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

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Representative site 2qan:A2016, See in JSmolMgRNA representative site for type 2PO-2BO        Click on the image to toggle views


Site type: 2Pout·2Bout

Schematic drawing for
2Pout·2Bout

MgRNA type 2PO-2BO
List of all 279 Mg2+ binding sites with the site type 2Pout·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 9 of 12 | | | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4ji5 A1702 2Pout·2Bout A1941, A1942, A1943, A1944, A1945, A1946 G:A361, G:A362 G:A362, G:A361
4ji6 A1932 2Pout·2Bout A3187, A3188, A3189, A3190, A3191, A3192 U:A580, G:A581 G:A581, G:A758
4ji6 A1832 2Pout·2Bout A2617, A2618, A2619, A2620, A2621, A2622 G:A953, G:A963 A:A964, G:A963
4ji6 A1887 2Pout·2Bout A2940, A2941, A2942, A2943, A2944, A2945 A:A353, A:A53 A:A53, A:A353
4ji6 A1745 2Pout·2Bout A2171, A2172, A2173, A2174 A:A608, A:A607 A:A609, G:A610
4ji7 A1859 2Pout·2Bout A2671, A2672, A2673, A2674, A2675, A2676 G:A361, G:A362 G:A362, G:A361
4ji7 A1775 2Pout·2Bout A2273, A2274, A2275, A2276 A:A608, A:A607 A:A609, G:A610
4kiy A1611 2Pout·2Bout A1751, A1752, A1754, A1755, A1756 G:A803, U:A804 G:A771, U:A772
4m4o B103 2Pout·2Bout B245, B246, B247, B248, B277 C:B39, U:B38 A:B25, G:B26
4nvv A3518 2Pout·2Bout A4618, A4619, A4620, A4621 A:A1399, A:A1400 G:A1402, C:A1421
4nvv A3404 2Pout·2Bout A4318, A4319, A4320, A4321, A4322 G:A1378, C:A1379 U:A1381, G:A1380
4nvw A3090 2Pout·2Bout A4038, A4039, A4040, A4041 U:A804, G:A803 G:A771, U:A772
4nvx A3321 2Pout·2Bout A4218, A4219, A4220, A4221 C:A1370, G:A1358 G:A1358, G:A1371
4nvx A3373 2Pout·2Bout A4338, A4339, A4340, A4341, A4342 A:A1354, A:A1353 G:A1355, G:A1356
4nw1 A3367 2Pout·2Bout A4337, A4338, A4339, A4340, A4341 A:A1354, A:A1353 G:A1355, G:A1356
4nxm A1793 2Pout·2Bout A2123, A2124, A2125, T201 U:A264, G:A265 G:A190, G:A260
4pe9 A1602 2Pout·2Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A329, A:A315 G:A318, G:A319
4pe9 A1601 2Pout·2Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260, G:A259
4peb A3119 2Pout·2Bout A3739, A3740, A3741, A3742, A3743, A3744 A:A1000, A:A1001 G:A1003, G:A1002
4peb A3084 2Pout·2Bout A3592, A3593, A3594, A3595, A3596, A3597 G:A976, G:A977 G:A978, G:A977
4pec A3025 2Pout·2Bout A3314, A3315, A3316, A3317, A3318, A3319 C:A796, G:A797 G:A798, G:A797
4pec A3119 2Pout·2Bout A3730, A3731, A3732, A3733, A3734, A3735 A:A1000, A:A1001 G:A1003, G:A1002
4pec A3084 2Pout·2Bout A3583, A3584, A3585, A3586, A3587, A3588 G:A976, G:A977 G:A977, G:A978
4pec A3092 2Pout·2Bout A3621, A3622, A3623, A3624, A3625, A3626 A:A1572, G:A1422 G:A1423, G:A1425
4qcm A1745 2Pout·2Bout A4071, A4072, A4073, A4074, A4075, A4076 U:A804, G:A803 U:A772, G:A771

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>