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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qov:B2933, See in JSmolMgRNA representative site for type OP-3PO Click on the image to toggle views


Site type: Oph·3Pout

Schematic drawing for
Oph·3Pout
MgRNA type OP-3PO
List of all 867 Mg2+ binding sites with the site type Oph·3Pout 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 3 of 35 | | | 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
1m90 A8037 Oph·3Pout A:A2553(OP2) A3177, A7396, A8597, A9657, A9735 A:A2576, U:A2554, C:A2575 C:A2552 A:A2576
1n8r A8032 Oph·3Pout U:A2115(OP1) A3380, A4121, A4184, A4582, C8640 G:A2272, C:A2273, U:A2116
1n8r A8045 Oph·3Pout G:A1979(OP2) A8312, A8423, A8424, A8425 G:A1998, C:A1999, A:A1978
1n8r A8017 Oph·3Pout G:A456(OP2) A7772, A8248, A9809, E8359, E8363 A:A455, U:A457, G:A458
1n8r A8035 Oph·3Pout G:A1484(OP2) A4111, A8293, A8294, A8417, A8418 C:A1456, A:A1485, C:A1455 G:A1484, U:A1457
1n8r A8091 Oph·3Pout G:A918(OP1) A3714, A6870, A8406, A9495, A9937 C:A2294, C:A2391, A:A2465 A:A2465
1n8r A8021 Oph·3Pout G:A2304(OP2) A3353, A4033, A4034, A8254, A8255 A:A2301, A:A2303, A:A2305 U:A2306, A:A2305, G:A2304
1nji A8037 Oph·3Pout A:A2553(OP2) A3132, A3206, A3641, A7858, A9079 C:A2575, A:A2576, U:A2554 C:A2552 A:A2576
1nji A8032 Oph·3Pout U:A2115(OP1) A3716, A3779, A4181, A9984, C8629 U:A2116, G:A2272, C:A2273
1nji A8021 Oph·3Pout G:A2304(OP2) A3631, A3632, A7761, A7762, A9958 A:A2301, A:A2305, A:A2303 A:A2305, G:A2304, U:A2306
1nji A8072 Oph·3Pout U:A954(OP1) A3228, A3987, A7412, A7829, A7888 C:A2298, G:A2299, A:A2301
1q7y A8040 Oph·3Pout U:A392(OP2) A3297, A7340, A7341, A9208 C:A171, U:A172, U:A391
1q7y A8058 Oph·3Pout G:A2013(OP2) A3272, A7296, A7297, C8630, C8632 G:A1884, U:A1883, C:A2626
1q7y A8032 Oph·3Pout U:A2115(OP1) A3235, A3296, A3696, A9506, C8629 U:A2116, G:A2272, C:A2273
1q7y A8021 Oph·3Pout G:A2304(OP2) A3149, A7244, A7245, A9479 A:A2305, A:A2303, A:A2301 A:A2305, G:A2304, U:A2306
1q7y A8035 Oph·3Pout G:A1484(OP2) A3225, A7280, A7281, A7336, A7337 C:A1455, C:A1456, A:A1485 C:A1483 G:A1484, U:A1457
1q81 A8037 Oph·3Pout A:A2553(OP2) A3161, A7347, A8603, A9646, A9725 A:A2576, U:A2554, C:A2575 C:A2552 A:A2576
1q81 A8017 Oph·3Pout G:A456(OP2) A3134, A7246, A8926, E8361, E8464 A:A455, U:A457, G:A458
1q81 A8032 Oph·3Pout U:A2115(OP1) A3238, A3301, A9504, C8565, C8641 U:A2116, G:A2272, C:A2273 G:A2271
1q81 A8035 Oph·3Pout G:A1484(OP2) A3228, A7289, A7290, A7345, A7346 C:A1456, A:A1485, C:A1455 G:A1484, U:A1457
1q81 A8040 Oph·3Pout U:A392(OP2) A4148, A7349, A7350, A9204 C:A171, U:A172, U:A391
1q81 A8091 Oph·3Pout G:A918(OP1) A5984, A7333, A8617, A9060, A9837 C:A2294, C:A2391, A:A2465 A:A2465
1q81 A8021 Oph·3Pout G:A2304(OP2) A3151, A3152, A7252, A7253, A9479 A:A2301, A:A2305, A:A2303 A:A2305, G:A2304, U:A2306
1q82 A8058 Oph·3Pout G:A2013(OP2) A3274, A7296, A7297, C8646, C8648 G:A1884, U:A1883, C:A2626
1q82 A8091 Oph·3Pout G:A918(OP1) A5969, A7323, A8613, A9834 C:A2294, C:A2391, A:A2465 A:A2465

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>