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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qam:B3090, See in JSmolMgRNA representative site for type OP-2PO Click on the image to toggle views


Site type: Oph·2Pout

Schematic drawing for
Oph·2Pout
MgRNA type OP-2PO
List of all 1607 Mg2+ binding sites with the site type Oph·2Pout 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
1vs6 B2925 Oph·2Pout G:B1187(OP2) B3116, B3117, B3118, B3119, B3120 C:B816, C:B817 G:B1185 G:B1187, G:B818
1vs6 B2905 Oph·2Pout A:B802(OP1) B3015, B3016, B3017, B3018, B3019 G:B674, A:B675 U:B803, A:B804
1vs6 B2974 Oph·2Pout G:B1776(OP2) B3346, B3347, B3348, B3349, B3350 U:B1775, A:B1981 G:B1776
1vs6 B2952 Oph·2Pout U:B567(OP1) B3241, B3242, B3243, B3244, L343 G:B808, G:B809 U:B810
1vs6 B2949 Oph·2Pout U:B120(OP1) B3227, B3228, B3229, B3230, B3231 G:B122, G:B123 G:B123, G:B124
1vs6 B2975 Oph·2Pout C:B2025(OP2) B3351, B3352, B3353, B3354, B3355 G:B2024, U:B2034
1vs6 B2927 Oph·2Pout A:B1970(OP2) B3125, B3126, B3127, B3128, B3129 G:B1835, A:B1900 U:B1834 G:B1835
1vs6 B2981 Oph·2Pout A:B2270(OP2) B3377, B3378, B3379, B3380, B3381 G:B2269, A:B2267 G:B2271
1vs6 B3000 Oph·2Pout A:B1938(OP2) B3451, B3452, B3453, B3454, B3455 C:B1958, C:B1957
1vs6 B2973 Oph·2Pout C:B1774(OP1) B3341, B3342, B3343, B3344, B3345 U:B1775, A:B1786 A:B1772 A:B1772, G:B1776
1vs6 B2929 Oph·2Pout U:B1313(OP1) B3133, B3134, B3135, B3136, B3137 G:B1333, G:B1334
1vs7 A1598 Oph·2Pout C:A536(OP1) A1868, A1869, A1870, A1871, A1872 C:A504, G:A537 C:A522
1vs7 A1544 Oph·2Pout U:A891(OP2) A1606, A1607, A1608, A1609, A1610 A:A892, G:A903 U:A905, A:A906, U:A904
1vs7 A1554 Oph·2Pout C:A1195(OP1) A1655, A1656, A1657, A1658, A1659 A:A1196, A:A1398 A:A1398
1vs7 A1588 Oph·2Pout A:A1110(OP2) A1821, A1822, A1823, A1824, A1825 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
1vs7 A1591 Oph·2Pout U:A1224(OP1) A1834, A1835, A1836, A1837 G:A951, U:A952 C:A1223
1vs8 B2912 Oph·2Pout G:B1776(OP2) B3052, B3053, B3054, B3055, B3056 U:B1775, A:B1981 G:B1776
1vs8 B2944 Oph·2Pout A:B574(OP2) B3206, B3207, B3208, B3209, B3210 U:B573, U:B576 U:B576, G:B577
1vs8 B2973 Oph·2Pout U:B1313(OP1) B3351, B3352, B3353, B3354, B3355 G:B1333, G:B1334
1vs8 B2906 Oph·2Pout C:B1774(OP1) B3020, B3021, B3022, B3023, B3024 U:B1775, A:B1786 A:B1772 A:B1772
1vs8 B2939 Oph·2Pout A:B2270(OP2) B3186, B3187, B3188, B3189, B3190 A:B2267, G:B2271 G:B2271
1vs8 B2911 Oph·2Pout A:B1970(OP2) B3047, B3048, B3049, B3050, B3051 G:B1835, A:B1900 U:B1834 G:B1835
1vs8 B2983 Oph·2Pout G:B2588(OP2) B3396, B3397, B3398, B3399, B3400 A:B2587, A:B2589 G:B2588, A:B2589
1vs8 B2948 Oph·2Pout G:B297(OP2) B3225, B3226, B3227, B3228, B3229 U:B296, G:B338 G:B298
1vs8 B2972 Oph·2Pout A:B802(OP1) B3346, B3347, B3348, B3349, B3350 G:B674, A:B675 U:B803, A:B804

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>