`

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 1vqk



1VQK (2.3Å) -- RIBOSOME : The structure of ccda-phe-cap-bio bound to the a site of the ribosomal subunit of haloarcula marismortui
List of all 19 Mg2+ binding sites in the PDB structure 1vqk 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
1vqk 08068 Nb A:02569(N7) 04355, 05413, 08453, E920, E6236 A:02568, A:02569, G:02567 C:02565 A:02568
1vqk 08020 Oph·2Pout C:01830(OP1) 08333, 08352, 09748, 09751, 09825 U:01831, A:01842 G:01828 G:01828, G:01832
1vqk 08017 Oph·3Pout G:0456(OP2) 03044, 08330, C9164, C9167, C9271 U:0457, A:0455, G:0458
1vqk 08032 Oph·3Pout U:02115(OP1) 03606, 04392, 04790, 08367, A9535 G:02272, C:02273, U:02116 G:02271
1vqk 08036 Oph·3Pout G:0956(OP2) 04274, 08371, 08372, 08373, 09993 A:01006, A:0955, A:0957 G:0956, A:0957
1vqk 08012 Oph·4Pout G:028(OP1) 03264, 03837, 04251, 08418, 09665 C:01343, G:01344, C:01305, U:01304
1vqk 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03393, 04386, 08329, 09673 A:0477, A:0455, A:0460 A:0455
1vqk 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04475, 04615, 04756, 08423 G:0267, U:0268
1vqk 08028 Oph·Ob A:01448(OP2) U:01677(O4) 04282, 04303, 04314, S9502 G:01676
1vqk 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 04244, 08331, 08332, 08342 G:02585, G:02584
1vqk 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 03062, 08335, 08382, 08383 A:0169, U:0163
1vqk 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04225, 08353, 09633, 09650 G:01688 A:0844, A:01689, A:0882, C:01692
1vqk 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04270, A9499, A9520
1vqk 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08357, 08358, 08359 C:02542
1vqk 08029 fac-3Oph U:01503(OP1), A:01504(OP2), C:01679(OP1) 08362, 08364
1vqk 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04216, 08345, 08346 G:01837 A:01839
1vqk 08002 fac-3Oph·Ob A:02483(OP1), C:02534(OP1), U:02535(OP2) G:0627(O6) 08323, 09888 C:02071
1vqk 08056 Mg2+ bound by non-RNA A:02757(OP1) 04272, 08401, B9539 ASN:B335(O) A:02719, C:02720, G:02758
1vqk 08079 poly-nuclear Mg2+ site A:0167(OP1), C:0168(OP2) A:0165(N7) 04215, 04220, 04232 G:0164, A:0165 G:0164

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>