`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 1kd1




1KD1 (3Å) -- RIBOSOME : Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui
List of all 44 Mg2+ binding sites in the PDB structure 1kd1 in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 2 of 3 | | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1kd1 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3635, A7761, A7762, A7772 G:A2585, G:A2584
1kd1 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5872, A6258, A7872, A7910 C:A2745, U:A2749
1kd1 A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7826, A7827, A7828, A9814 A:A2649 U:A1371
1kd1 A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A4200, A4483, A7843, A7896 C:A1431 A:A1691 U:A1722, A:A1691
1kd1 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4319, A7752, A7753 U:A625 U:A626
1kd1 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3606, A3612, A3624 G:A164, A:A165 G:A164
1kd1 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7848, A7898, A7899
1kd1 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3611, A7774, A9173 U:A2484 A:A2532
1kd1 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3662, C8511, C8536
1kd1 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3613, A3750, A9805 G:A856, U:A855
1kd1 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3742, A7777, A7778
1kd1 A8005 mer-3Oph A:A1836(OP1), U:A1838(OP1), A:A1839(OP2) A3607, A7775, A7776 G:A1837 A:A1839
1kd1 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3357, A7764, A9008
1kd1 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3625, A7768, A7854 G:A2466
1kd1 A8033 fac-3Oph·Ob A:A1747(OP2), U:A1748(OP2), G:A2585(OP1) U:A1749(O4) A3811, A9668 U:A2586
1kd1 C8065 Rout A3963, A9915, C8523, C8553, C8605, C8635 G:A782
1kd1 A8063 2Bout A4175, A7001, A7436, A7758, A7837, A7889 G:A1364, G:A1363
1kd1 A8071 2Pout·3Bout A4105, A6048, A7421, A7555, A7835, A7836 A:A1815, C:A1816 U:A1813, C:A1818, U:A1817
1kd1 L8069 Mg2+ bound by non-RNA A4236, A6039, L1797, L2121, L7871 ASN:L42(OD1) U:A1749, A:A2583, G:A2584, U:A2546
1kd1 A8056 Mg2+ bound by non-RNA A:A2757(OP1) A3664, A3968, A7838, A9974 ASN:D335(O) A:A2719, C:A2720, G:A2758

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>