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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 4dhc




4DHC (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome
List of all 719 Mg2+ binding sites in the PDB structure 4dhc in the full dataset (switch to benchmark dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "Site type" or "Mg2+ ID"
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Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
4dhc A3172 Or 1  0.02 0  0.76no
4dhc A3068 Or 1  0.02 0  0.73no
4dhc A3278 Or 1  0.01 0  0.83no
4dhc A3185 Or 1  0.01 0  0.95no
4dhc A3115 Or 1  0.02 0  0.80no
4dhc A3208 Or 1  0.03 0  0.84no
4dhc A3126 Or 1  0.05 0  0.78no
4dhc A3254 Or 1  0.01 0  0.78no
4dhc A3373 Or 1  0.02 0  0.72no
4dhc A3460 Or 4  0.40  0.65  0.98no
4dhc A3051 Or 1  0.01 0  0.90no
4dhc A3024 Ob 1  0.03 0  0.93no
4dhc A3283 Ob 1  0.02 0  0.87no
4dhc A3031 Ob 1  0.01 0  0.66no
4dhc A3020 Ob 2  0.04  0.21  0.93no
4dhc B201 Ob 1  0.01 0  0.77no
4dhc A3135 Ob 1  0.02 0  0.92no
4dhc A3624 Ob 3  0.27  0.54  0.93no
4dhc A3120 Ob 1  0.04 0  0.86no
4dhc A3525 Ob 4  0.38  0.68  0.78no

# Validation parameters Qv, Qs, Qe are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Qv measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg2+ (+2)
Qs measures the geometrical symmetry of the ligands distribution around the Mg2+ required for octahedral geometry
Qe measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg2+ compared to those of all atoms in its environment

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>