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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qov:B2933, See in JSmolMgRNA representative site for type OP-3PO Click on the image to toggle views


Site type: Oph·3Pout

Schematic drawing for
Oph·3Pout
MgRNA type OP-3PO
List of all 867 Mg2+ binding sites with the site type Oph·3Pout 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 6 of 35 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qct A3287 Oph·3Pout A:A2062(OP2) A4122, A4123, A4124, A4125, A4126 G:A2444, C:A2443, G:A2061 G:A2444, G:A2445
4qcs A3096 Oph·3Pout C:A578(OP1) A4056, A4057, A4058, A4059, A4060 U:A820, C:A817, G:A576
4qcr A3565 Oph·3Pout G:A1859(OP2) A4842, A4843, A4844, A4845, A4846 C:A1858, A:A1994, C:A1819 G:A1859
4qcr A3427 Oph·3Pout U:A2096(OP1) A4427, A4428, A4429, D401 G:A2251, C:A2252, U:A2097 G:A2250
4qcr A3540 Oph·3Pout G:A586(OP2) A4751, A4752, A4753, A4754, A4755 C:A587, A:A595, G:A1021 C:A1020
4qcr A3347 Oph·3Pout U:A2039(OP1) A4190, A4191, A4192, A4193, A4194 A:A601, G:A602, G:A2040
4qcr A3408 Oph·3Pout U:A2418(OP1) A4348, A4349, A4350, A4351, A4352 G:A2419, U:A2420, G:A2421 G:A2417 G:A2422, U:A2420, G:A2421
4qcr A3307 Oph·3Pout U:A1008(OP1) A4073, A4074, A4075, A4076, A4077 C:A2510, A:A2509, G:A992
4qcr A3512 Oph·3Pout C:A2464(OP1) A4664, A4665, A4666, A4667, A5380 U:A2505, G:A2506, A:A2465
4qcr A3515 Oph·3Pout C:A1463(OP2) A4672, A4673, A4674, A4675 G:A1464, C:A1624, U:A1625 G:A1464
4qcr A3348 Oph·3Pout A:A2084(OP2) A4195, A4196, A4197, A4198, A4199 G:A2456, C:A2455, G:A2083 G:A2456, G:A2457
4qcr A3410 Oph·3Pout C:A238(OP1) A4357, A4358, A4359, A4360, A4361 G:A239, U:A2443, A:A2444 G:A239 C:A2406
4qcq A3125 Oph·3Pout A:A768(OP2) A4041, A4042, A4043, A4044, A4045 U:A804, C:A805, A:A767 A:A768, G:A769
4qcp A3429 Oph·3Pout G:A1647(OP2) A4493, A4494, A4495, A4496, A4497 G:A1325, A:A1272, C:A1617 A:A1616, C:A1646 A:A1616
4qcp A3395 Oph·3Pout C:A1417(OP2) A4402, A4403, A4404, A4405 C:A1577, U:A1578, G:A1418 G:A1416 G:A1418
4qcp A3441 Oph·3Pout G:A1828(OP2) A4526, A4527, A4528, A4529, D413 C:A1827, A:A1972, C:A1788 G:A1828
4qcp A3251 Oph·3Pout U:A963(OP1) A4040, A4041, A4042, A4043, A4044 C:A2498, A:A2497, G:A947
4qcp A3282 Oph·3Pout A:A2062(OP2) A4121, A4122, A4123, A4124, A4125 G:A2444, C:A2443, G:A2061 G:A2444, G:A2445
4qcp A3578 Oph·3Pout C:A2452(OP1) A4835, A4836, A4837, A4838, 0201 A:A2453, G:A2494, U:A2493
4qcp A3579 Oph·3Pout C:A1636(OP2) A4839, A4840, A4841, A4842, A4843 U:A1300, G:A1635, A:A1637 U:A1300
4qcn A3542 Oph·3Pout G:A1859(OP2) A4820, A4821, A4822, A4823, A4824 C:A1858, A:A1994, C:A1819 G:A1859
4qcn A3404 Oph·3Pout U:A2096(OP1) A4405, A4406, A4407, D3102 C:A2252, U:A2097, G:A2251 G:A2250
4qcn A3504 Oph·3Pout U:A2504(OP1) A4696, A4697, A4698, A4699, A4700 U:A2505, A:A2465, G:A2466 C:A2585 C:A2585
4qcn A3488 Oph·3Pout C:A2464(OP1) A4645, A4646, A4647, 03102, 03103 U:A2505, G:A2506, A:A2465
4qcn A3328 Oph·3Pout U:A2039(OP1) A4177, A4178, A4179, A4180, A4181 A:A601, G:A602, G:A2040

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>