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

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Representative site 2qal:A2136, See in JSmolMgRNA representative site for type 3PO-RO         Click on the image to toggle views


Site type: 3Pout·Rout

Schematic drawing for
3Pout·Rout

MgRNA type 3PO-RO
List of all 51 Mg2+ binding sites with the site type 3Pout·Rout 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ofa A1573 3Pout·Rout A1763, A1764, A1765, A1766, A1767, A1768 C:A504, C:A503, C:A536 C:A522
3ofq A2964 3Pout·Rout A3322, A3323, A3324, A3325 G:A1968, G:A2592, G:A1973 C:A1967
3ofx A1573 3Pout·Rout A1763, A1764, A1765, A1766, A1767, A1768 C:A504, C:A536, C:A503 C:A522
3or9 A1574 3Pout·Rout A1763, A1764, A1765, A1766, A1767, A1768 C:A504, C:A503, C:A536 C:A522
3r8t A2918 3Pout·Rout A3138, A3139, A3140, A3141, A3142, A3143 U:A2017, U:A2016, G:A578 U:A1255
3v23 A3339 3Pout·Rout A4031, A4032, A4033, A4034, A4035, A4036 C:A1990, G:A1989, G:A1667 G:A1667
3v26 A1721 3Pout·Rout A1994, A1995, A1996, A1997, A1998, A1999 G:A406, A:A432, A:A496 A:A495
3v27 A3450 3Pout·Rout A4429, A4430, A4431, A4432, A4433, A4434 A:A71, G:A113, U:A72 U:A112
3v2d A3250 3Pout·Rout A4382, A4383, A4384, A4385, A4386 C:A1990, G:A1989, G:A1667 G:A1667
4bpe A5037 3Pout·Rout A2062, A2063, A2064, A2065, A2066, A2302 G:A353, G:A354, G:A368 A:A351
4bpn A5050 3Pout·Rout A6159, A6160, A6161, A6162, A6163, A6164 C:A524, A:A508, U:A523 U:A34
4bpn A5037 3Pout·Rout A6068, A6069, A6070, A6071, A6072, A6073 G:A353, A:A369, G:A368 A:A351
4dr2 A1676 3Pout·Rout A2167, A2168, A2169, L302 C:A536, G:A537, A:A523 C:A522
4dr5 A1824 3Pout·Rout A2334, A2335, A2336, A2337, A2338, A2339 C:A904, U:A891, G:A903 G:A890
4duz A1628 3Pout·Rout A1956, A1957, A1958, A1959 A:A563, U:A560, C:A562 A:A559
4duz A1810 3Pout·Rout A2102, A2103, A2104, A2105, A2106 C:A150, A:A151, G:A168 G:A167
4dv0 A1787 3Pout·Rout A2134, A2135, A2136, A2137, A2138 C:A150, A:A151, G:A168 G:A167
4dv0 A1823 3Pout·Rout A2260, A2261, A2262, A2263, A2264 C:A48, U:A49, G:A115 C:A47
4dv6 A1853 3Pout·Rout A2344, A2345, A2346, A2347, A2348 C:A328, C:A330, C:A314 A:A329
4gaq A1629 3Pout·Rout A1836, A1837, A1838, A1839 G:A1198, G:A1053, C:A1054 G:A1198
4gas A1615 3Pout·Rout A1768, A1769, A1770, A1771, A1772, A1773 C:A536, G:A537, C:A504 C:A522
4gd2 A1631 3Pout·Rout A1846, A1847, A1848, A1849, N204, N205 U:A1049, G:A1048, A:A1204 C:A1203
4ji7 A1976 3Pout·Rout A3360, A3361, A3362, A3363, A3364, L307 C:A536, G:A537, C:A503 C:A522
4pec A3015 3Pout·Rout A3268, A3269, A3270, A3271, A3272, A3273 U:A2016, U:A2017, G:A579 U:A1255
4ton A1615 3Pout·Rout A1765, A1766, A1767, A1768, A1769, A1770 C:A504, C:A503, C:A536 C:A522

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>