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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qam:B3600, See in JSmolMgRNA representative site for type 3PO-RO-2BO Click on the image to toggle views


Site type: 3Pout·Rout·2Bout

Schematic drawing for
3Pout·Rout·2Bout
MgRNA type 3PO-RO-2BO
List of all 58 Mg2+ binding sites with the site type 3Pout·Rout·2Bout 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
3i1t A3028 3Pout·Rout·2Bout A3594, A3595, A3596, A3597, A3598, A3599 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821
3oas A3027 3Pout·Rout·2Bout A3593, A3594, A3595, A3596, A3597, A3598 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568
3ofd A3027 3Pout·Rout·2Bout A3594, A3595, A3596, A3597, A3598, A3599 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568
3ofq A3028 3Pout·Rout·2Bout A3594, A3595, A3596, A3597, A3598, A3599 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568
3ofr A3032 3Pout·Rout·2Bout A3610, A3611, A3612, A3613, A3614, A3615 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821
3oxd A101 3Pout·Rout·2Bout A138, A139, A140, A141, A142, A143 C:A35, A:A65, A:A34 A:A81 G:A36, A:A37
3oxd B106 3Pout·Rout·2Bout A144, A145, B137, B138, B139, B140 C:A66, C:B66, A:B33 A:B65 A:B33, A:A65
3r8s A3033 3Pout·Rout·2Bout A3680, A3681, A3682, A3683, A3684, A3685 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821
3r8t A2950 3Pout·Rout·2Bout A3286, A3287, A3288, A3289, A3290 G:A1455, A:A1453, G:A1456 C:A1454 G:A1456, U:A1457
3r8t A3032 3Pout·Rout·2Bout A3649, A3650, A3651, A3652, A3653, A3654 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821
3v23 A3606 3Pout·Rout·2Bout A5030, A5031, A5032, A5033, A5034, A5035 G:A570, A:A973, U:A569 G:A972 A:A820, A:A821
3v27 A3629 3Pout·Rout·2Bout A5230, A5231, A5232, A5233, A5234, A5235 G:A570, A:A973, U:A569 G:A972 A:A820, A:A821
3v2f A3192 3Pout·Rout·2Bout A3894, A3895, A3896, A3897 A:A1937, U:A1956, G:A1945 A:A1936 G:A1945, U:A1946
4bpe A5063 3Pout·Rout·2Bout A2372, A2373, A2374, A2375, A2434, A2438 G:A1173, G:A1172, G:A1170 C:A1574 A:A1168, C:A1574
4bpn A5063 3Pout·Rout·2Bout A6507, A6508, A6509, A6510, A6511, A6512 G:A1173, G:A1170, G:A1172 C:A1574 A:A1168, C:A1574
4bpo A5063 3Pout·Rout·2Bout A2220, A2221, A2222, A2223, A2294, A2298 G:A1173, G:A1172, G:A1170 C:A1574 A:A1168, C:A1574
4gar A3127 3Pout·Rout·2Bout A3775, A3776, A3777, A3778, A3779, A3780 G:A570, A:A973, U:A569 A:A972 A:A821, A:A820
4gau A3126 3Pout·Rout·2Bout A3779, A3780, A3781, A3782, A3783, A3784 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821
4ji8 A1959 3Pout·Rout·2Bout A3258, A3259, A3260, A3261, A3262, A3263 C:A857, G:A869, C:A868 G:A858 G:A858, G:A869
4peb A3129 3Pout·Rout·2Bout A3778, A3779, A3780, A3781, A3782, A3783 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821
4qcr A3498 3Pout·Rout·2Bout A4618, A4619, A4620, A4621, A4622, A4623 G:A593, A:A1018, U:A592 G:A1017 A:A867, A:A868
4qct A3389 3Pout·Rout·2Bout A4387, A4388, A4389, A4390, A4391, A4392 G:A570, U:A569, A:A973 G:A972 A:A820, A:A821
4qcx A3389 3Pout·Rout·2Bout A4320, A4321, A4322, A4323, A4324, A4325 G:A570, A:A973, U:A569 G:A972 A:A820, A:A821
4qcz A3479 3Pout·Rout·2Bout A4562, A4563, A4564, A4565, A4566 U:A592, G:A593, A:A1018 G:A1017 A:A867, A:A868
4qd1 A3402 3Pout·Rout·2Bout A4310, A4311, A4312, A4313, A4314, A4315 G:A570, U:A569, A:A973 G:A972 A:A820, A:A821

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>