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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2945, See in JSmolMgRNA representative site for type OP-PO Click on the image to toggle views


Site type: Oph·Pout

Schematic drawing for
Oph·Pout
MgRNA type OP-PO
List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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
1m90 A8051 Oph·Pout G:A641(OP2) A3633, A7350, A7351 A:A1355 G:A642, A:A1355, G:A641
1m90 A8084 Oph·Pout A:A1742(OP2) A3164, A7378, A8771, A8895, A9272 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1m90 A8039 Oph·Pout U:A115(OP2) A3493, A4642, A7346, A7347, A9429 G:A112 A:A114 A:A119, G:A118, A:A117
1m90 A8083 Oph·Pout A:A1754(OP2) A3235, A3684, A5894, A7377, A7430 C:A1753 A:A1755, A:A1754
1n8r A8084 Oph·Pout A:A1742(OP2) A3146, A4030, A8402, A9647, A9768 G:A2033 G:A2033, G:A1744, G:A1745, A:A1742, G:A1743
1n8r A8083 Oph·Pout A:A1754(OP2) A4102, A4544, A6744, A8401, A8453 C:A1753 A:A1755, A:A1754
1n8r A8039 Oph·Pout U:A115(OP2) A3300, A4363, A5493, A8300, A8304 G:A112 A:A114 G:A118, A:A119, A:A117
1nji A8051 Oph·Pout G:A641(OP2) A4094, A7812, A7813 A:A1355 A:A1355, G:A642, G:A641
1nji A8039 Oph·Pout U:A115(OP2) A3956, A5094, A7807, A7808, A9904 G:A112 A:A119, G:A118, A:A117
1nji A8083 Oph·Pout A:A1754(OP2) A3698, A4142, A6356, A7839, A7895 C:A1753 A:A1755, A:A1754
1pjo A32 Oph·Pout G:A5(OP2) A136, A137, A138, A139, A140 A:A6 G:A5, A:A6
1q7y A8051 Oph·Pout G:A641(OP2) A3610, A7292, A7293 A:A1355 G:A642, G:A641
1q7y A8019 Oph·Pout A:A2011(OP2) A3658, A6726, A7257, A7258, A7259 A:A1941 C:A1940, U:A1890 G:A1891, C:A1892
1q7y A8083 Oph·Pout A:A1754(OP2) A3216, A3659, A5845, A7319, A7369 C:A1753 A:A1755, A:A1754
1q7y A8084 Oph·Pout A:A1742(OP2) A3145, A7320, A8768, A8888, A9267 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1q81 A8051 Oph·Pout G:A641(OP2) A3614, A7301, A7302 A:A1355 A:A1355, G:A642
1q81 A8019 Oph·Pout A:A2011(OP2) A3660, A6726, A7265, A7266, A7267 A:A1941 U:A1890 G:A1891, C:A1892
1q81 A8083 Oph·Pout A:A1754(OP2) A3219, A3661, A5866, A7328, A7380 C:A1753 A:A1755, A:A1754
1q82 A8084 Oph·Pout A:A1742(OP2) A3147, A7319, A8768, A8892, A9261 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1q82 A8083 Oph·Pout A:A1754(OP2) A3218, A3662, A5841, A7318, A7369 C:A1753 A:A1755, A:A1754
1q82 A8039 Oph·Pout U:A115(OP2) A3477, A4604, A7288, A7289, A9419 G:A112 A:A114 A:A119, G:A118, A:A117
1q86 A8083 Oph·Pout A:A1754(OP2) A3233, A3679, A5875, A7349, A7400 C:A1753 A:A1754, A:A1755
1q86 A8039 Oph·Pout U:A115(OP2) A3496, A4614, A7318, A7319, A9431 G:A112 A:A114 A:A119, G:A118, A:A117
1qu2 T1203 Oph·Pout A:T14(OP2) T1304, T1305, T1306, T1307, A2198 G:T7 U:T8
1qvf 08039 Oph·Pout U:0115(OP2) 03476, 04595, 07264, 07265, 09429 G:0112 A:0114 A:0119, G:0118, A:0117

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>