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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2i2t:B2987, See in JSmolMgRNA representative site for type cis-2OP-OB Click on the image to toggle views


Site type: cis-2Oph·Ob

Schematic drawing for
cis-2Oph·Ob
MgRNA type cis-2OP-OB
List of all 98 Mg2+ binding sites with the site type cis-2Oph·Ob 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
3ccu 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04347, 07790, 07791 U:02535 U:0625 U:0626
3ccv 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04345, 07765, 07766 U:02535 U:0625 U:0626
3cxc 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 05265, 08651, 08652 U:02535 U:0625 U:0626
3df2 B3505 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B4506, B4507, B4508 G:B2581 G:B2583, G:B2608
3df4 B3496 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B4497, B4498, B4499 C:B2498 A:B2030
3df4 B3521 cis-2Oph·Ob G:B2582(OP2), G:B2583(OP2) U:B2584(O4) B4522, B4523, B4524 G:B2581 G:B2583
3i1n A3009 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3536, A3537, A3538 U:A569, A:A2030
3i1r A3008 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3533, A3534, A3535 U:A569, A:A2030
3i1t A3005 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3515, A3516, A3517 U:A569, A:A2030
3i1t A3016 cis-2Oph·Ob C:A1670(OP2), G:A2550(OP1) U:A1671(O4) A3288, A3550, A3551 U:A1671, C:A2551, A:A1669
3i20 A3008 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3534, A3535, A3536 A:A2030, A:A945
3oat A3006 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3516, A3517, A3518 U:A569, A:A2030
3ofc A3013 cis-2Oph·Ob G:A2582(OP2), G:A2583(OP2) U:A2584(O4) A3548, A3549, A3550 G:A2581 G:A2583, G:A2608
3ofr A3008 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3525, A3526, A3527 U:A569, A:A2030
3orb A3007 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3529, A3530, A3531 U:A569, A:A2030
3q3z V4 cis-2Oph·Ob A:V61(OP1), G:V62(OP2) U:V63(O4) V97, V98, V99
3q3z A82 cis-2Oph·Ob A:A61(OP1), G:A62(OP2) U:A63(O4) A87, A89, A90
3r8t A3008 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3560, A3561, A3562 C:A2498 U:A569, A:A2030
3v27 B215 cis-2Oph·Ob A:B57(OP2), A:B58(OP2) G:B23(O6) B316, B317, B318 G:B56 A:B59, C:B60, A:B58, U:B22
4qcr A3752 cis-2Oph·Ob A:A2460(OP1), C:A2511(OP1) G:A593(O6) A5262, A5263, A5264 U:A591 U:A592
4tov A3107 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3689, A3690, A3691 U:A2500 U:A569, A:A2030
4tox A3107 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3685, A3686, A3687 C:A2498 A:A2030, A:A945
4tpf A3107 cis-2Oph·Ob A:A2448(OP1), C:A2499(OP1) G:A570(O6) A3684, A3685, A3686 A:A2030

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>