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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbg:B2930, See in JSmolMgRNA representative site for type PO-4BO Click on the image to toggle views


Site type: Pout·4Bout

Schematic drawing for
Pout·4Bout
MgRNA type PO-4BO
List of all 135 Mg2+ binding sites with the site type Pout·4Bout 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 6 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1hr2 B17 Pout·4Bout B362, B363, B364, B365, B366, B367 A:B114 A:B115, G:B116, U:B205, G:B117
1vs5 A1549 Pout·4Bout A1629, A1630, A1631, A1632, A1633, A1634 U:A644 G:A645, U:A593, U:A644, G:A646
1vs8 B2923 Pout·4Bout B3105, B3106, B3107, B3108, B3109, B3110 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009
1vt2 A2980 Pout·4Bout A3401, A3402, A3403, A3404, A3405, A3406 G:A2454 G:A2455, C:A2496, G:A2454, A:A2453
1vt2 A2943 Pout·4Bout A3224, A3225, A3226, A3227, A3228, A3229 U:A1267 A:A2009, G:A2010, U:A2011, G:A2012
2aw4 B2983 Pout·4Bout B3384, B3385, B3386, B3387, B3388, B3389 C:B2452 G:B2454, A:B2497, G:B2455, C:B2496
2awb B2923 Pout·4Bout B3106, B3107, B3108, B3109, B3110, B3111 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009
2awb B2930 Pout·4Bout B3140, B3141, B3142, B3143, B3144, B3145 A:B2453 A:B2453, G:B2454, A:B2497, G:B2455
2i2p A1562 Pout·4Bout A1697, A1698, A1699, A1700, A1701, A1702 G:A266 G:A257, G:A259, G:A258, U:A268
2i2v B2930 Pout·4Bout B3150, B3151, B3152, B3153, B3154, B3155 A:B2453 A:B2453, G:B2454, A:B2497, G:B2455
2i2v B2923 Pout·4Bout B3115, B3116, B3117, B3118, B3119, B3120 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009
2qal A2115 Pout·4Bout A2116, A2117, A2118, A2119, A2120, A2121 G:A266 G:A257, U:A268, G:A258, G:A259
2qal A2129 Pout·4Bout A2130, A2131, A2132, A2133, A2134, A2135 A:A559 U:A24, G:A9, A:A10, A:A559
2qam B3103 Pout·4Bout B3694, B3695, B3696, B3697, B3698, B3699 U:B1267 G:B2010, U:B2011, G:B2012, A:B2009
2qan A2141 Pout·4Bout A2142, A2143, A2144, A2145, A2146, A2147 G:A266 G:A257, G:A258, U:A268, G:A259
2qao B3110 Pout·4Bout B3708, B3709, B3710, B3711, B3712, B3713 U:B1267 A:B2009, U:B2011, G:B2012, G:B2010
2qba B3103 Pout·4Bout B3694, B3695, B3696, B3697, B3698, B3699 U:B1267 G:B2010, U:B2011, G:B2012, A:B2009
2qbc B3110 Pout·4Bout B3710, B3711, B3712, B3713, B3714, B3715 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009
2qbe B3103 Pout·4Bout B3695, B3696, B3697, B3698, B3699, B3700 U:B1267 G:B2010, U:B2011, G:B2012, A:B2009
2qbg B2930 Pout·4Bout B3142, B3143, B3144, B3145, B3146, B3147 A:B2453 A:B2453, G:B2454, A:B2497, G:B2455
2qbg B2923 Pout·4Bout B3107, B3108, B3109, B3110, B3111, B3112 U:B1267 U:B2011, G:B2012, A:B2009, G:B2010
2qbi B2922 Pout·4Bout B3096, B3097, B3098, B3099, B3100, B3101 U:B1267 G:B2010, U:B2011, G:B2012, A:B2009
2qbj A1562 Pout·4Bout A1693, A1694, A1695, A1696, A1697, A1698 U:A644 G:A592, U:A593, G:A646, G:A645
2qbk B2923 Pout·4Bout B3106, B3107, B3108, B3109, B3110, B3111 U:B1267 A:B2009, U:B2011, G:B2012, G:B2010
2qox B2923 Pout·4Bout B3104, B3105, B3106, B3107, B3108, B3109 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009

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>