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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 5 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
1m90 A8074 cis-2Oph A:A1286(OP1), A:A1287(OP1) A7364, A7365, A7426, X7874 A:A1287
1m90 A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3398, A7306, A8631, A8978 A:A2095 A:A2096 G:A2097
1m90 A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7409, A7410, A7411, A7412 C:A1103, C:A1104 A:A1107
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 A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3261, A3502, A7379, A7380 C:A534 A:A2814, U:A10
1m90 A8087 cis-2Oph A:A682(OP2), G:A683(OP2) A3205, A7438
1m90 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3171, A3183, A7318, A8540 C:A2475, A:A2624 G:A885
1m90 A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3187, A3696, A7285, A8553 G:A2481 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1mms C257 cis-2Oph A:C1070(OP2), C:C1072(OP1) C258, C259, C260, C261 G:C1062 G:C1062, G:C1074, G:C1063
1mms D380 cis-2Oph A:D1070(OP2), C:D1072(OP1) D381, D382, D383, D384 G:D1062 G:D1074, G:D1062, G:D1063
1n8r A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A8431, A8432, A8433, A8434 C:A1103, C:A1104 A:A1107
1n8r A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A4597, A4881, A8400, A8452 C:A1431 A:A1691, C:A1692 U:A1722, A:A1691
1n8r A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A4129, A4372, A8403, A8404 C:A534 A:A2814, U:A10
1n8r A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A4035, A8249, A8250, A8260 G:A2585, G:A2584
1n8r A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A4023, A4216, A8275, A8276 G:A2616 G:A2618
1n8r A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A4267, A8259, A9512, A9853 A:A2095 A:A2096 G:A2097
1n8r A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A4019, A4254, A8443, A9983 C:A1126 C:A1129, G:B3090
1n8r A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A4054, A4556, A8238, A9436 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1n8r A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A3211, A8380, A8383, A8386 U:A1371
1n8r A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3610, A4009, A7844, A8413 C:A910, U:A909 G:A911, G:A1292
1n8r A8074 cis-2Oph A:A1286(OP1), A:A1287(OP1) A8389, A8390, A8448, X7874 A:A1287
1nji A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3621, A3811, A7782, A7783 G:A2616 G:A2618
1nji A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5876, A6262, A7868, A7906 C:A2745, U:A2749
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

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>