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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qam:B3090, See in JSmolMgRNA representative site for type OP-2PO Click on the image to toggle views


Site type: Oph·2Pout

Schematic drawing for
Oph·2Pout
MgRNA type OP-2PO
List of all 1607 Mg2+ binding sites with the site type Oph·2Pout 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 3 of 65 | | | 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
1q7y A8092 Oph·2Pout C:A1844(OP2) A3155, A3169, A7372 A:A1843, A:A1845
1q81 A8092 Oph·2Pout C:A1844(OP2) A3158, A3173, A7383 A:A1843, A:A1845 A:A1845
1q81 A8039 Oph·2Pout U:A115(OP2) A4611, A7296, A7297, A9425 G:A112, G:A116 A:A119, G:A118, A:A117
1q81 A8068 Oph·2Pout A:A2568(OP2) A3265, A4330, A5735, A7374, A9248 A:A2569, G:A2567 A:A2569, A:A2568
1q81 A8036 Oph·2Pout G:A956(OP2) A3183, A7291, A7292, A7293, A8881 A:A1006, A:A955 A:A957, G:A956
1q86 A8068 Oph·2Pout A:A2568(OP2) A3278, A4341, A5745, A7394, A9257 A:A2569, G:A2567 A:A2569, A:A2568
1q86 A8040 Oph·2Pout U:A392(OP2) A3317, A4166, A7370, A7371, A9215 U:A391, C:A171
1q86 A8036 Oph·2Pout G:A956(OP2) A3196, A7313, A7314, A7315, A8893 A:A1006, A:A955 A:A957, G:A956
1q86 A8019 Oph·2Pout A:A2011(OP2) A3678, A6751, A7286, A7287, A7288 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1q86 A8020 Oph·2Pout C:A1830(OP1) A7270, A7289, A8643, A8646, A8719 U:A1831, A:A1842 G:A1828 G:A1828, G:A1832
1qu2 T1205 Oph·2Pout C:T25(OP1) T1312, T1313, T1314, A2199 G:T40, G:T26
1qvf 08092 Oph·2Pout C:01844(OP2) 03161, 03175, 07348 A:01843, A:01845 A:01845
1qvf 08045 Oph·2Pout G:01979(OP2) 07267, 07318, 07319, 07320 G:01998, C:01999
1qvf 08019 Oph·2Pout A:02011(OP2) 03662, 06709, 07234, 07235, 07236 A:01941, G:01891 U:01890 G:01891, C:01892
1qvf 08020 Oph·2Pout C:01830(OP1) 07220, 07237, 08643, 08646, 08720 U:01831, A:01842 G:01828 G:01828, G:01832
1qvf 08068 Oph·2Pout A:02568(OP2) 03266, 04316, 05710, 07340, 09256 A:02569, G:02567 A:02569, A:02568
1qvg 08083 Oph·2Pout A:01754(OP2) 03212, 03648, 05791, 07227, 07275 C:01753, A:01755 A:01755, A:01754
1qvg 08092 Oph·2Pout C:01844(OP2) 03151, 03166, 07278, 08908 A:01843, A:01845 A:01845
1qvg 08058 Oph·2Pout G:02013(OP2) 07204, 07205, A8622, A8624 U:01883, C:02626
1qvg 08019 Oph·2Pout A:02011(OP2) 03647, 06645, 07168, 07169, 07170 A:01941, G:01891 U:01890 G:01891
1qvg 08068 Oph·2Pout A:02568(OP2) 03257, 04300, 05662, 07270, E920 A:02569, G:02567 A:02569, A:02568
1qvg 08020 Oph·2Pout C:01830(OP1) 07153, 07171, 08644, 08647, 08721 U:01831, A:01842 G:01828 G:01828, A:01845, G:01832
1qvg 08039 Oph·2Pout U:0115(OP2) 03463, 04578, 07197, 09416 G:0112, G:0116 A:0114 A:0119, A:0117, G:0118
1qvg 08052 Oph·2Pout U:01125(OP1) 03128, 03357, 98390, 98530 C:01126, G:93092 C:01129, G:93090
1s72 08083 Oph·2Pout A:01754(OP2) 03229, 03676, 05881, 07349, 07403 C:01753, A:01755 A:01755, A:01754

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>