`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
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
Oph·Pout
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"
Page 1 of 53 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2otl 08092 Oph·Pout C:01844(OP2) 03656, 03671, 07882, 09387 A:01843 A:01845
1k9m A8084 Oph·Pout A:A1742(OP2) A3626, A7858, A9249, A9370, A9741 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1yij 08084 Oph·Pout A:01742(OP2) 03644, 07818, 09250, 09377, 09755 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1s72 08084 Oph·Pout A:01742(OP2) 03156, 07350, 08769, 08893, 09274 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
2otj 08084 Oph·Pout A:01742(OP2) 03654, 07841, 09255, 09382, 09763 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1m1k A8084 Oph·Pout A:A1742(OP2) A3229, A7436, A8841, A8964, A9347 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1yi2 08084 Oph·Pout A:01742(OP2) 03632, 07805, 09249, 09376, 09754 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
3cc2 08084 Oph·Pout A:01742(OP2) 03188, 07408, 08778, 08906, 09290 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1vq6 08084 Oph·Pout A:01742(OP2) 03068, 03943, 08129, 09575, 09696 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1q82 A8084 Oph·Pout A:A1742(OP2) A3147, A7319, A8768, A8892, A9261 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1vq5 08084 Oph·Pout A:01742(OP2) 03074, 03951, 08165, 09573, 09699 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1vql 08084 Oph·Pout A:01742(OP2) 03365, 04227, 08374 G:02033 G:02033, G:01743, G:01744, G:01745, A:01742
1k8a A8084 Oph·Pout A:A1742(OP2) A3225, A7397, A8844, A8963, A9342 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1qvf 08084 Oph·Pout A:01742(OP2) 03151, 08772, 08895, 09273 G:02033 G:01744, G:01745, G:01743, G:02033
1k73 A8084 Oph·Pout A:A1742(OP2) A3629, A7859, A9248, A9374, A9750 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1vqm 08084 Oph·Pout A:01742(OP2) 03367, 04234, 08375 G:02033 G:02033, G:01743, G:01744, G:01745, A:01742
3cxc 08084 Oph·Pout A:01742(OP2) 03236, 03361, 03727, 04583, 08740 G:02033 G:01743, G:01744, G:01745, G:02033, A:01742
2otl 08084 Oph·Pout A:01742(OP2) 03646, 07828, 09250, 09375, 09757 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1vq7 08084 Oph·Pout A:01742(OP2) 03073, 03959, 08160, 09577, 09699 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1yj9 08084 Oph·Pout A:01742(OP2) 03449, 07628, 09070, 09193, 09569 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1vq4 08084 Oph·Pout A:01742(OP2) 03067, 03940, 08121, 09569, 09694 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
2qex 08084 Oph·Pout A:01742(OP2) 03459, 07680, 09074, 09198, 09582 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1vqp 08084 Oph·Pout A:01742(OP2) 03376, 04246, 08395 G:02033 G:02033, G:01743, G:01744, G:01745, A:01742
1vqn 08084 Oph·Pout A:01742(OP2) 03363, 04230, 08367 G:02033 G:02033, G:01743, G:01744, G:01745, A:01742
1n8r A8084 Oph·Pout A:A1742(OP2) A3146, A4030, A8402, A9647, A9768 G:A2033 G:A2033, G:A1744, G:A1745, A:A1742, G:A1743

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
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>