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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"
Page 1 of 53 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1hr2 A9 Oph·Pout A:A173(OP2) A337, A338, A339, A340, A341 A:A172 A:A171 A:A173, G:A174
1hr2 B10 Oph·Pout A:B173(OP2) B341, B342, B343, B344, B345 A:B172 A:B171 G:B174, A:B173, G:B175
1hr2 B13 Oph·Pout G:B112(OP2) B351, B352, B353, B354, B355 C:B204 A:B113, G:B112
1pjo A32 Oph·Pout G:A5(OP2) A136, A137, A138, A139, A140 A:A6 G:A5, A:A6
2i2p X62 Oph·Pout U:X6(OP1) A1897, X366, X367, X368, X369 U:X5 U:X2, U:X6 G:A1497, U:A1498
4m2z C101 Oph·Pout A:C2(OP1) A606, C204, C205 C:C103
3oxb A101 Oph·Pout A:A34(OP1) A132, A133, A134, A135, A136 G:A35 G:A35, G:A36
4m2z D101 Oph·Pout A:D2(OP1) B403, D207, D208 C:D103
1xjr A101 Oph·Pout A:A12(OP1) A203, A204, A205, A206, A207 G:A13 G:A34, G:A36, G:A35
3ox0 A101 Oph·Pout A:A34(OP1) A131, A132, A133, A134, A135 G:A35 G:A35, G:A36
4oji A105 Oph·Pout DU:A6(OP1) A209, A210, A211, A212, A213 C:A5 G:A47
3owz A105 Oph·Pout C:A70(OP2) A135, A136, A137, A138 A:A71 U:A69 A:A71, G:A72
4enb A111 Oph·Pout A:A40(OP2) A214, A221, A223, A224, A225 G:A39 A:A40 U:A7, A:A49, C:A50
3ox0 B115 Oph·Pout A:B34(OP1) B144, B145, B146, B147, B148 G:B35 G:B36, G:B35
3oww A116 Oph·Pout A:A78(OP2) A177, A178, A179, A180, A181 A:A77 A:A78, G:A79, G:A80
3owi A116 Oph·Pout A:A78(OP2) A177, A178, A179, A180, A181 A:A77 A:A78, G:A79, G:A80
3oww B117 Oph·Pout U:B23(OP1) B152, B153, B154, B155, B156 C:B24 G:B26, G:B25
3owi B117 Oph·Pout U:B23(OP1) B153, B154, B155, B156, B157 G:B25 G:B26, G:B25
4jf2 A118 Oph·Pout U:A53(OP1) A317, A318, A319, A320 U:A54
3oww B118 Oph·Pout A:B78(OP2) B157, B158, B159, B160, B161 A:B77 G:B79, G:B80, A:B78
3owi A118 Oph·Pout A:A21(OP2) A182, A183, A184, A185, A186 A:A51 U:A19 A:A21, A:A22, U:A23, A:B53
3oww A120 Oph·Pout A:A21(OP2) A187, A188, A189, A190, A191 A:A51 U:A19 A:A21, A:A22, U:A23, A:B53
3oww B121 Oph·Pout A:B52(OP2) B162, B163, B164, B165, B166 A:B51 A:B52, G:B49
3i1r B123 Oph·Pout G:B100(OP2) B661, B662, B663, B664, B665 A:B101 A:B101, G:B102
3oxb B129 Oph·Pout A:B34(OP1) B136, B137, B138, B139, B140 G:B35 G:B35, G:B36

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>