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

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Representative site 2qam:B3090, See in JSmolMgRNA representative site for type OP-2PO         Click on the image to toggle views

Site type: Oph·2Pout

Schematic drawing for

MgRNA type OP-2PO
List of all 1607 Mg2+ binding sites with the site type Oph·2Pout 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
1dul B802 Oph·2Pout C:B141(OP1) B817, B845, B883, B884, B885 A:B164, C:B142 G:B144
1dul B803 Oph·2Pout G:B149(OP2) B806, B886, B887, B888, B889 A:B148, G:B150 G:B149, G:B150, U:B151
1f27 A36 Oph·2Pout A:A9(OP2) A65, A165, A166, A167, A168 G:A12, A:A11 G:A12, G:A13
1feu F324 Oph·2Pout G:F100(OP2) F333, F345, F358, F359, F360 A:E73, A:F101 A:F101, G:F102
1ffy T1205 Oph·2Pout C:T25(OP1) T1312, T1313, T1314, A2199 G:T40, G:T26
1hq1 B1802 Oph·2Pout C:B141(OP1) B9040, B9062, B9164, B9282, B9283 C:B142, A:B164 G:B144
1jj2 08036 Oph·2Pout G:0956(OP2) 03197, 07358, 07359, 07360, 08886 A:01006, A:0955 A:0957, G:0956
1jj2 08020 Oph·2Pout C:01830(OP1) 07316, 07335, 08641, 08644, 08715 U:01831, A:01842 G:01828 G:01828, G:01832
1jj2 08068 Oph·2Pout A:02568(OP2) 03279, 04357, 05768, 07441, 09259 A:02569, G:02567 A:02569, A:02568
1jj2 08019 Oph·2Pout A:02011(OP2) 03678, 06783, 07332, 07333, 07334 A:01941, G:01891 U:01890 G:01891, C:01892
1jj2 08083 Oph·2Pout A:01754(OP2) 03234, 03679, 05901, 07394, 07448 C:01753, A:01755 A:01755, A:01754
1jj2 08045 Oph·2Pout G:01979(OP2) 07366, 07418, 07419, 07420 G:01998, C:01999
1k73 A8083 Oph·2Pout A:A1754(OP2) A3702, A4148, A6364, A7858, A7911 C:A1753, A:A1755 A:A1755, A:A1754
1k73 A8068 Oph·2Pout A:A2568(OP2) A3746, A4820, A6231, A7905, G920 A:A2569, G:A2567 A:A2569, A:A2568
1k73 A8045 Oph·2Pout G:A1979(OP2) A7830, A7882, A7883, A7884 G:A1998, C:A1999
1k73 A8092 Oph·2Pout C:A1844(OP2) A3640, A3655, A7914 A:A1843, A:A1845 A:A1845
1k73 A8019 Oph·2Pout A:A2011(OP2) A4147, A7250, A7796, A7797, A7798 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1k8a A8091 Oph·2Pout G:A918(OP1) A6048, A7401, A8693, A9137, A9911 C:A2294, A:A2465 A:A2465
1k8a A8083 Oph·2Pout A:A1754(OP2) A3294, A3738, A5924, A7396, A7448 C:A1753, A:A1755 A:A1755, A:A1754
1k8a A8019 Oph·2Pout A:A2011(OP2) A3737, A6792, A7333, A7334, A7335 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1k8a A8020 Oph·2Pout C:A1830(OP1) A7318, A7336, A8721, A8724, A8793 U:A1831, A:A1842 G:A1828 G:A1828, G:A1832
1k8a A8068 Oph·2Pout A:A2568(OP2) A3338, A4403, A5792, A7441, A9324 A:A2569, G:A2567 A:A2569, A:A2568
1k9m A8092 Oph·2Pout C:A1844(OP2) A3636, A3651, A7911 A:A1843, A:A1845 A:A1845
1k9m A8068 Oph·2Pout A:A2568(OP2) A3742, A4816, A6230, A7902, A9724 A:A2569, G:A2567 A:A2569, A:A2568
1kc8 A8068 Oph·2Pout A:A2568(OP2) A3756, A4818, A6223, A7892, G920 A:A2569, G:A2567 A:A2569, A:A2568

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>