`

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 1vq5



1VQ5 (2.6Å) -- RIBOSOME : The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
List of all 67 Mg2+ binding sites in the PDB structure 1vq5 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
1vq5 08075 2Or A:0907(O2'), A:0908(O4') 03953, 04229, 05243, 08153 U:01270 A:01328, A:0907
1vq5 08011 2Nb G:0824(N7), G:0854(N7) 04272, 04604, 04736, 04836 G:0854, U:0823, G:0824, C:0853
1vq5 08019 Oph·Pout A:02011(OP2) 04464, 07478, 07996, 07997, 07998 A:01941 U:01890 G:01891, C:01892
1vq5 08047 Oph·Pout A:01098(OP2) 03451, 06544, 08205 A:01097 G:01099
1vq5 08039 Oph·Pout U:0115(OP2) 03231, 04278, 05401, 08133, 08134 G:0112 A:0114 G:0118, A:0119
1vq5 08084 Oph·Pout A:01742(OP2) 03074, 03951, 08165, 09573, 09699 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1vq5 08051 Oph·2Pout G:0641(OP2) 04418, 08137, 08138 A:01355, G:0640 G:0642, A:01355
1vq5 08045 Oph·2Pout G:01979(OP2) 08136, 08189, 08190, 08191 G:01998, C:01999 C:01826
1vq5 08068 Oph·2Pout A:02568(OP2) 04066, 05128, 06501, 08209, E920 A:02569, G:02567 A:02569, A:02568
1vq5 08083 Oph·2Pout A:01754(OP2) 04021, 04465, 06622, 08164, 08215 C:01753, A:01755 A:01755, A:01754
1vq5 08020 Oph·2Pout C:01830(OP1) 07980, 07999, 09445, 09448, 09520 U:01831, A:01842 G:01828 G:01828, A:01845, G:01832
1vq5 08036 Oph·3Pout G:0956(OP2) 03986, 08128, 08129, 08130, 09693 A:01006, A:0955, A:0957 A:0957, G:0956
1vq5 08032 Oph·3Pout U:02115(OP1) 03311, 04103, 04504, A9343, A9422 C:02273, U:02116, G:02272
1vq5 08037 Oph·3Pout A:02553(OP2) 03457, 03532, 03965, 08184, 09399 C:02575, A:02576, U:02554 C:02552 A:02576
1vq5 08021 Oph·3Pout G:02304(OP2) 03286, 03954, 03955, 07983, 07984 A:02301, A:02303, A:02305 U:02306, A:02305, G:02304
1vq5 08040 Oph·3Pout U:0392(OP2) 03017, 04104, 04949, 08186, 08187 U:0172, U:0391, C:0171
1vq5 08017 Oph·3Pout G:0456(OP2) 04257, 07977, 09738, C9155, C9261 G:0458, A:0455, U:0457
1vq5 08012 Oph·4Pout G:028(OP1) 03548, 03964, 08175, 09361, 09962 C:01305, U:01304, C:01343, G:01344
1vq5 08035 Oph·4Pout G:01484(OP2) 04030, 08126, 08127, 08182, 08183 C:01483, A:01485, C:01455, C:01456 G:01484, U:01457
1vq5 08060 Oph·5Pout G:0175(OP2) 08143, 08144, 08145, 09493 C:0173, G:0225, U:0172, G:0393, U:0392

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>