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

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List of Mg2+ binding sites in structure 4bpp




4BPP (3.7Å) -- RIBOSOME : The crystal structure of the eukaryotic 40s ribosomal subunit in complex with eif1 and eif1a - complex 4
List of all 77 Mg2+ binding sites in the PDB structure 4bpp in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4bpp A5052 Rout A7843, A7844, A7845, A7846, A7847, A7848 A:A675
4bpp A5032 Bout A7523, A7524, A7525, A7526, A7527, A7528 G:A926
4bpp A5013 2Bout A7219, A7220, A7221, A7222, A7223, A7224 U:A1622, G:A1621
4bpp A5045 2Bout A7731, A7732, A7733, A7734, A7735, A7736 C:A1026, U:A1027
4bpp A5035 2Bout A7571, A7572, A7573, A7574, A7575, A7576 G:A1028, G:A1029
4bpp A5059 2Bout A7955, A7956, A7957, A7958, A7959, A7960 C:A1691, C:A1692
4bpp A5068 2Bout A8099, A8100, A8101, A8102, A8103, A8104 U:A1561, G:A1562
4bpp A5034 2Bout A7555, A7556, A7557, A7558, A7559, A7560 G:A902, A:A901
4bpp A5027 2Bout A7443, A7444, A7445, A7446, A7447, A7448 G:A268, G:A269
4bpp A5036 2Bout A7587, A7588, A7589, A7590, A7591, A7592 U:A515, G:A514
4bpp A5016 2Bout A7267, A7268, A7269, A7270, A7271, A7272 G:A194, G:A195
4bpp A5067 2Bout A8083, A8084, A8085, A8086, A8087, A8088 G:A1479, G:A1478
4bpp A5014 2Bout A7235, A7236, A7237, A7238, A7239, A7240 G:A1707, G:A1617
4bpp A5077 Rout·2Bout A8243, A8244, A8245, A8246, A8247, A8248 U:A1277 U:A1277, U:A1286
4bpp A5011 3Bout A7187, A7188, A7189, A7190, A7191, A7192 U:A1732, G:A1730, G:A1731
4bpp A5000 3Bout A7011, A7012, A7013, A7014, A7015, A7016 G:A374, U:A94, G:A375
4bpp A5024 3Bout A7395, A7396, A7397, A7398, A7399, A7400 G:A1267, G:A1266, U:A1274
4bpp A5031 3Bout A7507, A7508, A7509, A7510, A7511, A7512 G:A863, G:A903, A:A904
4bpp A5074 3Bout A8195, A8196, A8197, A8198, A8199, A8200 G:A1389, U:A1385, A:A1388
4bpp A5023 3Bout A7379, A7380, A7381, A7382, A7383, A7384 A:A456, G:A459, G:A457

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/)
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