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

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Representative site 2r8s:R1004, See in JSmolMgRNA representative site for type 2OB            Click on the image to toggle views

Site type: 2Ob

Schematic drawing for

MgRNA type 2OB
List of all 16 Mg2+ binding sites with the site type 2Ob 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
1jj2 08097 2Ob G:0863(O6), U:0864(O4) 03199, 03203, 05094, 09865 U:0862, G:0782
1nji A8097 2Ob G:A863(O6), U:A864(O4) A3336, A3664, A3668, A5551 G:A782, U:A862
1yjw 78097 2Ob G:0863(O6), U:0864(O4) 05757, 05969, 05977, 05980 G:0782, U:0862
2otj 08097 2Ob G:0863(O6), U:0864(O4) 03356, 03690, 03694, 05590 G:0782, U:0862
2r8s R1004 2Ob G:R257(O6), U:R258(O4) R1015, R1016, R1017, R1018 A:R256, C:R255 G:R215
3v23 A3357 2Ob G:A538(O6), U:A555(O4) A4105, A4106, A4107, A4108 G:A539, U:A554
3v23 A3310 2Ob U:A594(O4), G:A662(O6) A3925, A3926, A3927, A3928 G:A593, G:A663, C:A664
3v2d A3258 2Ob G:A1488(O6), U:A1489(O4) A4405, A4406, A4407, A4408 C:A1498 G:A1487, G:A1500
4dr2 A1761 2Ob U:A1510(O4), G:A1511(O6) A2423, A2424, A2425, A2426 U:A1512, U:A1522, A:A1513, G:A1523, C:A1524
4dr3 A1632 2Ob U:A304(O4), G:A305(O6) A1963, A1964, A1965 G:A293
4dv5 A1625 2Ob U:A304(O4), G:A305(O6) A1944, A1945, A1946 A:A303, G:A293
4dv5 A1686 2Ob G:A1370(O6), G:A1371(O6) A2047, A2048, A2049 U:A1372
4dv7 A1626 2Ob U:A304(O4), G:A305(O6) A1951, A1952, A1953 G:A293
4ji3 A1784 2Ob U:A304(O4), G:A305(O6) A2114, A2115, A2116 G:A293
4ji7 A1654 2Ob G:A886(O6), G:A887(O6) A2199, A2200, A2201 G:A885, U:A911, G:A888
4nxn A1629 2Ob U:A304(O4), G:A305(O6) A1961, A1962, A1963 G:A293

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>