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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 7 of 69 | | | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1q81 A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7360, A7361, A7362, A7363 C:A1103, C:A1104 A:A1107
1q81 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3153, A7247, A7248, A7258 G:A2585, G:A2584
1q81 A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3140, A3334, A7272, A7273 G:A2616 G:A2618
1q81 A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A3136, A7372, B8389, B8417 C:A1126 C:A1129, G:B3090
1q81 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5386, A5774, A7357, A7392 C:A2745, U:A2749
1q81 A8034 cis-2Oph A:A2302(OP1), A:A2303(OP1) A3156, A3282, A4374, A7288 A:A2301, G:A2304
1q82 A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A3714, A4001, A7317, A7368 C:A1431 A:A1691, C:A1692 U:A1722, A:A1691
1q82 A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3244, A3486, A7320, A7321 C:A534 A:A2814, U:A10
1q82 A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3380, A7247, A8630, A8975 A:A2095 A:A2096 G:A2097
1q82 A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3172, A3674, A7226, A8553 G:A2481 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1q82 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3126, A6944, A7330, A9731 C:A910, U:A909 G:A1292, G:A911
1q82 A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A3136, A7360, A9106, B8416 C:A1126 C:A1129, G:B3090
1q82 A8054 cis-2Oph C:A162(OP1), U:A2276(OP1) A7241, A7294, A7295, A8950 U:A163, A:A169
1q86 A8034 cis-2Oph A:A2302(OP1), A:A2303(OP1) A3168, A3297, A4384, A7310 A:A2301 A:A2301, G:A2304
1q86 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3165, A7268, A7269, A7279 G:A2585, G:A2584
1q86 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5394, A5784, A7378, A7413 C:A2745, U:A2749
1q86 A8029 cis-2Oph U:A1503(OP1), C:A1679(OP1) A7302, A7303, A7304, A7305 A:A1504
1q86 A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7381, A7382, A7383, A7384 C:A1103, C:A1104 C:A1105 A:A1107
1q86 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3167, A3180, A7290, A8542 C:A2475, A:A2624 G:A885
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
1q86 A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A3733, A4016, A7348, A7399 C:A1431 A:A1684, A:A1691, C:A1692 U:A1722, A:A1691
1q86 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3139, A6980, A7361, A9743 C:A910, U:A909 G:A1292, G:A911
1q86 A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3153, A3348, A7294, A7295 G:A2616 G:A2618
1q86 A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7331, A7332, A7333, A9341 A:A2649 U:A1371
1q86 A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3259, A3505, A7351, A7352 C:A534 A:A2814, U:A10

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>