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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2aw4:B2955, See in JSmolMgRNA representative site for type 4PO-RO         Click on the image to toggle views


Site type: 4Pout·Rout

Schematic drawing for
4Pout·Rout

MgRNA type 4PO-RO
List of all 51 Mg2+ binding sites with the site type 4Pout·Rout 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1hr2 A14 4Pout·Rout A347, A348, A349, A350, A351, A352 A:A113, U:A202, C:A128, C:A203 C:A127
1vs8 B2966 4Pout·Rout B3315, B3316, B3317, B3318, B3319, B3320 G:B559, A:B1008, G:B2038, C:B560 C:B1007
1vs8 B2935 4Pout·Rout B3165, B3166, B3167, B3168, B3169, B3170 U:B2017, G:B579, U:B2016, G:B578 U:B1255
2aw4 B2955 4Pout·Rout B3251, B3252, B3253, B3254, B3255, E206 G:B579, U:B2017, U:B2016, A:B2058 U:B1255
2awb B2936 4Pout·Rout B3169, B3170, B3171, B3172, B3173, B3174 U:B2017, G:B579, U:B2016, G:B578 U:B1255
2qam B3295 4Pout·Rout B3851, B3852, B3853, B3854, B3855, B3856 G:B578, U:B2016, G:B579, U:B2017 U:B1255
2qao B3189 4Pout·Rout B3774, B3775, B3776, B3777, B3778, B3779 G:B579, U:B2017, U:B2016, G:B578 U:B1255
2qba B3295 4Pout·Rout B3853, B3854, B3855, B3856, B3857, B3858 G:B578, U:B2016, G:B579, U:B2017 U:B1255
2qbc B3189 4Pout·Rout B3774, B3775, B3776, B3777, B3778, B3779 G:B579, U:B2017, U:B2016, G:B578 U:B1255
2qbe B3295 4Pout·Rout B3851, B3852, B3853, B3854, B3855, B3856 G:B578, U:B2016, G:B579, U:B2017 U:B1255
2qbf A1596 4Pout·Rout A1868, A1869, A1870, A1871, A1872 C:A536, G:A537, A:A523, C:A503 C:A522
2qbg B2968 4Pout·Rout B3326, B3327, B3328, B3329, B3330, B3331 G:B559, C:B560, G:B2038, A:B1008 C:B1007
2qbg B2936 4Pout·Rout B3173, B3174, B3175, B3176, B3177, B3178 U:B2017, G:B578, G:B579, U:B2016 U:B1255
2qbi B2955 4Pout·Rout B3252, B3253, B3254, B3255, B3256, B3257 G:B578, G:B579, U:B2016, U:B2017 U:B1255
2qov B2955 4Pout·Rout B3255, B3256, B3257, B3258, B3259, B3260 G:B578, U:B2016, G:B579, U:B2017 U:B1255
2qox B2936 4Pout·Rout B3170, B3171, B3172, B3173, B3174, B3175 G:B578, U:B2017, U:B2016, G:B579 U:B1255
2qoz B2955 4Pout·Rout B3746, B3747, B3748, B3749, B3750, B3751 G:B578, G:B579, U:B2016, U:B2017 U:B1255
2qp1 B2936 4Pout·Rout B3676, B3677, B3678, B3679, B3680, B3681 G:B579, U:B2017, U:B2016, G:B578 U:B1255
2z4l B2909 4Pout·Rout B3033, B3034, B3035, B3036, B3037, B3038 C:B560, A:B1008, G:B559, G:B2038 C:B1007
2z4n B2969 4Pout·Rout B3324, B3325, B3326, B3327, B3328, B3329 C:B560, A:B1008, G:B2038, G:B559 C:B1007
2z4n B2937 4Pout·Rout B3172, B3173, B3174, B3175, B3176, B3177 G:B579, U:B2017, U:B2016, G:B578 U:B1255
3df4 B3375 4Pout·Rout B4376, B4377, B4378, B4379, B4380, B4381 G:B559, C:B560, G:B2038, A:B1008 C:B1007
3df4 B3189 4Pout·Rout B4190, B4191, B4192, B4193, B4194, B4195 G:B579, U:B2017, G:B578, U:B2016 U:B1255
3i1p A2998 4Pout·Rout A3481, A3482, A3483, A3484, A3485, A3486 U:A1636, G:A1300, G:A1299, A:A1637 A:A1635
3i1t A2914 4Pout·Rout A3089, A3090, A3091, A3092, A3093, A3094 C:A560, A:A1008, G:A559, G:A2038 C:A1007

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>