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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 1vq7



1VQ7 (2.5Å) -- RIBOSOME : The structure of the transition state analogue "dca" bound to the large ribosomal subunit of haloarcula marismortui
List of all 63 Mg2+ binding sites in the PDB structure 1vq7 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vq7 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 07977, 08135, 08136, 09758 U:0163, A:0169
1vq7 B8055 2Pout 06681, 07927, B9356, B9470, U2221 C:02720, U:02721
1vq7 B8056 Mg2+ bound by non-RNA A:02757(OP1) 03992, 04299, 08153, B9344 ASN:B335(O) A:02719, C:02720, G:02758
1vq7 08058 poly-nuclear Mg2+ site G:02013(OP2) 04088, 08137, 08138, A9425, A9427 G:01884, U:01883, C:02626 U:02012
1vq7 08060 Oph·5Pout G:0175(OP2) 08139, 08140, 08141, 09498 C:0173, G:0225, U:0172, G:0393, U:0392
1vq7 08061 cis-2Oph A:01369(OP2), U:02650(OP1) 03141, 08142, 08143, 08144 A:02649 U:01371
1vq7 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03956, 04282, 06447, 09721 G:01490, A:01487 G:01489, G:01490
1vq7 A8065 Pout·Rout 03248, 04294, A9320, A9350, A9397, A9426 C:0783 G:0782
1vq7 08068 Oph·2Pout A:02568(OP2) 04076, 05138, 06496, 08205, E920 A:02569, G:02567 A:02569, A:02568
1vq7 K8069 Mg2+ bound by non-RNA 03742, 04567, 06321, K2121, K7871 ASN:K42(OD1) U:02546, U:01749, A:02583, G:02584
1vq7 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 08147, W7803, W7873, W7874 A:01287
1vq7 08076 Pout·Rout·2Bout 07100, 08154, 08155, 08207, 08208, 27875 U:01419 U:01418 G:01443, G:01444
1vq7 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03946, 08156, 08157, 09568 A:0882, C:0884 U:0883, A:01836
1vq7 38078 Mg2+ bound by non-RNA 39326, 39377, 39378 GLY:345(O), GLY:347(O), ASP:349(OD1) G:02121, C:02122
1vq7 08079 poly-nuclear Mg2+ site A:0167(OP1), C:0168(OP2) A:0165(N7) 03934, 03940, 03952 G:0164, A:0165 G:0164
1vq7 08080 cis-2Oph A:01684(OP2), U:01724(OP2) 04532, 04813, 08158, 08209 C:01431 A:01684, A:01691, C:01692 U:01722, A:01691
1vq7 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04424, 09933
1vq7 08083 Oph·2Pout A:01754(OP2) 04031, 04478, 06621, 08159, 08210 C:01753, A:01755 A:01755, A:01754
1vq7 08084 Oph·Pout A:01742(OP2) 03073, 03959, 08160, 09577, 09699 G:02033 G:02033, G:01744, G:01745, A:01742, G:01743
1vq7 08086 cis-2Oph A:0532(OP1), U:0533(OP1) 04056, 04300, 08161, 08162 C:0534 A:02814, U:010

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>