T1310, T1311 U:T42, G:T26, A:T44 1qu2 T1204 Ob G:T43(O6) T1218, T1308, T1309, T1310, T1311 U:T42, G:T26, A:T44 3ofb A1536 Ob G:A362(O6) A1584, A1585, A1586, A1587, A1588 G:A361 3ora A1536 Ob G:A362(O6) A1588, A1589, A1590, A1591, A1592 G:A361 3oar A1536 Ob G:A362(O6) A1583, A1584, A1585, A1586, A1587 G:A361 3ofy A1536 Ob G:A362(O6) A1584, A1585, A1586, A1587, A1588 G:A361 3i1o A1550 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1415, G:A1416, G:A1482 3i1s A1550 Ob G:A1417(O6) A1668, A1669, A1670, A1671, A1672 G:A1482 3i21 A1550 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1415

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].

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