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

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Representative site 4bpp:A5052, See in JSmolMgRNA representative site for type RO             Click on the image to toggle views

Site type: Rout

Schematic drawing for

MgRNA type RO
List of all 25 Mg2+ binding sites with the site type Rout 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
1k8a C8065 Rout A3557, C8522, C8541, C8553, C8611, C8646 G:A782
1kc8 C8065 Rout A3974, A9921, C8523, C8552, C8606, C8634 G:A782
1kd1 C8065 Rout A3963, A9915, C8523, C8553, C8605, C8635 G:A782
1kqs A8065 Rout 03476, 09435, A8522, A8555, A8608, A8639 G:0782
1m1k C8065 Rout A3564, C8524, C8539, C8552, C8603, C8636 G:A782
1n8r C8065 Rout A4367, C8522, C8541, C8555, C8609, C8642 G:A782
1q81 C8065 Rout A3482, A9441, C8521, C8558, C8616, C8643 G:A782
1q82 C8065 Rout A3480, C8524, C8543, C8556, C8615, C8647 G:A782
1q86 C8065 Rout A3500, A9448, C8520, C8549, C8596, C8624 G:A782
1qvf A8065 Rout 03480, A8549, A8601, A8631 G:0782
1qvg A8065 Rout 03468, 09431, A8519, A8546, A8595, A8623 G:0782
1vq4 A8065 Rout 03242, 04275, A9320, A9348, A9395, A9423 G:0782
1vq6 A8065 Rout 03239, 04276, A9320, A9346, A9398, A9427 G:0782
1yhq A8050 Rout 04462, A8988, A9002, A9016, A9063, A9092 G:0782
1yi2 A8065 Rout 03966, 09932, A8823, A8849, A8899, A8928 G:0782
1yjw A8065 Rout 05760, 05761, A4013, A4017, A4067, A4069 G:0782
2otj A8065 Rout 03997, 09938, A8821, A8846, A8892, A8920 G:0782
3cxc A8065 Rout 04917, A8523, A8538, A8554, A8611, A8643 G:0782
3v27 A3459 Rout A4466, A4467, A4468, A4469, A4470 A:A528
4a17 08 Rout 05075, 05076, 05077, 05078, 05079, 05080 A:237
4bpe A5052 Rout A2140, A2141, A2319, A2320, A2321, A2322 A:A675
4bpp A5052 Rout A7843, A7844, A7845, A7846, A7847, A7848 A:A675
4ji7 A1894 Rout A2880, A2881, A2882, A2883, A2884, A2885 G:A799
4lfb H202 Rout A1907, A1908, H301, H302, H303, H304 U:A5
4lfc A1737 Rout A1836, A1837, A1838, A1839, A1840, A1841 G:A867

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>