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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3r8s:A3026, See in JSmolMgRNA representative site for type cis-2OP Click on the image to toggle views


Site type: cis-2Oph

Schematic drawing for
cis-2Oph
MgRNA type cis-2OP
List of all 1720 Mg2+ binding sites with the site type cis-2Oph 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 8 of 69 | | | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1q86 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3167, A3180, A7290, A8542 C:A2475, A:A2624 G:A885
1q86 A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7381, A7382, A7383, A7384 C:A1103, C:A1104 C:A1105 A:A1107
1q86 A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3185, A3691, A7257, A8555 G:A2481 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1qu2 T1209 cis-2Oph C:T48(OP1), G:T50(OP1) T1323, T1324, T1325, T1326 U:T51
1qvf 08080 cis-2Oph A:01684(OP2), U:01724(OP2) 03716, 03995, 07294, 07344 C:01431 A:01684, A:01691, C:01692 U:01722, A:01691
1qvf 08061 cis-2Oph A:01369(OP2), U:02650(OP1) 07277, 07278, 07279, 09339 A:02649 U:01371
1qvf 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 07282, 07283, V7873, V7874 A:01287
1qvf 08086 cis-2Oph A:0532(OP1), U:0533(OP1) 03246, 03486, 07296, 07297 C:0534 A:02814, U:010
1qvf 08034 cis-2Oph A:02302(OP1), A:02303(OP1) 03159, 03284, 04361, 07256 A:02301 A:02301, G:02304
1qvf 08030 cis-2Oph U:01748(OP1), U:01749(OP2) 03156, 07218, 07219, 07227 G:02585, G:02584
1qvf 08052 cis-2Oph U:01125(OP1), G:93092(OP1) 03142, 07337, 98388, 98416 C:01126 C:01129, G:93090
1qvf 08018 cis-2Oph A:01291(OP1), G:01292(OP2) 03133, 06933, 07306, 09736 C:0910, U:0909 G:01292, G:0911
1qvf 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03382, 07226, 08632, 08977 A:02095 A:02096 G:02097
1qvf 08107 cis-2Oph A:01106(OP2), A:01107(OP2) 07325, 07326, 07327, 07328 C:01103, C:01104 C:01105 A:01107
1qvf 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 07270, 07271, 08952 A:0169
1qvf 08023 cis-2Oph G:02617(OP2), G:02618(OP2) 03333, 07241, 07242 G:02616 G:02618
1qvf 08013 cis-2Oph G:0877(OP1), G:02623(OP1) 03158, 03170, 08540, A8628 C:02475, A:02624 G:0885
1qvf 08014 cis-2Oph G:02102(OP2), G:02537(OP2) 03174, 03675, 07207, 08552 C:02536, A:02101 G:02480, G:02481, A:02101
1qvf 08029 cis-2Oph U:01503(OP1), C:01679(OP1) 07248, 07249, 07250, 07251 A:01504
1qvg 08087 cis-2Oph A:0682(OP2), G:0683(OP2) 03182, 07285
1qvg 08086 cis-2Oph A:0532(OP1), U:0533(OP1) 03237, 03473, 07229, 07230 C:0534 A:02814, U:010
1qvg 08074 cis-2Oph A:01286(OP1), A:01287(OP1) 07214, 07215, V7873, V7874 A:01287
1qvg 08080 cis-2Oph A:01684(OP2), U:01724(OP2) 03700, 03976, 07226, 07274 C:01431 A:01684, A:01691, C:01692 U:01722, A:01691
1qvg 08107 cis-2Oph A:01106(OP2), A:01107(OP2) 07257, 07258, 07259, 07260 C:01103, C:01104 C:01105 A:01107
1qvg 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03371, 07160, 08633, 08978 A:02095 A:02096 G:02097

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>