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

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Representative site 3q3z:A6, See in JSmolMgRNA representative site for type trans-2OP      Click on the image to toggle views


Site type: trans-2Oph

Schematic drawing for
trans-2Oph

MgRNA type trans-2OP
List of all 282 Mg2+ binding sites with the site type trans-2Oph 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 6 of 12 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1n A2926 trans-2Oph A:A751(OP1), A:A1614(OP1) A3152, A3153, A3154, A3155 G:A1613 A:A751, C:A1617, A:A1614, A:A789
3i1p A2940 trans-2Oph U:A999(OP2), C:A1153(OP2) A3209, A3210, A3211, A3212 C:A998 C:A1152 G:A1154
3i1p A2927 trans-2Oph A:A751(OP1), A:A1614(OP1) A3157, A3158, A3159, A3160 G:A1613 C:A1615, A:A789
3i1r A2977 trans-2Oph C:A2579(OP1), C:A2611(OP2) A3385, A3386, A3387, A3388 U:A2580 G:A2576, C:A2610
3i1r A2982 trans-2Oph G:A370(OP2), A:A422(OP2) A3405, A3406, A3407, A3408 U:A369 A:A423, G:A370
3i1r A2926 trans-2Oph A:A751(OP1), A:A1614(OP1) A3150, A3151, A3152, A3153 G:A1613 A:A751, C:A1617, A:A1614, C:A1615, A:A789
3i1t A2927 trans-2Oph A:A751(OP1), A:A1614(OP1) A3158, A3159, A3160, A3161 A:A789
3i1t A2940 trans-2Oph U:A999(OP2), C:A1153(OP2) A3211, A3212, A3213, A3214 C:A998 C:A1152 G:A1154
3i20 A2926 trans-2Oph A:A751(OP1), A:A1614(OP1) A3152, A3153, A3154, A3155 G:A1613 A:A751, C:A1617, A:A1614, A:A789
3i20 A2977 trans-2Oph C:A2579(OP1), C:A2611(OP2) A3385, A3386, A3387, A3388 U:A2580 G:A2576, C:A2610
3i20 A2982 trans-2Oph G:A370(OP2), A:A422(OP2) A3405, A3406, A3407, A3408 G:A370, A:A423
3oar A1545 trans-2Oph G:A577(OP2), A:A814(OP2) A1628, A1629, A1630, A1631 A:A815
3oas A2927 trans-2Oph A:A751(OP1), A:A1614(OP1) A3156, A3157, A3158, A3159 G:A1613 A:A751, C:A1615
3ofc A2924 trans-2Oph A:A751(OP1), A:A1614(OP1) A3145, A3146, A3147, A3148 G:A1613 A:A751, C:A1617, A:A1614, C:A1615, A:A789
3ofc A2992 trans-2Oph A:A1359(OP1), G:A1360(OP2) A3456, A3457, A3458, A3459 G:A1361
3ofd A2927 trans-2Oph A:A751(OP1), A:A1614(OP1) A3156, A3157, A3158, A3159 G:A1613 A:A751, C:A1615, A:A789
3ofq A2928 trans-2Oph A:A751(OP1), A:A1614(OP1) A3155, A3156, A3157, A3158 G:A1613 A:A751, C:A1615, A:A789
3ofr A2993 trans-2Oph A:A1359(OP1), G:A1360(OP2) A3453, A3454, A3455, A3456 G:A1361
3ofr A2981 trans-2Oph G:A370(OP2), A:A422(OP2) A3398, A3399, A3400, A3401 U:A369 A:A423, G:A370
3ofr A2926 trans-2Oph A:A751(OP1), A:A1614(OP1) A3145, A3146, A3147, A3148 G:A1613 A:A751, C:A1617, A:A1614, A:A789
3ofz A2924 trans-2Oph A:A751(OP1), A:A1614(OP1) A3142, A3143, A3144, A3145 G:A1613 A:A751, A:A789, C:A1617, A:A1614
3og0 A2926 trans-2Oph A:A751(OP1), A:A1614(OP1) A3154, A3155, A3156, A3157 G:A1613 A:A751, A:A789
3orb A3026 trans-2Oph C:A787(OP1), U:A790(OP2) A3598, A3599, A3600, A3601 A:A789, C:A791 U:A790
3orb A2925 trans-2Oph A:A751(OP1), A:A1614(OP1) A3146, A3147, A3148, A3149 G:A1613 A:A751, C:A1617, A:A1614, C:A1615, A:A789
3owi A103 trans-2Oph A:A22(OP1), A:A75(OP2) A139, A140, A141, A142 C:A74 A:A75

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>