MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2t:B2935, See in JSmolClick on the image to toggle views Site type: 3Pout·Bout Schematic drawing for 3Pout·Bout List of all 155 Mg2+ binding sites with the site type 3Pout·Bout 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" Page 3 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3oas A2952 3Pout·Bout A3265, A3266, A3267, A3268, A3269 G:A1456, A:A1453, G:A1455 G:A1456 3ofd A2948 3Pout·Bout A3246, A3247, A3248, A3249, A3250, A3251 C:A1351, C:A1376, G:A1377 G:A1377 3ofq A3023 3Pout·Bout A3576, A3577, A3578, A3579 U:A790, C:A787, C:A791 U:A1781 3ofq A2915 3Pout·Bout A3088, A3089, A3090, A3091, A3092, A3093 A:A1008, G:A2038, C:A560 A:A1008 3ofr A2947 3Pout·Bout A3237, A3238, A3239, A3240, A3241, A3242 C:A1351, U:A1352, C:A1376 G:A1377 3r8s A2965 3Pout·Bout A3382, A3383, A3384, A3385, A3386, A3387 A:A2614, A:A2051, G:A2578 A:A2051 3ud3 R1 3Pout·Bout R671, R672, R673, R674, R675, R676 G:R40, G:R41, A:R23 G:R42 3v23 A3383 3Pout·Bout A4203, A4204, A4205, A4206, A4207, A4208 C:A2885, U:A2832, U:A2884 G:A2886 3v24 A1662 3Pout·Bout A1781, A1782, A1783, A1784 A:A621, G:A617, C:A620 G:A617 3v25 A3360 3Pout·Bout A3947, A3948, A3949, A3950 U:A306, G:A307, G:A309 G:A307 3v25 A3367 3Pout·Bout A3966, A3967, A3968, A3969 G:A1358, C:A1370, U:A1357 G:A1371 3v26 A1712 3Pout·Bout A1953, A1954, A1955, A1956, A1957 G:A15, A:A16, U:A13 U:A14 3v27 A3631 3Pout·Bout A5242, A5243, A5244, A5245, A5246 U:A2613, G:A2578, C:A2050 A:A2614 3v27 A3604 3Pout·Bout A5090, A5091, A5092, A5093 C:A2551, A:A1669, G:A1987 G:A1954 3v27 B218 3Pout·Bout B330, B331, B332, B333, B334 U:B74, A:B100, G:B75 G:B76 3v27 A3356 3Pout·Bout A4055, A4056, A4057, A4058 C:A2755, U:A2746, G:A2747 G:A2747 3v29 A3485 3Pout·Bout A4337, A4338, A4339, A4340 A:A861, G:A862, A:A910 A:A863 3v29 A3502 3Pout·Bout A4400, A4401, A4402, A4403, A4404 A:A2738, G:A2763, G:A2762 A:A2738 3v2d A3172 3Pout·Bout A4173, A4174, A4175, A4176, P310 G:A831, G:A944, U:A568 A:A2448 3v2f A3263 3Pout·Bout A4140, A4141, A4142, A4143, A4144 U:A475, A:A478, G:A476 G:A476 3v2f A3221 3Pout·Bout A4003, A4004, A4005, P304 G:A831, G:A944, U:A568 A:A2448 3v2f A3327 3Pout·Bout A4346, A4347, A4348, A4349 C:A1615, C:A1617, A:A1610 C:A1612 4bpe A5012 3Pout·Bout A2174, A2175, A2181, A2182, A2183, A2347 C:A968, A:A969, C:A988 G:A989 4bpe A5030 3Pout·Bout A2042, A2043, A2044, A2045, A2046, A2285 U:A140, A:A141, G:A159 G:A159 4bpn A5030 3Pout·Bout A6415, A6463, A6464, A6465, A6467, A6468 U:A140, G:A159, A:A141 G:A159

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>