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

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Representative site 2i2t:B2987, See in JSmolMgRNA representative site for type cis-2OP-OB     Click on the image to toggle views


Site type: cis-2Oph·Ob

Schematic drawing for
cis-2Oph·Ob

MgRNA type cis-2OP-OB
List of all 98 Mg2+ binding sites with the site type cis-2Oph·Ob 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 1 of 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1ffk 02926 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 02930, 02931, 02932 U:0625 U:0626
1jj2 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03854, 07305, 07306 U:0625 U:0626
1k73 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4319, A7769, A7770 U:A625 U:A626
1k8a A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A3910, A7307, A7308 U:A625 U:A626
1k9m A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4317, A7766, A7767 U:A625 U:A626
1kc8 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4325, A7756, A7757 U:A2535 U:A625 U:A626
1kd1 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4319, A7752, A7753 U:A625 U:A626
1kqs 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03825, 07240, 07241 U:02535 U:0625 U:0626
1m1k A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A3922, A7344, A7345 U:A2535 U:A625 U:A626
1m90 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A3858, A7287, A7288 U:A2535 U:A625 U:A626
1n8r A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4714, A8240, A8241 U:A2535 U:A625 U:A626
1nji A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4314, A7747, A7748 U:A2535 U:A625 U:A626
1q81 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A3830, A7238, A7239 C:A2533 U:A625 U:A626
1q82 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A3835, A7228, A7229 U:A2535 U:A625 U:A626
1q86 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A3852, A7259, A7260 U:A625 U:A626
1qvf 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03832, 07209, 07210 U:0625 U:0626
1qvg 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03817, 07142, 07143 U:0625 U:0626
1s72 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 03851, 07260, 07261 U:02535 U:0625 U:0626
1vq4 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04631, 07924, 07925 U:02535 U:0625 U:0626
1vq5 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04637, 07969, 07970 U:02535 U:0625 U:0626
1vq6 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04627, 07933, 07934 U:02535 U:0625 U:0626
1vq7 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04649, 07964, 07965 U:02535 U:0625 U:0626
1vq8 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 08282, 08283, 09881 U:02535 U:0625, G:02482 C:02071
1vql 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 08288, 08289, 09884 U:02535, G:02482 U:0625
1vqm 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 08288, 08289, 09886 U:02535, G:02482 U:0625

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>