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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
Oph
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
3ofp A1547 Oph C:A934(OP1) A1638, A1639, A1640, A1641, A1642
3ofp A1551 Oph C:A1054(OP2) A1657, A1658, A1659, A1660 G:A1053 G:A1198
3ofq A2958 Oph A:A1678(OP2) A3291, A3292, A3293, A3294, A3295 A:A1678, A:A1679
3ofq A2987 Oph A:A299(OP2) A3432, A3433, A3434, U491, U495 A:A299, G:A338, U:A339, A:A300
3ofq A2911 Oph U:A419(OP1) A3070, A3071, A3072, A3073, A3074 G:A230
3ofq A2941 Oph A:A1156(OP2) A3215, A3216, A3217, A3218, A3219 C:A998, G:A1157, G:A997
3ofq A2923 Oph A:A621(OP2) A3132, A3133, L147, L148
3ofq A2914 Oph G:A536(OP2) A3083, A3084, A3085, A3086, A3087
3ofr A2911 Oph U:A419(OP1) A3072, A3073, A3074, A3075, A3076 G:A230
3ofr A2930 Oph A:A800(OP1) A3162, A3163, A3164, A3165, A3166 G:A799 A:A191, C:A192, A:A800
3ofr A2980 Oph A:A299(OP2) A3393, A3394, A3395, A3396, A3397 A:A299, G:A338, U:A339
3ofr A2956 Oph A:A1678(OP2) A3279, A3280, A3281, A3282, A3283 A:A1678, A:A1679
3ofx A1557 Oph G:A21(OP1) A1693, A1694, A1695, A1696, A1697 G:A568, G:A567 G:A567, A:A573, A:A574
3ofx A1548 Oph A:A937(OP2) A1647, A1648, A1649, A1650, A1651 A:A937, A:A938, G:A939
3ofy A1563 Oph A:A1433(OP2) A1715, A1716, A1717, A1718, A1719 C:A1466, A:A1434
3ofy A1558 Oph G:A21(OP1) A1692, A1693, A1694, A1695, A1696 G:A568, G:A567 A:A573, G:A567
3ofy A1547 Oph C:A934(OP1) A1638, A1639, A1640, A1641, A1642
3ofy A1571 Oph G:A100(OP2) A1750, A1751, A1752, A1753, A1754 G:A64, G:A100, A:A101
3ofz A2978 Oph A:A299(OP2) A3385, A3386, A3387, A3388, A3389 U:A339, A:A299, G:A338
3ofz A2928 Oph A:A800(OP1) A3157, A3158, A3159, A3160, A3161 A:A191, C:A192, A:A800
3ofz A2910 Oph U:A419(OP1) A3069, A3070, A3071, A3072, A3073 G:A230
3og0 A2908 Oph U:A120(OP2) A3059, A3060, A3061, A3062, A3063 G:A123, G:A124
3og0 A2985 Oph A:A299(OP2) A3430, A3431, A3432, A3433, U491 A:A299, G:A338, U:A339, A:A300
3og0 A2929 Oph A:A800(OP1) A3170, A3171, A3172, A3173, A3174 G:A799, A:A203 A:A191
3og0 A2956 Oph A:A1678(OP2) A3288, A3289, A3290, A3291, A3292 A:A1679

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>