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

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Representative site 3i20:A2945, See in JSmolMgRNA representative site for type OP-PO          Click on the image to toggle views

Site type: Oph·Pout

Schematic drawing for

MgRNA type OP-PO
List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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
1feu C314 Oph·Pout G:C100(OP2) C343, C344, C345, C346, C347 A:C101 A:C101, G:C100, G:C102
1ffy T1203 Oph·Pout A:T14(OP2) T1304, T1305, T1306, T1307, A2198 G:T7 U:T8
1hr2 B10 Oph·Pout A:B173(OP2) B341, B342, B343, B344, B345 A:B172 A:B171 G:B174, A:B173, G:B175
1hr2 B13 Oph·Pout G:B112(OP2) B351, B352, B353, B354, B355 C:B204 A:B113, G:B112
1hr2 A9 Oph·Pout A:A173(OP2) A337, A338, A339, A340, A341 A:A172 A:A171 A:A173, G:A174
1jj2 08084 Oph·Pout A:01742(OP2) 03161, 07395, 08769, 08893, 09276 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1jj2 08039 Oph·Pout U:0115(OP2) 03493, 04637, 07363, 07364, 09434 G:0112 A:0114 A:0119, G:0118, A:0117
1k73 A8039 Oph·Pout U:A115(OP2) A3962, A5102, A7827, A7828, A9909 G:A112 A:A114 A:A119, G:A118, A:A117
1k73 A8084 Oph·Pout A:A1742(OP2) A3629, A7859, A9248, A9374, A9750 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1k8a A8039 Oph·Pout U:A115(OP2) A3554, A4682, A7364, A7365, A9500 G:A112 A:A119, G:A118, A:A117
1k8a A8084 Oph·Pout A:A1742(OP2) A3225, A7397, A8844, A8963, A9342 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1k9m A8039 Oph·Pout U:A115(OP2) A3957, A5102, A7825, A7826, A9897 G:A112 A:A114 A:A119, G:A118, A:A117
1k9m A8084 Oph·Pout A:A1742(OP2) A3626, A7858, A9249, A9370, A9741 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1k9m A8019 Oph·Pout A:A2011(OP2) A4143, A7246, A7793, A7794, A7795 A:A1941 U:A1890 G:A1891, C:A1892
1k9m A8083 Oph·Pout A:A1754(OP2) A3697, A4144, A6366, A7857, A7908 C:A1753 A:A1755, A:A1754
1kc8 A8083 Oph·Pout A:A1754(OP2) A3712, A4154, A6358, A7846, A7899 C:A1753 A:A1755, A:A1754
1kc8 A8039 Oph·Pout U:A115(OP2) A3970, A5106, A7815, A7816, A9906 G:A112 A:A114 A:A119, G:A118, A:A117
1kd1 A8039 Oph·Pout U:A115(OP2) A3959, A5105, A7812, A7813, A9900 G:A112 A:A114 A:A119, G:A118, A:A117
1kqs 08083 Oph·Pout A:01754(OP2) 03216, 03657, 05858, 07329, 07381 C:01753 A:01755, A:01754
1kqs 08039 Oph·Pout U:0115(OP2) 03472, 04602, 07298, 07299, 09419 G:0112 A:0114 A:0119, G:0118, A:0117
1kqs 08084 Oph·Pout A:01742(OP2) 03143, 07330, 08767, 08884, 09264 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1m1k A8047 Oph·Pout A:A1098(OP2) A5872, A7476, A9730 A:A1097 G:A1099
1m1k A8039 Oph·Pout U:A115(OP2) A3560, A4701, A7403, A7404, A9508 G:A112 A:A114 A:A119, G:A118, A:A117
1m1k A8083 Oph·Pout A:A1754(OP2) A3302, A3749, A5957, A7435, A7485 C:A1753 A:A1755, A:A1754
1m1k A8084 Oph·Pout A:A1742(OP2) A3229, A7436, A8841, A8964, A9347 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033

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>