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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qp1:B2994, See in JSmolMgRNA representative site for type OP-4PO Click on the image to toggle views


Site type: Oph·4Pout

Schematic drawing for
Oph·4Pout
MgRNA type OP-4PO
List of all 231 Mg2+ binding sites with the site type Oph·4Pout 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 10 | | | 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
2i2t B2920 Oph·4Pout G:B1828(OP1) B3094, B3095, B3096, B3097, B3098 A:B1773, G:B1972, G:B1973, A:B1772
2i2t B2917 Oph·4Pout G:B1333(OP2) B3079, B3080, B3081, B3082, B3083 C:B1314, G:B1332, G:B1334, U:B1313 G:B1334, G:B1333, C:B1335
2i2t B2992 Oph·4Pout C:B31(OP1) B3427, B3428, B3429, B3430, B3431 G:B1239, U:B1240, U:B1199, C:B1200
2i2v B2979 Oph·4Pout G:B1828(OP1) B3383, B3384, B3385, B3386, B3387 G:B1972, G:B1973, A:B1773, A:B1772
2i2v B2975 Oph·4Pout G:B1333(OP2) B3366, B3367, B3368, B3369, B3370 C:B1314, G:B1334, U:B1313, G:B1332 G:B1334, C:B1335
2otj 08091 Oph·4Pout G:0918(OP1) 03338, 06506, 07845, 09092, 09558 C:02294, C:02391, A:02465, U:0919 A:02465
2otl 08012 Oph·4Pout G:028(OP1) 03236, 03659, 07838, 09040, 09637 C:01305, U:01304, C:01343, G:01344
2qal A2038 Oph·4Pout A:A560(OP2) A2039, A2040, A2041, A2042, A2043 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
2qam B3499 Oph·4Pout C:B31(OP1) B4018, B4019, B4020, B4021, B4022 G:B1239, U:B1199, C:B1200, U:B1240
2qan A2023 Oph·4Pout A:A560(OP2) A2024, A2025, A2026, A2027, A2028 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
2qba B3499 Oph·4Pout C:B31(OP1) B4015, B4016, B4017, B4018, B4019 G:B1239, U:B1240, C:B1200, U:B1199
2qbb A2023 Oph·4Pout A:A560(OP2) A2388, A2389, A2390, A2391, A2392 U:A562, A:A563, G:A558, G:A557 A:A559 G:A566
2qbc B3515 Oph·4Pout C:B31(OP1) B4037, B4038, B4039, B4040, B4041 C:B1200, G:B1239, U:B1240, U:B1199
2qbc B3425 Oph·4Pout G:B1333(OP2) B3967, B3968, B3969, B3970, B3971 C:B1314, G:B1332, G:B1334, U:B1313 G:B1334, G:B1333
2qbd A2038 Oph·4Pout A:A560(OP2) A2039, A2040, A2041, A2042, A2043 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
2qbe B3072 Oph·4Pout G:B1333(OP2) B3669, B3670, B3671, B3672, B3673 C:B1314, G:B1332, G:B1334, U:B1313 G:B1333, C:B1335
2qbe B3499 Oph·4Pout C:B31(OP1) B4015, B4016, B4017, B4018, B4019 G:B1239, C:B1200, U:B1199, U:B1240 A:B1214
2qbh A1549 Oph·4Pout A:A560(OP2) A1635, A1636, A1637, A1638, A1639 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
2qbi B2920 Oph·4Pout G:B1828(OP1) B3085, B3086, B3087, B3088, B3089 A:B1773, G:B1972, G:B1973, A:B1772
2qbi B2992 Oph·4Pout C:B31(OP1) B3417, B3418, B3419, B3420, B3421 G:B1239, U:B1240, C:B1200, U:B1199
2qbj A1547 Oph·4Pout A:A560(OP2) A1623, A1624, A1625, A1626, A1627 U:A562, A:A563, G:A557, G:A558 A:A559
2qbk B2976 Oph·4Pout G:B1333(OP2) B3363, B3364, B3365, B3366, B3367 C:B1314, G:B1332, G:B1334, U:B1313 G:B1333
2qbk B3015 Oph·4Pout U:B963(OP1) B3511, B3512, B3513, B3514, B3515 C:B964, C:B2498, A:B2497, A:B947
2qex 08012 Oph·4Pout G:028(OP1) 03059, 03472, 07690, 08862, 09461 C:01305, U:01304, C:01343, G:01344
2qou A1549 Oph·4Pout A:A560(OP2) A1928, A1929, A1930, A1931, A1932 U:A562, A:A563, G:A557, G:A558 A:A559

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>