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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 1vq6



1VQ6 (2.7Å) -- RIBOSOME : The structure of c-hpmn and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui
List of all 61 Mg2+ binding sites in the PDB structure 1vq6 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
1vq6 08111 Nb G:02609(N7) 03605, 04005, 04029, 06005, B9411 G:02609 U:02610, G:02606
1vq6 08112 Nb A:0187(N1) 04035, 04075, 09452, 09655, 09892 U:0207, C:0155 G:0206 C:0438, C:0188
1vq6 08011 2Nb G:0824(N7), G:0854(N7) 04265, 04594, 04722, 04822 G:0854, U:0823, G:0824, C:0853
1vq6 08019 Oph·Pout A:02011(OP2) 04458, 07437, 07960, 07961, 07962 A:01941 U:01890 G:01891, C:01892
1vq6 08084 Oph·Pout A:01742(OP2) 03068, 03943, 08129, 09575, 09696 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1vq6 08047 Oph·Pout A:01098(OP2) 03438, 06512, 08168 A:01097 G:01099
1vq6 08040 Oph·2Pout U:0392(OP2) 03010, 04096, 04934, 08150, 08151 U:0172, C:0171
1vq6 08020 Oph·2Pout C:01830(OP1) 07944, 07963, 09446, 09449, 09522 U:01831, A:01842 G:01828 G:01828, G:01832
1vq6 08068 Oph·2Pout A:02568(OP2) 04060, 05109, 06467, 08171, E920 A:02569, G:02567 A:02569, A:02568
1vq6 08017 Oph·3Pout G:0456(OP2) 03929, 04249, 07941, 09736, C9263 A:0455, G:0458, U:0457
1vq6 08036 Oph·3Pout G:0956(OP2) 03978, 07985, 07986, 07987, 09690 A:01006, A:0955, A:0957 A:0957, G:0956
1vq6 08032 Oph·3Pout U:02115(OP1) 03300, 04095, 04496, A9345, A9425 C:02273, U:02116, G:02272
1vq6 08021 Oph·3Pout G:02304(OP2) 03275, 03946, 03947, 07947, 07948 A:02301, A:02305, A:02303 U:02306, A:02305, G:02304
1vq6 08035 Oph·4Pout G:01484(OP2) 04024, 07983, 07984, 08146, 08147 C:01483, C:01455, A:01485, C:01456 U:01457
1vq6 08012 Oph·4Pout G:028(OP1) 03534, 03956, 08139, 09361, 09957 C:01305, U:01304, C:01343, G:01344
1vq6 08091 Oph·5Pout G:0918(OP1) 03631, 06713, 08133, 09414, 09870 G:02293, C:02294, C:02391, A:02465, U:0919 A:02465
1vq6 08014 Oph·Or G:02537(OP2) G:02102(O5') 03967, 04472, 07931, 09355 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1vq6 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03986, 04007, 04019, S9147 G:01676
1vq6 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04178, 04320, 04463, 08144 G:0267, U:0268
1vq6 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03092, 04089, 07940, 09369 A:0477, A:0455, A:0460 A:0455

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/)
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