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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 4nvy




4NVY (3.1Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic ge82832 bound to 70s ribosome
List of all 10 Mg2+ binding sites in the PDB structure 4nvy 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"
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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
4nvy A3187 Ob·Nb G:A1432(O6) A4092, A4093, A4094, A4095 C:A1466 G:A1467
4nvy A3175 Oph C:A352(OP2) A4066, A4067, A4068, A4069 G:A331, C:A352 C:A330, A:A59, G:A354
4nvy A3182 Oph G:A21(OP1) A4080, A4081, A4082, A4083, A4084 G:A568, G:A567 A:A563, G:A567, A:A573
4nvy A3151 Oph·2Pout A:A768(OP2) A4022, A4023, A4024, A4025 U:A804, A:A767 A:A768
4nvy A3155 3Bout A4033, A4034, A4035, P101 G:A44, U:A45, G:A396
4nvy A3165 Pout·Bout A4048, A4049, A4050, A4051 G:A803 G:A771
4nvy A3221 Pout·Rout·2Bout A4150, A4151, A4152, V201 C:A1496 U:V17 G:A1497, U:A1498
4nvy A3205 2Pout A4129, A4130, A4131, E203 A:A864, U:A863
4nvy A3145 2Pout·3Bout A4011, A4012, A4013, A4014 U:A582, A:A583 G:A585, G:A584, U:A757
4nvy A3192 4Pout A4104, A4105, A4106, A4107, A4108, A4109 U:A13, U:A14, A:A16, G:A15

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>