MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 4qcu 4QCU (2.9Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing short substrate- mimic cytidine-puromycin in the a site and acylated trna in the p site. this entry contains the 30s subunit of the List of all 12 Mg2+ binding sites in the PDB structure 4qcu 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 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4qcu A3147 Ob G:A1417(O6) A4087, A4088, A4089, A4090, A4091 G:A1416, G:A1415 U:A1481, G:A1482, G:A1416 4qcu A3120 Oph·3Pout G:A576(OP1) A4028, A4029, A4030, A4031 G:A577, G:A575, A:A815 4qcu A3148 Oph·Ob C:A352(OP2) C:A330(O2) A4092, A4093, A4094, A4095 G:A354 C:A352, C:A330 A:A59, G:A354 4qcu A3129 cis-2Oph A:A782(OP1), A:A794(OP2) A4049, A4050, A4051, A4052 C:A783 G:A1521, U:A1522 G:A1521 4qcu A3017 cis-2Oph·2Ob C:A979(OP1), C:A980(OP2) U:A981(O4), G:A1222(O6) 4qcu A3127 3Bout A4042, A4043, A4044, A4045, P101 G:A44, G:A396, C:A43 4qcu A3140 Pout·2Bout A4071, A4072, A4073, A4074, A4075, A4076 G:A803 U:A772, G:A771 4qcu A3139 Pout·3Bout A4066, A4067, A4068, A4069, A4070 A:A781 G:A799, G:A800, G:A798 4qcu A3163 2Pout·2Bout A4127, A4128, A4129, V101, V102 G:A1401, G:V18 G:A1401, C:A1399 4qcu A3117 3Pout·2Bout A4021, A4022, A4023, A4024 C:A779, A:A780, G:A799 G:A800, A:A780 4qcu A3161 4Pout A4118, A4119, A4120, A4121, A4122, A4123 U:A13, U:A14, G:A15, A:A16 4qcu A3031 poly-nuclear Mg2+ site A:A116(OP2) G:A117(N7)

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].

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