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

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Representative site 3r8s:A3026, See in JSmolMgRNA representative site for type cis-2OP        Click on the image to toggle views

Site type: cis-2Oph

Schematic drawing for

MgRNA type cis-2OP
List of all 1720 Mg2+ binding sites with the site type cis-2Oph 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
1ehz A540 cis-2Oph G:A20(OP1), A:A21(OP2) A722, A723, A724
1evv A902 cis-2Oph G:A20(OP1), A:A21(OP2) A1105, A1114
1ffy T1209 cis-2Oph C:T48(OP1), G:T50(OP1) T1323, T1324, T1325, T1326 U:T51
1jj2 08034 cis-2Oph A:02302(OP1), A:02303(OP1) 03169, 03297, 04404, 07355 A:02301 A:02301, A:02303, G:02304
1jj2 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03168, 03181, 08541, A8630 C:02475, A:02624 G:0885
1jj2 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 07318, 07369, 07370, 08951 U:0163, A:0169
1jj2 08080 cis-2Oph A:01684(OP2), U:01724(OP2) 03733, 04025, 07393, 07447 C:01431 A:01691, C:01692 U:01722, A:01691
1jj2 08023 cis-2Oph G:02617(OP2), G:02618(OP2) 03154, 03346, 07339, 07340 G:02616 G:02618
1jj2 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 03166, 07314, 07315, 07325 G:02585, G:02584
1jj2 08086 cis-2Oph A:0532(OP1), U:0533(OP1) 03260, 03503, 07396, 07397 C:0534 A:02814, U:010
1jj2 08052 cis-2Oph U:01125(OP1), G:992(OP1) 03150, 07438, 98389, 98416 C:01126 C:01129, G:990
1jj2 08061 cis-2Oph A:01369(OP2), U:02650(OP1) 07376, 07377, 07378, 09344 A:02649 U:01371
1jj2 08029 cis-2Oph U:01503(OP1), C:01679(OP1) 07347, 07348, 07349, 07350 A:01504
1jj2 08107 cis-2Oph A:01106(OP2), A:01107(OP2) 07426, 07427, 07428, 07429 C:01103, C:01104 A:01107
1jj2 08014 cis-2Oph G:02102(OP2), G:02537(OP2) 03186, 03691, 07303, 08553 C:02536, A:02101 G:02480, G:02481, A:02101
1jj2 08048 cis-2Oph A:02746(OP2), G:02750(OP2) 05419, 05807, 07423, 07459 C:02745, U:02749
1jj2 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03140, 07017, 07406, 09744 C:0910, U:0909 G:01292, G:0911
1jj2 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03396, 07324, 08630, 08976 A:02095 A:02096 G:02097
1jj2 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 07381, 07382, 07443, 07444 A:01287
1k73 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3637, A3649, A9020, C8631 C:A2475, A:A2624 G:A885
1k73 A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3654, A4160, A7767, A9032 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1k73 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3219, A3609, A7481, A7870 C:A910, U:A909 G:A911, G:A1292
1k73 A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3728, A3972, A7860, A7861 C:A534 A:A2814, U:A10
1k73 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5882, A6270, A7887, A7923 C:A2745, U:A2749
1k73 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3635, A7778, A7779, A7789 G:A2585, G:A2584

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>