`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
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 5 of 35 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1s72 08017 Oph·3Pout G:0456(OP2) 03465, 07268, 08933, C8356, C8466 G:0458, A:0455, U:0457
1s72 08032 Oph·3Pout U:02115(OP1) 03311, 03714, 09512, A8551, A8632 U:02116, G:02272, C:02273 G:02271
1s72 08037 Oph·3Pout A:02553(OP2) 03170, 07369, 08598, 09655, 09730 A:02576, U:02554, C:02575 C:02552 A:02576
1vq4 08017 Oph·3Pout G:0456(OP2) 03926, 04250, 07932, 09735, C9267 A:0455, G:0458, U:0457
1vq4 08021 Oph·3Pout G:02304(OP2) 03278, 03943, 03944, 07938, 07939 A:02301, A:02303, A:02305 U:02306, A:02305, G:02304
1vq4 08035 Oph·3Pout G:01484(OP2) 04020, 07975, 07976, 08137, 08138 C:01455, C:01456, A:01485 G:01484, U:01457
1vq4 08037 Oph·3Pout A:02553(OP2) 03445, 03517, 03954, 08139, 09397 C:02575, A:02576, U:02554 C:02552 A:02576
1vq4 08040 Oph·3Pout U:0392(OP2) 03010, 04094, 04941, 08141, 08142 U:0172, U:0391, C:0171
1vq4 08032 Oph·3Pout U:02115(OP1) 03304, 04093, 04499, A9347, A9421 C:02273, U:02116, G:02272
1vq4 08036 Oph·3Pout G:0956(OP2) 03975, 07977, 07978, 07979, 09688 A:01006, A:0955, A:0957 A:0957, G:0956
1vq5 08040 Oph·3Pout U:0392(OP2) 03017, 04104, 04949, 08186, 08187 U:0172, U:0391, C:0171
1vq5 08032 Oph·3Pout U:02115(OP1) 03311, 04103, 04504, A9343, A9422 C:02273, U:02116, G:02272
1vq5 08036 Oph·3Pout G:0956(OP2) 03986, 08128, 08129, 08130, 09693 A:01006, A:0955, A:0957 A:0957, G:0956
1vq5 08021 Oph·3Pout G:02304(OP2) 03286, 03954, 03955, 07983, 07984 A:02301, A:02303, A:02305 U:02306, A:02305, G:02304
1vq5 08017 Oph·3Pout G:0456(OP2) 04257, 07977, 09738, C9155, C9261 G:0458, A:0455, U:0457
1vq5 08037 Oph·3Pout A:02553(OP2) 03457, 03532, 03965, 08184, 09399 C:02575, A:02576, U:02554 C:02552 A:02576
1vq6 08032 Oph·3Pout U:02115(OP1) 03300, 04095, 04496, A9345, A9425 C:02273, U:02116, G:02272
1vq6 08017 Oph·3Pout G:0456(OP2) 03929, 04249, 07941, 09736, C9263 A:0455, G:0458, U:0457
1vq6 08036 Oph·3Pout G:0956(OP2) 03978, 07985, 07986, 07987, 09690 A:01006, A:0955, A:0957 A:0957, G:0956
1vq6 08021 Oph·3Pout G:02304(OP2) 03275, 03946, 03947, 07947, 07948 A:02301, A:02305, A:02303 U:02306, A:02305, G:02304
1vq7 08021 Oph·3Pout G:02304(OP2) 03286, 03962, 03963, 07978, 07979 A:02301, A:02305, A:02303 U:02306, A:02305, G:02304
1vq7 08036 Oph·3Pout G:0956(OP2) 03994, 08124, 08125, 08126, 09693 A:01006, A:0955, A:0957 A:0957, G:0956
1vq7 08017 Oph·3Pout G:0456(OP2) 04268, 07622, 07972, 09740, C9155 G:0458, A:0455, U:0457
1vq7 08032 Oph·3Pout U:02115(OP1) 03312, 04112, 04516, A9349, A9424 C:02273, U:02116, G:02272
1vq7 08037 Oph·3Pout A:02553(OP2) 03459, 03533, 03973, 08179, 09398 C:02575, A:02576, U:02554 C:02552 A:02576

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>