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

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Representative site 2qoy:A1567, See in JSmolMgRNA representative site for type 2BO            Click on the image to toggle views

Site type: 2Bout

Schematic drawing for

MgRNA type 2BO
List of all 555 Mg2+ binding sites with the site type 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
1egk A22 2Bout B55, B56, B57, B58, B59, B60 G:A9, DG:B31
1egk C4 2Bout B62, B63, C34, C35, C36, C37 G:C103, G:C102
1egk A21 2Bout A28, A29, A30, A31, A32, A33 G:A2, G:A3
1egk A26 2Bout A49, A50, A51, A52, A53, A54 U:A15, G:A16
1egk A23 2Bout A34, A35, A36, A37, A38, A39 C:A17, G:A18
1egk A27 2Bout A55, A56, A57, A58, A59, A60 G:A13, G:A12
1hr2 A22 2Bout A371, A372, A373, A374, A375, A376 G:A242, U:A243
1hr2 A18 2Bout A359, A360, A361, A362, A363, A364 G:A129, G:A191
1hr2 B19 2Bout B368, B369, B370, B371, B372, B373 G:B129, G:B191
1ik5 B99 2Bout A74, A77, B75, B76, B93 G:B15, G:B16
1jj2 08063 2Bout 03708, 06551, 06986, 07311, 07387, 07440 G:01364, G:01363
1k73 A8063 2Bout A4177, A7016, A7450, A7775, A7851, A7904 G:A1364, G:A1363
1k8a A8063 2Bout A3767, A6567, A6993, A7313, A7389, A7440 G:A1364, G:A1363
1k9m A8063 2Bout A4174, A7013, A7448, A7772, A7850, A7901 G:A1364, G:A1363
1kc8 A8063 2Bout A4183, A7005, A7439, A7761, A7839, A7891 G:A1364, G:A1363
1kd1 A8063 2Bout A4175, A7001, A7436, A7758, A7837, A7889 G:A1364, G:A1363
1kqs 08063 2Bout 03686, 06502, 06927, 07246, 07322, 07373 G:01364, G:01363
1l2x A52 2Bout A53, A54, A55, A56, A57, A58 G:A4, G:A2
1m90 A8063 2Bout A3713, A6540, A6971, A7293, A7370, A7423 G:A1364, G:A1363
1nji A8063 2Bout A4171, A7001, A7431, A7753, A7832, A7886 G:A1364, G:A1363
1o3z B304 2Bout B566, B577, B599, B600, B601 G:B4, U:B3
1o3z B305 2Bout B519, B558, B559, B567, B574, B586 G:B7, U:B6
1pjo A35 2Bout A150, A151, A152, A154, B153, B155 A:A4, A:A3
1q7y A8063 2Bout A3687, A6496, A6922, A7236, A7312, A7363 G:A1364, G:A1363
1q81 A8063 2Bout A3691, A6500, A6926, A7244, A7321, A7373 G:A1364, G:A1363

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>