`

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 4qcq




4QCQ (2.55Å) -- RIBOSOME : Crystal structure of the thermus thermophilus 70s ribosome in the post-catalysis state of peptide bond formation containing dipeptydil- trna in the a site and deacylated trna in the p site. this entry contains the 50s subunit of the first 70s ribosome in
List of all 20 Mg2+ binding sites in the PDB structure 4qcq 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 1
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4qcq A3152 Ob G:A1417(O6) A4111, A4112, A4113, A4114, A4115 G:A1416, G:A1415 U:A1481, G:A1482, G:A1415, G:A1416
4qcq A3154 Nb G:A362(N7) A4120, A4121, A4122, L201 G:A361, G:A362 G:A361
4qcq A3163 Ob·Nb G:A1432(O6) A4138, A4139, A4140, A4141 C:A1466 G:A1467
4qcq A3159 Oph G:A21(OP1) A4129, A4130, A4131, A4132, A4133 G:A568, G:A567 G:A567, A:A573
4qcq A3126 Oph A:A766(OP2) A4046, A4047, A4048, A4049 C:A811, C:A812, U:A813, A:A767
4qcq A3153 Oph C:A352(OP2) A4116, A4117, A4118, A4119 C:A352, C:A330, G:A331 G:A354, A:A59, C:A330
4qcq A3123 Oph·Pout G:A903(OP1) A4036, A4037, A4038, A4039 C:A904 G:A890
4qcq A3125 Oph·3Pout A:A768(OP2) A4041, A4042, A4043, A4044, A4045 U:A804, C:A805, A:A767 A:A768, G:A769
4qcq A3131 trans-2Oph A:A782(OP1), A:A794(OP2) A4064, A4065, A4066, A4067 C:A783 G:A1521, U:A1522, C:A1515
4qcq A3129 2Bout A4054, A4055, A4056, A4057, A4058 G:A44, G:A396
4qcq A3180 Pout A4178, A4179, E301, E302 A:A864
4qcq A3110 Pout·Bout A4006, A4007, A4008, A4009 U:A871 G:A853
4qcq A3143 Pout·3Bout A4085, A4086, A4087, A4088, A4089 A:A781 G:A799, G:A798, G:A800
4qcq A3172 2Pout A4162, A4163, A4164, A4165 A:A814, C:A904
4qcq A3130 2Pout·Rout·Bout A4059, A4060, A4061, A4062, A4063 A:A915, G:A916 U:A13 G:A916
4qcq A3145 2Pout·2Bout A4092, A4093, A4094, A4095, A4096, A4097 U:A804, G:A803 U:A772, G:A771
4qcq A3169 2Pout·Rout·2Bout A4154, A4155, A4156, V101 C:A1496, G:A1497 U:V17 G:A1497, U:A1498
4qcq A3170 2Pout·3Bout A4157, A4158, A4159, V102, V103 G:A1401, G:V18 G:A1401, C:A1399, G:V18
4qcq A3117 3Pout·2Bout A4019, A4020, A4021, A4022, A4023 C:A779, A:A780, G:A799 G:A800, A:A780
4qcq A3168 4Pout A4148, A4149, A4150, A4151, A4152, A4153 U:A13, U:A14, G:A15, A:A16

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>