`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
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 6 of 69 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1nji A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3216, A3606, A7462, A7851 C:A910, U:A909 G:A911, G:A1292
1nji A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3862, A7766, A9110, A9450 A:A2095 A:A2096 G:A2097
1nji A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3621, A3811, A7782, A7783 G:A2616 G:A2618
1nji A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7871, A7872, A7873, A7874 C:A1103, C:A1104 A:A1107
1nji A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5876, A6262, A7868, A7906 C:A2745, U:A2749
1pjo B34 cis-2Oph G:A10(OP1), DT:B18(OP1) A147, A148, A149, B146 G:A10, DT:B18, DT:B18, G:A10 DT:B19
1pjo A31 cis-2Oph A:A9(OP1), DT:B18(OP2) A132, A133, A134, B135 G:A10, DT:B17, DG:B20, DT:B17, DT:B18
1q7y A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3168, A3671, A7228, A8555 G:A2481 G:A2102, C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1q7y A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3137, A3328, A7264, A7265 G:A2616 G:A2618, U:A2619
1q7y A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3124, A6951, A7331, A9732 C:A910, U:A909 G:A1292, G:A911
1q7y A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7301, A7302, A7303, A9335 A:A2649 U:A1371
1q7y A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3152, A3163, A8541, C8628 C:A2475, A:A2624 G:A885
1q7y A8029 cis-2Oph U:A1503(OP1), C:A1679(OP1) A7271, A7272, A7273, A7274 A:A1504
1q7y A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A3710, A7318, A7368 A:A1691
1q7y A8034 cis-2Oph A:A2302(OP1), A:A2303(OP1) A3153, A3278, A4369, A7279 A:A2301, G:A2304
1q81 A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3385, A7257, A8634, A8970 A:A2095 A:A2096 G:A2097
1q81 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3155, A3167, A8541, C8640 C:A2475, A:A2624 G:A885
1q81 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3125, A6957, A7340, A9735 C:A910, U:A909 G:A1292, G:A911
1q81 A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3140, A3334, A7272, A7273 G:A2616 G:A2618
1q81 A8025 cis-2Oph U:A1120(OP2), G:A1121(OP2) A3679, A7274, A7275, A7342 G:A1121
1q81 A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3172, A3674, A7236, A8554 G:A2481 G:A2102, C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1q81 A8029 cis-2Oph U:A1503(OP1), C:A1679(OP1) A7280, A7281, A7282, A7283 A:A1504
1q81 A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7310, A7311, A7312, A9335 A:A2649 U:A1371
1q81 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3153, A7247, A7248, A7258 G:A2585, G:A2584
1q81 A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A3136, A7372, B8389, B8417 C:A1126 C:A1129, G:B3090

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>