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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
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 5 of 53 | | | 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
1vt2 A3035 Oph·Pout A:A943(OP2) A3634, A3635, A3636, A3637, A3638 U:A832
1vt2 A2931 Oph·Pout A:A800(OP1) A3171, A3172, A3173, A3174, A3175 A:A204 G:A799, A:A203 A:A190, A:A191
1vt2 A2908 Oph·Pout U:A120(OP2) A3056, A3057, A3058, A3059, A3060 G:A121 A:A119 G:A122, G:A123
1vt2 A2955 Oph·Pout A:A1664(OP2) A3276, A3277, A3278, A3279, A3280 G:A1992 G:A1667, A:A1664, A:A1665, G:A1992, G:A1666
1vt2 A2989 Oph·Pout A:A572(OP1) A3442, A3443, A3444, A3445, A3446 A:A983 U:A573
1vt2 A2996 Oph·Pout A:A1327(OP2) A3476, A3477, A3478, A3479, A3480 U:A1326 G:A1324
1vt2 A2970 Oph·Pout G:A2502(OP2) A3353, A3354, A3355, A3356 G:A2061 A:A2060, G:A2502 G:A2446
1vt2 A2918 Oph·Pout A:A574(OP2) A3104, A3105, A3106, A3107, A3108 U:A576 U:A576, G:A577
1vt2 A2909 Oph·Pout U:A120(OP1) A3061, A3062, A3063, A3064, A3065 G:A123 G:A123, G:A124
1xjr A101 Oph·Pout A:A12(OP1) A203, A204, A205, A206, A207 G:A13 G:A34, G:A36, G:A35
1yhq 08065 Oph·Pout A:01742(OP2) 03254, 04130, 08358, 09749, 09873 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1yhq 08029 Oph·Pout U:0115(OP2) 03413, 04458, 05579, 08326, 08327 G:0112 A:0114 G:0118, A:0119
1yi2 08039 Oph·Pout U:0115(OP2) 03962, 05086, 07774, 07775, 09916 G:0112 A:0114 A:0119, G:0118, A:0117
1yi2 08051 Oph·Pout G:0641(OP2) 04099, 07778, 07779 A:01355 G:0642, A:01355
1yi2 08084 Oph·Pout A:01742(OP2) 03632, 07805, 09249, 09376, 09754 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yij 08084 Oph·Pout A:01742(OP2) 03644, 07818, 09250, 09377, 09755 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yij 08039 Oph·Pout U:0115(OP2) 03976, 05110, 07786, 07787, 09917 G:0112 A:0114 A:0119, G:0118
1yj9 08083 Oph·Pout A:01754(OP2) 03522, 03973, 06164, 07627, 07675 C:01753 A:01755, A:01754
1yj9 08084 Oph·Pout A:01742(OP2) 03449, 07628, 09070, 09193, 09569 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yjn 08039 Oph·Pout U:0115(OP2) 03982, 05118, 07799, 09919 G:0112 A:0114 A:0119, G:0118
1yjn 08068 Oph·Pout A:02568(OP2) 03766, 04842, 06236, 07875, E920 G:02567 A:02569, A:02568
1yjn 08051 Oph·Pout G:0641(OP2) 04119, 07803, 07804 A:01355 A:01355
1yjn 08084 Oph·Pout A:01742(OP2) 03647, 07831, 09253, 09378, 09757 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
1yls B241 Oph·Pout C:B233(OP2) B350, B351, B352, B353, B354 U:B234 G:B211, C:B235
2avy A1577 Oph·Pout A:A1433(OP2) A1767, A1768, A1769, A1770, A1771 A:A1434 A:A1434, G:A1435

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>