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

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List of Mg2+ binding sites in structure 4qcp




4QCP (2.6Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing acylated trna- substrates in the a and p sites. this entry contains the 50s subunit of the second 70s ribosome in the asu.
List of all 94 Mg2+ binding sites in the PDB structure 4qcp 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 5 of 5 | | Next » | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qcp A3313 3Pout·3Bout A4177, A4178, A4179, A4180, A4181 G:A1334, U:A1313, C:A1333 U:A1335, G:A1334, U:A1316
4qcp A3385 3Pout·Rout·3Bout A4380, A4381, A4382, A4383, A4384, A4385 G:A570, A:A973, U:A569 G:A972 A:A821, A:A820, U:A568
4qcp A3372 3Pout·2Rout·3Bout A4338, A4339, A4340, A4341, A4342 A:A1609, C:A1617, G:A1619 A:A1608, C:A1617 G:A1619, G:A1613, G:A1620
4qcp A3551 4Pout·2Bout A4762, A4763, A4764, A4765, A4766, A4767 A:A1936, C:A1958, G:A1959, A:A1937 A:A1960, G:A1959
4qcp A3575 5Pout·2Bout A4824, A4825, A4826, A4827, A4828, A4829 A:A2051, G:A2578, A:A2614, U:A2613, C:A2050 A:A2051, A:A2614
4qcp A3003 Mg2+ bound by non-RNA A:A2821(OP2), G:A2822(OP2) GLY:E110(O), HIS:R3(NE2)
4qcp A3331 poly-nuclear Mg2+ site G:A2588(OP2) A4241, A4242, A4243, D401, D402 A:A2587, A:A2589 A:A2589, G:A2588
4qcp A3330 poly-nuclear Mg2+ site G:A2685(O6) A4236, A4237, A4238, A4239, A4240 G:A2686, C:A2724, U:A2684
4qcp A3415 poly-nuclear Mg2+ site U:A576(OP1), A:A2503(OP1) A4458, A4459, A4460, A4461 G:A577, G:A2056, U:A2504, A:A2057
4qcp A3439 poly-nuclear Mg2+ site G:A1975(OP2) A4517, A4518, A4519, A4520 C:A1974, C:A1771
4qcp A3550 poly-nuclear Mg2+ site G:A2069(OP2) A4758, A4759, A4760, A4761 G:A2070, U:A2244
4qcp A3277 poly-nuclear Mg2+ site G:A2002(N7) A4102, A4103, A4104, A4105 G:A2002, A:A2001 G:A2003
4qcp A3267 poly-nuclear Mg2+ site G:A801(OP2) A4080, A4081, A4082, F401, F402 G:A798, G:A799 A:A800
4qcp A3230 poly-nuclear Mg2+ site U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1)

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].


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