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

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Representative site 2i2t:B2935, See in JSmolMgRNA representative site for type 3PO-BO         Click on the image to toggle views

Site type: 3Pout·Bout

Schematic drawing for

MgRNA type 3PO-BO
List of all 155 Mg2+ binding sites with the site type 3Pout·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 7 | « Previous | | 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
1vs5 A1598 3Pout·Bout A1866, A1867, A1868, A1869, A1870, A1871 A:A919, A:A1394, A:A918 A:A919
1vs7 A1574 3Pout·Bout A1757, A1758, A1759, A1760, A1761, A1762 A:A768, C:A805, A:A767 G:A769
1vs8 B2920 3Pout·Bout B3090, B3091, B3092, B3093, B3094, B3095 C:B1376, U:B1352, C:B1351 G:B1377
1vt2 A2949 3Pout·Bout A3249, A3250, A3251, A3252, A3253, A3254 C:A1351, C:A1376, G:A1377 G:A1377
2avy A1597 3Pout·Bout A1862, A1863, A1864, A1865, A1866, A1867 A:A919, A:A1394, A:A918 A:A919
2aw4 B2968 3Pout·Bout B3311, B3312, B3313, B3314, B3315, B3316 C:B1376, U:B1352, C:B1351 G:B1377
2aw4 B2931 3Pout·Bout B3140, B3141, B3142, B3143, B3144, B3145 A:B1937, A:B1936, G:B1959 G:B1959
2aw7 A1573 3Pout·Bout A1759, A1760, A1761, A1762, A1763, A1764 A:A768, C:A805, A:A767 G:A769
2awb B2910 3Pout·Bout B3042, B3043, B3044, B3045, B3046, B3047 C:B1986, A:B1987, C:B2551 G:B1954
2awb B2920 3Pout·Bout B3091, B3092, B3093, B3094, B3095, B3096 C:B1376, U:B1352, C:B1351 G:B1377
2i2p A1569 3Pout·Bout A1736, A1737, A1738, A1739, A1740 A:A768, A:A767, U:A804 G:A769
2i2t B2935 3Pout·Bout B3169, B3170, B3171, B3172, B3173, B3174 C:B2050, A:B2051, A:B2614 A:B2614
2qam B3369 3Pout·Bout B3912, B3913, B3914, B3915, B3916, B3917 C:B1376, G:B1377, C:B1351 G:B1377
2qan E2155 3Pout·Bout A2156, A2158, A2159, A2160, E2157 U:A20, G:A21, U:A561 G:A21
2qao B3092 3Pout·Bout B3693, B3694, B3695, B3696, B3697, B3698 C:B1351, G:B1377, C:B1376 G:B1377
2qb9 A2164 3Pout·Bout A2490, A2491, A2492, A2493, A2494 A:A767, A:A768, U:A804 G:A769
2qba B3369 3Pout·Bout B3909, B3910, B3911, B3912, B3913, B3914 C:B1376, C:B1351, G:B1377 G:B1377
2qbc B3092 3Pout·Bout B3695, B3696, B3697, B3698, B3699, B3700 C:B1376, C:B1351, G:B1377 G:B1377
2qbd A2129 3Pout·Bout A2131, A2133, A2134, A2135, E2130, E2132 G:A21, U:A20, U:A561 G:A21
2qbe B3282 3Pout·Bout B3841, B3842, B3843, B3844, B3845, L284 C:B944, G:B831, U:B568 A:B945
2qbe B3157 3Pout·Bout B3740, B3741, B3742, B3743, B3744, B3745 A:B1937, A:B1936, G:B1959 G:B1959
2qbe B3369 3Pout·Bout B3909, B3910, B3911, B3912, B3913, B3914 C:B1376, G:B1377, C:B1351 G:B1377
2qbg B2920 3Pout·Bout B3092, B3093, B3094, B3095, B3096, B3097 C:B1376, C:B1351, G:B1377 G:B1377
2qbg B2987 3Pout·Bout B3413, B3414, B3415, B3416, B3417, B3418 U:B2613, A:B2614, G:B2578 A:B2051
2qbh A1569 3Pout·Bout A1731, A1732, A1733, A1734, A1735 A:A768, U:A804, A:A767 G:A769

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>