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

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Representative site 3df2:B3382, See in JSmolMgRNA representative site for type 4PO-BO         Click on the image to toggle views


Site type: 4Pout·Bout

Schematic drawing for
4Pout·Bout

MgRNA type 4PO-BO
List of all 125 Mg2+ binding sites with the site type 4Pout·Bout 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 1 of 5 | « Previous | | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4gar C301 4Pout·Bout A3747, A3748, A3749, C406, C407 G:A1828, U:A1827, A:A1789, C:A1788 G:A1828
3ucz R670 4Pout·Bout R687, R688, R689, R690, R691, R692 U:R53, C:R52, U:R81, C:R44 A:R82
3mut R671 4Pout·Bout R715, R716, R717, R718, R719, R720 U:R53, U:R81, C:R52, C:R44 A:R82
2i2u A1556 4Pout·Bout A1662, A1663, A1664, A1665, A1666, A1667 A:A768, U:A804, C:A805, A:A767 G:A769
2i2p A1559 4Pout·Bout A1681, A1682, A1683, A1684, A1685, A1686 U:A13, A:A16, U:A14, G:A15 U:A14
4dr6 A1608 4Pout·Bout A2019, A2020, A2021, A2022 U:A751, U:A652, G:A752, C:A651 G:A752
4ji1 A1730 4Pout·Bout A2070, A2071, A2072, A2073, A2074, A2075 U:A751, G:A752, U:A652, C:A651 G:A752
3v28 A1749 4Pout·Bout A2007, A2008, A2009, A2010, A2011 A:A16, U:A13, U:A14, G:A15 U:A14
4duy A1793 4Pout·Bout A2143, A2144, A2145, A2146, A2147, A2148 A:A151, G:A167, G:A168, C:A150 G:A168
4ji1 A1797 4Pout·Bout A2473, A2474, A2475, A2476, A2477, A2478 C:A150, G:A168, G:A167, A:A151 G:A168
4dv6 A1804 4Pout·Bout A2155, A2156, A2157, A2158, A2159, A2160 A:A151, G:A168, G:A167, C:A150 G:A168
4dv1 A1812 4Pout·Bout A2217, A2218, A2219, A2220, A2221 A:A509, A:A510, G:A506, C:A507 A:A510
4dr7 A1818 4Pout·Bout A2474, A2475, A2476, A2477, A2478, A2479 C:A150, G:A168, A:A151, G:A167 G:A168
4duz A1829 4Pout·Bout A2198, A2199, A2200, A2201, A2202, A2203 A:A509, A:A510, G:A506, C:A507 A:A510
4dv7 A1829 4Pout·Bout A2115, A2116, A2117, A2118, A2119, A2120 C:A150, A:A151, G:A168, G:A167 G:A168
4dv3 A1837 4Pout·Bout A2201, A2202, A2203, A2204, A2205, A2206 A:A509, A:A510, C:A507, G:A506 A:A510
4dr6 A1840 4Pout·Bout A2505, A2506, A2507, A2508, A2509, A2510 A:A151, C:A150, G:A168, G:A167 G:A168
4ji8 A1951 4Pout·Bout A3211, A3212, A3213, A3214, A3215, A3216 C:A150, G:A167, G:A168, A:A151 G:A168
2awb B2909 4Pout·Bout B3036, B3037, B3038, B3039, B3040, B3041 A:B1937, G:B1959, A:B1936, C:B1958 G:B1959
1vs8 B2909 4Pout·Bout B3035, B3036, B3037, B3038, B3039, B3040 A:B1937, G:B1959, A:B1936, C:B1958 G:B1959
1vs8 B2910 4Pout·Bout B3041, B3042, B3043, B3044, B3045, B3046 C:B1986, A:B1669, A:B1987, C:B2551 G:B1954
2i2v B2910 4Pout·Bout B3051, B3052, B3053, B3054, B3055, B3056 C:B1986, A:B1669, A:B1987, C:B2551 G:B1954
2qbg B2910 4Pout·Bout B3043, B3044, B3045, B3046, B3047, B3048 A:B1669, C:B1986, C:B2551, A:B1987 G:B1954
2qp1 B2910 4Pout·Bout B3548, B3549, B3550, B3551, B3552, B3553 A:B1987, C:B1986, C:B2551, A:B1669 G:B1954
2z4n B2911 4Pout·Bout B3043, B3044, B3045, B3046, B3047, B3048 C:B2551, A:B1987, A:B1669, C:B1986 G:B1954

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>