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

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Representative site 2qbd:A2143, See in JSmolMgRNA representative site for type 2PO-RO         Click on the image to toggle views

Site type: 2Pout·Rout

Schematic drawing for

MgRNA type 2PO-RO
List of all 39 Mg2+ binding sites with the site type 2Pout·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
1vt2 A2964 2Pout·Rout A3323, A3324, A3325, A3326 G:A2592, G:A1973 C:A1967
2qbd A2143 2Pout·Rout A2144, A2145, A2146, A2147, A2148, A2149 A:A1357, G:A1356 A:A1254
3df3 A2324 2Pout·Rout A4325, A4326, A4327, A4328, A4329 C:A504, C:A536 C:A522
3i1p A2964 2Pout·Rout A3320, A3321, A3322, A3323 G:A2592, G:A1973 C:A1967
3i1t A2964 2Pout·Rout A3323, A3324, A3325, A3326 G:A1973, G:A2592 C:A1967
3i22 A2918 2Pout·Rout A3109, A3110, A3111, A3112, A3113, A3114 U:A2016, G:A1256 U:A1255
3i22 A2972 2Pout·Rout A3367, A3368, A3369, C476, C479 G:A2239, U:A2240 G:A2238
3i22 A2963 2Pout·Rout A3322, A3323, A3324, A3325 G:A2592, G:A1973 C:A1967
3oas A2963 2Pout·Rout A3321, A3322, A3323, A3324 G:A2592, G:A1973 C:A1967
3ofc A2949 2Pout·Rout A3251, A3252, A3253, A3254, A3255 G:A1455, A:A1453 C:A1454
3og0 A2962 2Pout·Rout A3319, A3320, A3321, A3322 G:A2592, G:A1973 C:A1967
3ora A1573 2Pout·Rout A1765, A1766, A1767, A1768, A1769 C:A536, A:A523 C:A522
3v27 A3372 2Pout·Rout A4116, A4117, A4118, A4119, A4120 G:A1989, C:A1990 G:A1667
3v27 A3484 2Pout·Rout A4570, A4571, A4572, A4573, A4574, A4575 A:A324, G:A323 A:A324
3v27 A3545 2Pout·Rout A4849, A4850, A4851, A4852, A4853 G:A1555, C:A698 A:A1554
3v27 A3424 2Pout·Rout A4321, A4322, A4323, 1201, 1202 U:A2233, U:A380 G:A379
3v29 A3455 2Pout·Rout A4238, A4239, A4240, A4241 C:A365, C:A404 U:A403
3v29 A3594 2Pout·Rout A4757, A4758, A4759, A4760, A4761, A4762 A:A529, G:A530 A:A528
3v29 A3448 2Pout·Rout A4211, A4212, B307, B308, B309, B310 A:B102, G:B72 C:A915
3v2d A3720 2Pout·Rout A5753, A5754, A5755, A5756 U:A1540, C:A1543 A:A1542
4a1e 08 2Pout·Rout 05075, 05076, 05077, 05078, 05079, 05080 C:238, A:237 G:236
4dr5 A1836 2Pout·Rout A2402, A2403, A2404, A2405, A2406, A2407 G:A450, A:A452 A:A451
4duy A1859 2Pout·Rout A2395, A2396, A2397, A2398, A2399, A2400 C:A972, C:A1366 G:A971
4duy A1838 2Pout·Rout A2318, A2319, M204, M205, M206, M207 C:A1322, A:A1225 G:A1224
4duy A1818 2Pout·Rout A2241, A2242, A2243, A2244, A2245 C:A1103, A:A1101 C:A1100

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>