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

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Representative site 3df1:A2096, See in JSmolMgRNA representative site for type 4PO            Click on the image to toggle views


Site type: 4Pout

Schematic drawing for
4Pout

MgRNA type 4PO
List of all 174 Mg2+ binding sites with the site type 4Pout 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 7 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qao B3375 4Pout B3927, B3928, B3929, B3930, B3931, B3932 C:B560, A:B1008, G:B2038, G:B559
2qb9 A2096 4Pout A2437, A2438, A2439, A2440, A2441, A2442 U:A13, U:A14, G:A15, A:A16
2qbb A2077 4Pout A2433, A2434, A2435, A2436, N2081, N2082 G:A1048, U:A1049, A:A1204, C:A1203
2qbb A2042 4Pout A2404, A2405, A2406, A2407, A2408, A2409 G:A350, C:A334, U:A333, A:A349
2qbb A2029 4Pout A2393, A2394, A2395, A2396, A2397, A2398 U:A13, U:A14, A:A16, G:A15
2qbd A2096 4Pout A2097, A2098, A2099, A2100, A2101, A2102 G:A15, A:A16, U:A14, U:A13
2qbe B3382 4Pout B3920, B3921, B3922, B3923, B3924, B3925 A:B1669, C:B1986, A:B1987, C:B2551
2qbf A1556 4Pout N101, N102, A1667, A1668, A1669, A1670 G:A1048, U:A1049, C:A1203, A:A1204
2qbh A1555 4Pout A1661, A1662, A1663, A1664, N101, N102 A:A1204, U:A1049, C:A1203, G:A1048
2qbh A1559 4Pout A1679, A1680, A1681, A1682, A1683, A1684 U:A13, U:A14, G:A15, A:A16
2qbj A1548 4Pout A1628, A1629, A1630, A1631, A1632, A1633 U:A13, U:A14, A:A16, G:A15
2qbj A1556 4Pout A1667, A1668, A1669, A1670, N101, N102 G:A1048, U:A1049, A:A1204, C:A1203
2qbj A1550 4Pout A1638, A1639, A1640, A1641, A1642, A1643 C:A334, U:A333, A:A349, G:A350
2qow A1550 4Pout A1916, A1917, A1918, A1919, A1920, A1921 U:A333, G:A350, C:A334, A:A349
2qox B2962 4Pout B3294, B3295, B3296, B3297, B3298, B3299 U:B1915, A:B1912, A:B1913, C:B1914
2qoy A1555 4Pout A1956, A1957, A1958, A1959, A1960, N101 A:A1204, G:A1048, U:A1049, C:A1203
2qoz B2970 4Pout B3816, B3817, B3818, B3819, B3820, B3821 A:B1669, C:B1986, A:B1987, C:B2551
2qp0 A1550 4Pout A1919, A1920, A1921, A1922, A1923, A1924 G:A350, C:A334, U:A333, A:A349
2z4k A1560 4Pout A1678, A1679, A1680, A1681, A1682, A1683 U:A13, U:A14, G:A15, A:A16
2z4k A1556 4Pout A1661, A1662, A1663, N101, N102, N1664 A:A1204, U:A1049, C:A1203, G:A1048
2z4m A1557 4Pout A1667, A1668, A1669, A1670, N101, N102 C:A1203, A:A1204, G:A1048, U:A1049
2z4m A1551 4Pout A1638, A1639, A1640, A1641, A1642, A1643 U:A333, G:A350, C:A334, A:A349
3cxc 08072 4Pout 04195, 04941, 08729, 08786, 08927 U:0954, C:02298, G:02299, A:02301
3df1 A2096 4Pout A4097, A4098, A4099, A4100, A4101, A4102 A:A16, U:A14, G:A15, U:A13
3df2 B3561 4Pout B4562, B4563, B4564, B4565, B4566, B4567 A:B203, G:B205, C:B383, C:B385

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>