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

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Representative site 3df2:B3464, See in JSmolMgRNA representative site for type 3BO            Click on the image to toggle views

Site type: 3Bout

Schematic drawing for

MgRNA type 3BO
List of all 341 Mg2+ binding sites with the site type 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
1dno A24 3Bout A215, A216, A217, A218, B219, B220 DT:A4, G:A3, DT:B16
1dno B22 3Bout A205, B203, B204, B206, B207, B208 DT:A6, G:B13, DT:B14
1dnt A21 3Bout A146, A147, A148, A149, A150, B151 DT:A4, DG:A3, DT:B16
1hr2 A24 3Bout A377, A378, A379, A380, A381, A382 G:A134, U:A135, U:A182
1hr2 B21 3Bout B374, B375, B376, B377, B378, B379 G:B158, U:B157, U:B144
1hr2 A26 3Bout A383, A384, A385, A386, A387, A388 G:A111, G:A112, G:A110
1hr2 B23 3Bout B380, B381, B382, B383, B384, B385 U:B243, G:B242, A:B230
1j1u B1502 3Bout B61, B288, B289, B290, B291, B292 G:B569, G:B504, G:B503
1jzv C300 3Bout C301, C302, C303, C304, C306, D305 A:C25, G:C24, C:C23
1n8r A8063 3Bout A4573, A7389, A7814, A8246, A8395, A8445 G:A1364, U:A1362, G:A1363
1nuj A417 3Bout A419, A420, A421, B420, B421, B422 G:A20, G:A19, U:B47
1nuj C425 3Bout C184, C307, C363, C391, C392, D364 A:C29, G:C30, G:D39
1nuj C426 3Bout C131, C137, C166, D160, D178, D371 G:C19, G:C20, U:D47
1nuj G420 3Bout G229, G230, G231, G232, G233, H228 G:G20, G:G19, U:H47
1nuj E423 3Bout E431, E432, E443, F68, F82, F99 G:E19, G:E20, U:F47
1nuj A418 3Bout A422, A423, A424, A425, B423, B424 A:A29, G:A30, G:B39
1nuj G421 3Bout G210, G211, G212, G213, G214, H209 A:G29, G:G30, G:H39
1nuj E424 3Bout E453, E454, E459, E469, E477, F81 A:E29, G:E30, G:F39
1nuv G414 3Bout G202, G203, G205, G206, H201, H204 A:G29, G:G30, G:H39
1nuv E417 3Bout E285, E287, E302, E367, E370, F293 A:E29, G:E30, G:F39
1nuv A410 3Bout A412, A413, A414, A415, A416, B425 G:A20, G:A19, U:B47
1nuv G413 3Bout G222, G224, G225, H221, H223, H226 G:G20, G:G19, U:H47
1nuv E416 3Bout E90, E93, E112, E117, E305, F294 G:E19, G:E20, U:F47
1nuv A411 3Bout A417, A418, A419, A420, B426, B427 A:A29, G:A30, G:B39
1vs6 B2947 3Bout B3216, B3217, B3218, B3219, B3220, B3221 G:B43, U:B434, A:B42

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>