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

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Representative site 2qbd:A2237, See in JSmolMgRNA representative site for type OP-OB          Click on the image to toggle views

Site type: Oph·Ob

Schematic drawing for

MgRNA type OP-OB
List of all 554 Mg2+ binding sites with the site type Oph·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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1jj2 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03159, 03485, 05718, 08915 G:01490, A:01487, U:01488 G:01489, G:01490
1jj2 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03309, 07312, 08567, 09303 A:0455, A:0460, A:0477 A:0455
1jj2 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03399, 03542, 03683, L8643 G:0267, U:0268
1k73 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3868, A4011, A4152, N8642 G:A267, U:A268
1k8a A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3460, A3600, A3742, A7411 G:A267, U:A268
1k9m A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3863, A4006, A4148, N8643 G:A267, U:A268
1k9m A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3624, A3948, A6180, A9390 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1kc8 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3637, A3962, A6173, A9397 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1kc8 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3877, A4018, A4158, N8650 G:A267, U:A268
1kd1 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3866, A4007, A4149, N8648 G:A267, U:A268
1kd1 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3628, A3952, A6168, A9388 A:A1487, U:A1488 G:A1489, G:A1490
1kqs 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03380, 03520, 03661, L8654 G:0267, U:0268
1kqs 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03291, 07247, 08568, 09290 A:0455, A:0460, A:0477 A:0455
1kqs 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03141, 03466, 05676, 08906 G:01490, A:01487, U:01488 G:01489, G:01490
1m1k A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3227, A3551, A5777, A8986 G:A1490, A:A1487, U:A1488 G:A1490, G:A1489
1m90 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3401, A3543, A3688, A7392 G:A267, U:A268
1m90 A8004 Oph·Ob A:A459(OP1) G:A456(O6) A3311, A7294, A8566, A9298 A:A455, A:A460, A:A477 A:A455
1n8r A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A4028, A4355, A6562, A9790 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1n8r A8027 Oph·Ob C:A240(OP1) G:A269(O6) A4270, A4409, A4548, N8656 G:A267, U:A268
1n8r A8028 Oph·Ob A:A1448(OP2) U:A1677(O4) A4073, A4094, A8283, A9967 G:A1676 G:A1676
1nji A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3626, A3949, A6173, A9389 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1nji A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3865, A4005, A4146, N8641 G:A267, U:A268
1nji A8004 Oph·Ob A:A459(OP1) G:A456(O6) A3773, A7754, A9048, A9772 A:A455, A:A460, A:A477 A:A455
1q7y A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3382, A3520, A3663, A7334 G:A267, U:A268
1q7y A8028 Oph·Ob A:A1448(OP2) U:A1677(O4) A3186, A3208, A3220, T8317 G:A1676

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>