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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2945, See in JSmolMgRNA representative site for type OP-PO Click on the image to toggle views


Site type: Oph·Pout

Schematic drawing for
Oph·Pout
MgRNA type OP-PO
List of all 1301 Mg2+ binding sites with the site type Oph·Pout 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
3oxe A135 Oph·Pout A:A21(OP2) A150, A151, A152, A153, A154 A:A51 U:A19 A:A21, A:A22, U:A23, A:B53
3hhn C158 Oph·Pout C:C47(OP2) C157, C159, C160, C161, C162 G:C46 G:C45 C:C30
3hhn C164 Oph·Pout C:C1009(OP1) C163, C165, C166, C167, C168 A:C1010 A:C32, U:C84
4tp3 B201 Oph·Pout A:B58(OP2) B301, B302, B303, B304 A:B57 G:B56 A:B58, A:B59, U:B22, G:B23, C:B60
4tox B201 Oph·Pout A:B58(OP2) B301, B302, B303, B304 A:B57 G:B56 A:B58, U:B22, G:B23, A:B59
4pec B201 Oph·Pout A:B58(OP2) B301, B302, B303, B304 A:B57 G:B56 A:B58, U:B22, G:B23, A:B59
4too B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tp1 B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B101 A:B73 A:B101, G:B102
4pec B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tp9 B203 Oph·Pout G:B100(OP2) B310, B311, B312, B313, B314 A:B101 A:B73 A:B101, G:B102
4peb B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B101 A:B73 A:B101, G:B102
4tom B203 Oph·Pout G:B100(OP2) B310, B311, B312, B313, B314 A:B73 A:B101
4gau B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tp3 B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tpb B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tpd B203 Oph·Pout G:B100(OP2) B310, B311, B312, B313, B314 A:B101 A:B73 A:B101, G:B102
2qbz X204 Oph·Pout A:X72(OP2) X315, X316, X317, X318, X319 A:X71 C:X69, A:X72, G:X73
2qbz X205 Oph·Pout A:X63(OP2) X320, X321, X322, X323, X324 A:X64 U:X65, G:X76, A:X64, C:X77, C:X78, A:X63
3v25 B205 Oph·Pout G:B101(OP2) B306, B307, B308, B309 A:B73 G:B103, A:B102
3v29 B208 Oph·Pout U:B35(OP2) B315, B316, B317, B318, B319 C:B36
3v23 B210 Oph·Pout A:B25(OP1) B308, B309, B310, B311, B312 U:B55 G:B24
3v2d B211 Oph·Pout A:B25(OP1) B314, B315, B316, B317 U:B55 G:B24
3v27 B216 Oph·Pout A:B25(OP1) B319, B320, B321, B322, B323 G:B56 G:B24
1yls B241 Oph·Pout C:B233(OP2) B350, B351, B352, B353, B354 U:B234 G:B211, C:B235
1feu C314 Oph·Pout G:C100(OP2) C343, C344, C345, C346, C347 A:C101 A:C101, G:C100, G:C102

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>