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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
1vs8 B2928 Oph·2Pout C:B2025(OP2) B3130, B3131, B3132, B3133, D231 G:B2024, U:B2034
1vs8 B2944 Oph·2Pout A:B574(OP2) B3206, B3207, B3208, B3209, B3210 U:B573, U:B576 U:B576, G:B577
1vs8 B2918 Oph·2Pout G:B1187(OP2) B3081, B3082, B3083, B3084, B3085 C:B817, C:B816 G:B1185 G:B818, G:B1187
1vs8 B2983 Oph·2Pout G:B2588(OP2) B3396, B3397, B3398, B3399, B3400 A:B2587, A:B2589 G:B2588, A:B2589
1vs8 B2974 Oph·2Pout G:B1333(OP2) B3356, B3357, B3358, B3359, B3360 C:B1314, G:B1332 G:B1333, G:B1334
1vt2 A2945 Oph·2Pout A:A2005(OP1) A3234, A3235, A3236, A3237 A:A1268, A:A1269
1vt2 A2959 Oph·2Pout C:A1774(OP1) A3296, A3297, A3298, A3299, A3300 U:A1775, A:A1786 A:A1772 G:A1776
1vt2 A2960 Oph·2Pout G:A1776(OP2) A3301, A3302, A3303, A3304, A3305 U:A1775, A:A1981 G:A1776
1vt2 A2999 Oph·2Pout C:A1658(OP1) A3491, A3492, A3493, A3494, A3495 G:A1659, U:A744 A:A743
1vt2 A3026 Oph·2Pout A:A1676(OP2) A3589, A3590, A3591, A3592, A3593 C:A1675, A:A1677 A:A1676, A:A1677
1vt2 A2976 Oph·2Pout A:A2270(OP2) A3380, A3381, A3382, A3383, A3384 A:A2267, G:A2271 G:A2271
1vt2 A2916 Oph·2Pout U:A567(OP1) A3094, A3095, A3096, A3097, A3098 G:A809, G:A808 U:A810, G:A809
1vt2 A2910 Oph·2Pout G:A297(OP2) A3066, A3067, A3068, A3069, U104 G:A338, G:A298 G:A297
1vt2 A2953 Oph·2Pout G:A1455(OP2) A3266, A3267, A3268, A3269, A3270 G:A1456, A:A1453 G:A1456
1vt2 A3017 Oph·2Pout G:A862(OP2) A3554, A3555, A3556, A3557, A3558 A:A861, A:A910 G:A862, A:A863
1vt2 A2965 Oph·2Pout A:A1970(OP2) A3327, A3328, A3329, A3330, A3331 A:A1900, G:A1835 U:A1834 G:A1835
1vt2 A2913 Oph·2Pout A:A526(OP1) A3079, A3080, A3081, A3082 A:A528, C:A527
1vt2 A2957 Oph·2Pout U:A1671(OP2) A3287, A3288, A3289, A3290 C:A1670, G:A2550
1vt2 A2993 Oph·2Pout A:A981(OP1) A3463, A3464, A3465, A3466, A3467 C:A982, G:A978
1xjr A201 Oph·2Pout A:A12(OP2) A208, A209, A210, A211, A212 G:A13, G:A11 C:A10 G:A13, U:A37, A:A38, G:A14, A:A12
1yhq 08026 Oph·2Pout G:0956(OP2) 04167, 08321, 08322, 08323, 09866 A:01006, A:0955 A:0957, G:0956
1yhq 08014 Oph·2Pout C:01830(OP1) 08282, 08301, 09619, 09622, 09696 U:01831, A:01842 G:01828 G:01828, G:01832
1yhq 08013 Oph·2Pout A:02011(OP2) 04643, 07691, 08298, 08299, 08300 A:01941, G:01891 U:01890 G:01891, C:01892
1yhq 08064 Oph·2Pout A:01754(OP2) 04204, 04644, 06828, 08357, 08414 C:01753, A:01755 A:01755, A:01754
1yi2 08020 Oph·2Pout C:01830(OP1) 07726, 07745, 09121, 09124, 09195 U:01831, A:01842 G:01828 G:01828, G:01832

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>