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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 1vs6:B2983, See in JSmolMgRNA representative site for type 3PO-3BO Click on the image to toggle views


Site type: 3Pout·3Bout

Schematic drawing for
3Pout·3Bout
MgRNA type 3PO-3BO
List of all 34 Mg2+ binding sites with the site type 3Pout·3Bout 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
1dul B801 3Pout·3Bout B810, B820, B826, B832, B881, B882 C:B163, G:B144, G:B145 U:B146, G:B144, G:B145
1hq1 B1801 3Pout·3Bout B9011, B9015, B9025, B9028, B9038, B9180 C:B163, G:B144, G:B145 U:B146, G:B144, G:B145
1vs6 B2983 3Pout·3Bout B3388, B3389, B3390, B3391, B3392, B3393 A:B2451, C:B2452, A:B2453 G:B2454, A:B2497, G:B2455
1vs8 B2917 3Pout·3Bout B3075, B3076, B3077, B3078, B3079, B3080 A:B2033, G:B2027, U:B2026 G:B2027, U:B2028, G:B2029
1vs8 B2958 3Pout·3Bout B3273, B3274, B3275, B3276, B3277, B3278 A:B582, G:B583, A:B1253 C:B584, A:B582, G:B583
1vt2 A2906 3Pout·3Bout A3044, A3045, A3046, A3047, A3048, A3049 A:A28, U:A29, A:A447 G:A473, U:A29, G:A30
2awb B2917 3Pout·3Bout B3076, B3077, B3078, B3079, B3080, B3081 A:B2033, G:B2027, U:B2026 G:B2027, U:B2028, G:B2029
2i2t B2957 3Pout·3Bout B3274, B3275, B3276, B3277, B3278, B3279 A:B616, G:B617, A:B608 G:B617, G:B619, G:B618
2i2v B2939 3Pout·3Bout B3194, B3195, B3196, B3197, B3198, B3199 A:B447, A:B28, U:B29 U:B29, G:B30, G:B474
2i2v B2927 3Pout·3Bout B3134, B3135, B3136, B3137, B3138, B3139 G:B617, A:B608, A:B616 G:B618, G:B617, G:B619
2qou A1584 3Pout·3Bout A2098, A2099, A2100, A2101, A2102 A:A1110, A:A1111, C:A1109 U:A1189, A:A1111, A:A1188
2qov B2923 3Pout·3Bout B3103, B3104, B3105, B3106, B3107, B3108 U:B29, A:B28, A:B447 G:B473, G:B30, G:B474
3df2 B3110 3Pout·3Bout B4111, B4112, B4113, B4114, B4115, B4116 U:B29, A:B28, A:B447 G:B473, G:B474, G:B30
3df4 B3207 3Pout·3Bout B4208, B4209, B4210, B4211, B4212, B4213 A:B447, A:B28, U:B29 G:B30, G:B473, G:B474
3i1o A2 3Pout·3Bout A1577, A1578, A1579, A1580, A1581, A1582 A:A329, A:A315, G:A319 G:A319, A:A320, G:A318
3i1r A2974 3Pout·3Bout A3369, A3370, A3371, A3372, A3373, A3374 A:A2453, A:A2451, C:A2452 A:A2497, G:A2455, A:A2453
3i1t A2905 3Pout·3Bout A3044, A3045, A3046, A3047, A3048, A3049 U:A29, A:A28, A:A447 G:A473, G:A474, G:A30
3i20 A3036 3Pout·3Bout A3638, A3639, A3640, 4779, 4782, 4784 A:A2740, A:A2741, G:A2742 G:A2742, G:A2763, U:A2743
3oar A1535 3Pout·3Bout A1577, A1578, A1579, A1580, A1581, A1582 A:A315, A:A329, G:A319 G:A319, A:A320, G:A318
3ofb A1535 3Pout·3Bout A1578, A1579, A1580, A1581, A1582, A1583 A:A315, A:A329, G:A319 G:A319, A:A320, G:A318
3ofy A1535 3Pout·3Bout A1578, A1579, A1580, A1581, A1582, A1583 A:A315, A:A329, G:A319 G:A319, A:A320, G:A318
3orb A2906 3Pout·3Bout A3046, A3047, A3048, A3049, A3050, A3051 A:A28, U:A29, A:A447 G:A473, G:A474, U:A29
3ucz R1 3Pout·3Bout R671, R672, R673, R674, R675, R676 A:R23, G:R41, G:R40 G:R42, A:R43, G:R41
3v23 A3605 3Pout·3Bout A5024, A5025, A5026, A5027, A5028, A5029 A:A2451, C:A2452, A:A2453 A:A2453, A:A2497, G:A2454
4bpe A5069 3Pout·3Bout A2368, A2369, A2370, A2371, A2376, A2377 G:A1148, C:A1428, C:A1149 A:A1174, U:A1159, G:A1172

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>