`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 2qoy:A1567, See in JSmolMgRNA representative site for type 2BO            Click on the image to toggle views


Site type: 2Bout

Schematic drawing for
2Bout

MgRNA type 2BO
List of all 555 Mg2+ binding sites with the site type 2Bout 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 7 of 23 | | | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qbk B2933 2Bout B3158, B3159, B3160, E202, E203, E204 G:B797, G:B798
2qbk B2971 2Bout B3339, B3340, B3341, B3342, B3343, B3344 A:B756, G:B757
2qbk B2999 2Bout B3448, B3449, B3450, B3451, B3452, B3453 G:B771, G:B770
2qou A1592 2Bout A2135, A2136, A2137, A2138, A2139, A2140 U:A37, G:A38
2qou A1568 2Bout A2023, A2024, A2025, A2026, A2027, A2028 G:A942, G:A941
2qou A1588 2Bout A2116, A2117, A2118, A2119, A2120, A2121 G:A1526, G:A1525
2qou A1599 2Bout A2168, A2169, A2170, A2171, A2172, A2173 G:A1401, C:A1402
2qov B2907 2Bout B3026, B3027, B3028, B3029, B3030, B3031 U:B580, U:B1258
2qov B2961 2Bout B3285, B3286, B3287, B3288, B3289, E333 G:B798, G:B797
2qow A1592 2Bout A2126, A2127, A2128, A2129, A2130, A2131 G:A941, G:A942
2qow A1559 2Bout A1966, A1967, A1968, A1969, A1970, A1971 G:A376, G:A377
2qow A1570 2Bout A2019, A2020, A2021, A2022, A2023, A2024 G:A1525, G:A1526
2qow A1590 2Bout A2112, A2113, A2114, A2115, A2116 G:A1050, G:A1207
2qow A1574 2Bout A2039, A2040, A2041, A2042, A2043, A2044 G:A38, U:A37
2qox B2933 2Bout B3156, B3157, B3158, B3159, B3160, B3161 G:B798, G:B797
2qoy A1592 2Bout A2137, A2138, A2139, A2140, A2141, A2142 U:A37, G:A38
2qoy A1588 2Bout A2118, A2119, A2120, A2121, A2122, A2123 G:A1525, G:A1526
2qoy A1568 2Bout A2025, A2026, A2027, A2028, A2029, A2030 G:A942, G:A941
2qoy A1567 2Bout A2019, A2020, A2021, A2022, A2023, A2024 G:A377, G:A378
2qoy A1574 2Bout A2054, A2055, A2056, A2057, A2058, A2059 G:A1385, G:A1386
2qoz B2937 2Bout B3664, B3665, B3666, B3667, B3668, B3669 C:B650, G:B651
2qoz B2984 2Bout B3884, B3885, B3886, B3887, B3888, B3889 G:B2550, G:B2557
2qp0 A1570 2Bout A2022, A2023, A2024, A2025, A2026, A2027 G:A1525, G:A1526
2qp0 A1594 2Bout A2134, A2135, A2136, A2137, A2138, A2139 G:A1385, G:A1386
2qp0 A1574 2Bout A2042, L192, L195, L1756, L1757, L1758 U:A37, G:A38

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>