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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 4 of 69 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1kqs 08054 cis-2Oph C:0162(OP1), U:02276(OP1) 07253, 07304, 07305, 08946 U:0163, A:0169
1kqs 08061 cis-2Oph A:01369(OP2), U:02650(OP1) 07311, 07312, 07313, 09332 A:02649 U:01371
1kqs 08023 cis-2Oph G:02617(OP2), G:02618(OP2) 03136, 03329, 07275, 07276 G:02616 G:02618, U:02619
1kqs 08022 cis-2Oph G:02097(OP2), G:02540(OP1) 03377, 07259, 08629, 08971 A:02095 A:02096 G:02097
1kqs 08029 cis-2Oph U:01503(OP1), C:01679(OP1) 07282, 07283, 07284, 07285 A:01504
1m1k A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A3803, A4090, A7434, A7484 C:A1431 A:A1691, C:A1692 A:A1691
1m1k A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3329, A3570, A7437, A7438 C:A534 A:A2814, U:A10
1m1k A8074 cis-2Oph A:A1286(OP1), A:A1287(OP1) A7422, A7423, X7873, X7874 A:A1287
1m1k A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7417, A7418, A7419, A9418 A:A2649 U:A1371
1m1k A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3222, A3414, A7379, A7380 G:A2616 G:A2618
1m1k A8029 cis-2Oph U:A1503(OP1), C:A1679(OP1) A7387, A7388, A7389, A7390 A:A1504
1m1k A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3209, A7061, A7447, A9819 C:A910, U:A909 G:A1292, G:A911
1m1k A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3465, A7363, A8706, A9051 A:A2095 A:A2096 G:A2097
1m1k A8034 cis-2Oph A:A2302(OP1), A:A2303(OP1) A3237, A3364, A4463, A7395 A:A2301, G:A2304
1m1k A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5480, A5864, A7463, A7497 C:A2745, U:A2749
1m1k A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3253, A3761, A7342, A8630 G:A2481 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1m90 A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7359, A7360, A7361, A9340 A:A2649 U:A1371
1m90 A8074 cis-2Oph A:A1286(OP1), A:A1287(OP1) A7364, A7365, A7426, X7874 A:A1287
1m90 A8034 cis-2Oph A:A2302(OP1), A:A2303(OP1) A3172, A3298, A4407, A7338 A:A2301 A:A2301, G:A2304
1m90 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5419, A5799, A7406, A7441 C:A2745, U:A2749
1m90 A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A3152, A7421, A9110, B2357 C:A1126 C:A1129, G:B3090
1m90 A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A3739, A4030, A7376, A7429 C:A1431 A:A1684, A:A1691, C:A1692 U:A1722, A:A1691
1m90 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3169, A7296, A7297, A7307 G:A2585, G:A2584
1m90 A8054 cis-2Oph C:A162(OP1), U:A2276(OP1) A7300, A7352, A7353, A8953 U:A163, A:A169
1m90 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3171, A3183, A7318, A8540 C:A2475, A:A2624 G:A885

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>