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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 4qd1



4QD1 (2.8Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the pre- attack state of peptide bond formation containing short substrate- mimic cytidine-cytidine-puromycin in the a site and acylated trna in the p site. this entry contains the 50s subunit
List of all 65 Mg2+ binding sites in the PDB structure 4qd1 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 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
4qd1 A3369 Ob U:A2419(O4) A4232, A4233, A4234, 8202 A:A2418
4qd1 A3364 Ob U:A2593(O4) A4219, A4220, A4221, A4222, D405 G:A2592, C:A2591 C:A2594, G:A2599, G:A2592, A:A1971, A:A2600
4qd1 A3307 Nb G:A2002(N7) A4085, A4086, A4087, A4088, A4089 G:A2002 G:A2003, G:A2004
4qd1 A3283 Nb G:A298(N7) A4031, A4032, A4033, A4034 G:A298, G:A338
4qd1 A3549 Oph A:A1890(OP2) A4593, A4594, A4595, A4596 C:A1852, A:A1890, G:A1891, U:A1851
4qd1 A3362 Oph A:A2598(OP1) A4214, A4215, D402, D403, D404
4qd1 A3539 Oph G:A1839(OP2) A4572, A4573, A4574, A4575 C:A1838 G:A1896, G:A1897, U:A1898
4qd1 A3451 Oph A:A800(OP1) A4412, A4413, A4414, A4415 C:A203 C:A192, A:A191
4qd1 A3465 Oph·Pout G:A770(OP2) A4446, A4447, A4448, A4449 G:A686 G:A770
4qd1 A3471 Oph·Pout U:A943(OP2) A4460, A4461, P304, P305 G:A832 G:A944
4qd1 A3310 Oph·Pout C:A574(OP1) A4095, A4096, A4097, A4098, A4099 C:A2055 G:A2035
4qd1 A3378 Oph·Pout A:A945(OP1) A4254, A4255, A4256, A4257 G:A831 G:A944, G:A831
4qd1 A3353 Oph·Pout A:A1676(OP2) A4192, A4193, A4194, A4195 C:A1675 G:A1674 A:A1676, A:A1677
4qd1 A3563 Oph·Pout A:A53(OP2) A4628, A4629, A4630, A4631 A:A52 G:A55
4qd1 A3347 Oph·Pout U:A588(OP2) A4176, A4177, A4178, A4179 C:A664
4qd1 A3435 Oph·2Pout G:A662(OP1) A4379, A4380, A4381, P303 A:A1247, A:A1246
4qd1 A3346 Oph·2Pout A:A567(OP1) A4172, A4173, A4174, A4175, P301 G:A809, G:A808 G:A809, U:A810
4qd1 A3342 Oph·2Pout C:A1327(OP2) A4158, A4159, A4160, A4161, A4162 U:A1326, G:A1328 G:A1324, G:A1328
4qd1 A3339 Oph·2Pout G:A987(OP2) A4146, A4147, A4148, 33101, 33102 A:A988, C:A986 A:A988
4qd1 A3303 Oph·2Pout G:A446(OP2) A4074, A4075, A4076, A4077, A4078 C:A445, C:A1200 U:A1199 G:A446

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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