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

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Representative site 2qoz:B2982, See in JSmolMgRNA representative site for type PO-3BO         Click on the image to toggle views


Site type: Pout·3Bout

Schematic drawing for
Pout·3Bout

MgRNA type PO-3BO
List of all 341 Mg2+ binding sites with the site type Pout·3Bout 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 14 | | | 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
2qox B2917 Pout·3Bout B3075, B3076, B3077, B3078, B3079, B3080 A:B2033 G:B2027, U:B2028, G:B2029
2qoy A1563 Pout·3Bout A1998, A1999, A2000, A2001, A2002, A2003 A:A781 U:A798, G:A799, G:A800
2qoy A1562 Pout·3Bout A1992, A1993, A1994, A1995, A1996, A1997 G:A266 U:A268, G:A257, G:A258
2qoz B2922 Pout·3Bout B3591, B3592, B3593, B3594, B3595, B3596 U:B1267 G:B2010, U:B2011, A:B2009
2qoz B2982 Pout·3Bout B3872, B3873, B3874, B3875, B3876, B3877 A:B2386 G:B2325, C:B2326, A:B2386
2qp0 A1557 Pout·3Bout A1957, A1958, A1959, A1960, A1961, A1962 A:A781 G:A800, U:A798, G:A799
2qp0 A1556 Pout·3Bout A1951, A1952, A1953, A1954, A1955, A1956 G:A266 G:A257, G:A258, G:A259
2qp0 A1589 Pout·3Bout A2109, A2110, A2111, A2112, N279, N281 A:A1360 C:A980, A:A1360, G:A1361
2qp0 A1555 Pout·3Bout A1945, A1946, A1947, A1948, A1949, A1950 A:A315 G:A318, G:A319, A:A320
2qp0 A1554 Pout·3Bout A1939, A1940, A1941, A1942, A1943, A1944 U:A644 G:A592, G:A645, G:A646
2qp1 B2923 Pout·3Bout B3611, B3612, B3613, B3614, B3615, B3616 U:B1267 G:B2010, U:B2011, A:B2009
2qp1 B2999 Pout·3Bout B3957, B3958, B3959, B3960, B3961, B3962 U:B769 G:B770, U:B769, G:B771
2qp1 B2927 Pout·3Bout B3630, B3631, B3632, B3633, B3634, E202 A:B616 G:B617, G:B618, G:B619
2z4k A1565 Pout·3Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A559 G:A9, A:A10, A:A559
2z4k A1564 Pout·3Bout A1700, A1701, A1702, A1703, A1704, A1705 A:A781 U:A798, G:A799, G:A800
2z4k A1563 Pout·3Bout A1694, A1695, A1696, A1697, A1698, A1699 G:A266 G:A257, G:A258, G:A259
2z4l B2947 Pout·3Bout B3207, B3208, B3209, B3210, B3211 C:B2310 G:B2304, U:B2302, G:B2303
2z4m A1568 Pout·3Bout A1721, A1722, A1723, A1724, A1725, A1726 A:A781 G:A800, U:A798, G:A799
2z4n B2958 Pout·3Bout B3269, B3270, B3271, B3272, B3273, B3274 A:B2386 C:B2326, U:B2387, A:B2386
2z75 B304 Pout·3Bout B411, B492, B493, B494, B544 A:B129 U:B100, G:B101, G:B102
3df1 A2122 Pout·3Bout A4123, A4124, A4125, A4126, A4127, A4128 A:A781 G:A799, G:A800, U:A798
3df3 A2148 Pout·3Bout A4149, A4150, A4151, A4152, A4153, A4154 A:A781 G:A800, U:A798, G:A799
3df3 A2114 Pout·3Bout A4115, A4116, A4117, A4118, A4119, A4120 U:A644 G:A592, G:A645, G:A646
3df3 A2091 Pout·3Bout A4093, A4094, A4096, N4092, N4095 A:A1360 C:A980, G:A1361, A:A1360
3df4 B3308 Pout·3Bout B4309, B4310, B4311, B4312, B4313, B4314 A:B2386 A:B2386, C:B2326, U:B2387

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>