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

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Representative site 1vs8:B2932, See in JSmolMgRNA representative site for type 3PO            Click on the image to toggle views


Site type: 3Pout

Schematic drawing for
3Pout

MgRNA type 3PO
List of all 207 Mg2+ binding sites with the site type 3Pout 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 4 of 9 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v27 A3393 3Pout A4196, A4197, A4198, A4199, A4200 C:A795, A:A677, G:A794
3v27 A3637 3Pout A5272, A5273, A5274, A5275, 3101 C:A850, G:A921, U:A851
3v27 A3551 3Pout A4876, A4877, A4878, A4879, A4880 U:A2519, C:A2464, C:A2538
3v27 5103 3Pout 5201, 5202, 5203, 5204, 5205 G:A16, G:A518, G:A17
3v27 A3614 3Pout A5141, A5142, A5143, A5144, A5145, A5146 C:A1499, G:A1500, G:A1484
3v29 A3445 3Pout A4200, A4201, A4202, A4203, A4204 A:A1971, A:A1970, A:A1969
3v29 A3345 3Pout A3796, A3797, A3798, A3799, A3800 C:A1670, U:A1671, G:A2549
3v29 A3503 3Pout A4405, A4406, A4407, A4408, A4409, A4410 C:A1370, U:A773, G:A1356
3v2d A3683 3Pout A5620, A5621, A5622, A5623, A5624 A:A866, U:A905, C:A865
3v2e A1798 3Pout A2289, A2290, A2291, A2292 G:A568, A:A864, U:A863
3v2f 8101 3Pout A4833, A4834, 6202, 6203, 8203 C:A2347, U:A2348, U:A2419
3v2f A3476 3Pout A4777, A4778, A4779, A4780, A4781 C:A1370, U:A773, G:A1356
4bpe A5053 3Pout A2176, A2177, A2178, A2323, A2324, A2325 C:A978, A:A979, G:A980
4bpe A5038 3Pout A2190, A2191, A2197, A2303, A2340, A2341 U:A1022, C:A1023, C:A1039
4bpe A5005 3Pout A2002, A2004, A2005, A2006, A2007, A2247 U:A8, U:A9, A:A11
4bpe A5054 3Pout A2155, A2156, A2179, A2180, A2326, A2348 U:A881, G:A986, U:A987
4bpe A5075 3Pout A2387, A2388, A2389, A2406, A2407, A2464 C:A1246, G:A1399, G:A1400
4bpe A5004 3Pout A2114, A2115, A2116, A2208, A2246, A2350 C:A567, A:A1111, A:A1110
4bpn A5049 3Pout A6152, A6153, A6154, A6155, A6156, A6157 A:A283, U:A114, A:A115
4bpn A5054 3Pout A6186, A6187, A6188, A6190, A6191, A6192 G:A986, U:A881, U:A987
4bpn A5038 3Pout A6075, A6076, A6077, A6078, A6079, A6080 C:A1039, C:A1023, U:A1022
4bpn A5075 3Pout A6592, A6593, A6594, A6595, A6596, A6597 C:A1246, G:A1399, G:A1400
4bpn A5005 3Pout A6030, A6031, A6032, A6039, A6046, A6053 U:A9, A:A11, U:A8
4bpo A5004 3Pout A2111, A2112, A2113, A2213, A2326, A2327 C:A567, A:A1111, G:A568
4bpo A5053 3Pout A2181, A2182, A2183, A2416, A2417, A2418 C:A978, A:A979, G:A980

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>