MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 3r8s:A2930, See in JSmolMgRNA representative site for type OP             Click on the image to toggle views

Site type: Oph

Schematic drawing for

MgRNA type OP
List of all 588 Mg2+ binding sites with the site type Oph 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
1evv A903 Oph G:A19(OP1) A918, A919, A920, A921, A922 G:A20, U:A59, C:A60, C:A56
1tra A79 Oph G:A19(OP1) A175, A176, A177, A178, A179 G:A20, U:A59, C:A60
1vs5 A1591 Oph G:A100(OP2) A1833, A1834, A1835, A1836, A1837 G:A64, C:A99, G:A100, A:A101
1vs5 A1555 Oph A:A937(OP2) A1656, A1657, A1658, A1659, A1660 G:A939
1vs5 A1572 Oph G:A21(OP1) A1743, A1744, A1745, A1746, A1747 G:A567, A:A573
1vs6 B2934 Oph U:B419(OP1) B3158, B3159, B3160, B3161, B3162 G:B230
1vs6 B2972 Oph A:B1678(OP2) B3336, B3337, B3338, B3339, B3340 A:B1678, A:B1679
1vs6 B2948 Oph U:B120(OP2) B3222, B3223, B3224, B3225, B3226 G:B122, G:B123, G:B121
1vs6 B3010 Oph A:B1676(OP2) B3494, B3495, B3496, B3497, B3498 C:B1675 A:B1677, A:B1676
1vs6 B2962 Oph A:B800(OP1) B3290, B3291, B3292, B3293, B3294 A:B191, C:B192
1vs7 A1575 Oph A:A572(OP1) A1763, A1764, A1765, A1766, A1767 A:A819
1vs7 A1587 Oph A:A608(OP2) A1816, A1817, A1818, A1819, A1820 A:A630, A:A609, C:A631, U:A610
1vs7 A1576 Oph G:A21(OP1) A1768, A1769, A1770, A1771, A1772 G:A568, G:A567 A:A573, G:A567
1vs7 A1604 Oph C:A980(OP1) A1896, A1897, A1898, A1899, A1900 G:A1221, G:A1220, A:A1219
1vs7 A1565 Oph A:A937(OP2) A1707, A1708, A1709, A1710, A1711 G:A939
1vs8 B2946 Oph A:B1678(OP2) B3216, B3217, B3218, B3219, B3220 A:B1679
1vs8 B2922 Oph A:B800(OP1) B3100, B3101, B3102, B3103, B3104 G:B799 A:B191, C:B192, A:B800
1vs8 B2945 Oph U:B120(OP2) B3211, B3212, B3213, B3214, B3215 G:B122, G:B123
1vs8 B2964 Oph U:B419(OP1) B3306, B3307, B3308, B3309, B3310 G:B230
1vt2 A2911 Oph U:A419(OP1) A3070, A3071, A3072, A3073, A3074 G:A230
1vt2 A2914 Oph G:A536(OP2) A3083, A3084, A3085, A3086, A3087
1vt2 A2987 Oph A:A299(OP2) A3434, A3435, A3436, A3437, U491 A:A299, G:A338, U:A339, A:A300
1vt2 A2958 Oph A:A1678(OP2) A3291, A3292, A3293, A3294, A3295 A:A1678, A:A1679
1vt2 A2922 Oph A:A621(OP2) A3133, A3134, A3135, L146 G:A620
1vt2 A2941 Oph A:A1156(OP2) A3214, A3215, A3216, A3217, A3218 C:A998, G:A1157, G:A997

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>