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 2vhn 2VHN (3.74Å) -- RIBOSOME : Structure of pdf binding helix in complex with the ribosome. (part 2 of 4) List of all 111 Mg2+ binding sites in the PDB structure 2vhn 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" Page 5 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2vhn Z4078 Oph 4   0.08   0.75   0.70 no 2vhn Z4079 Oph 4   0.08   0.50   0.40 no 2vhn Z4083 cis-2Oph 5   0.32   0.57   0.47 no 2vhn Z4087 cis-2Oph 4   0.21   0.43   0.83 no 2vhn Z4088 cis-2Oph·Nb 4   0.17   0.35   0.69 no 2vhn Z4089 cis-2Oph 5   0.20   0.71   0.96 no 2vhn Z4092 Oph·2Pout 4   0.19   0.70   0.07 no 2vhn Z4097 Pout·Rout 3   0.15   0.61   0.29 no 2vhn Z4098 Mg2+ bound by non-RNA 4   0.14   0.46   0.40 no 2vhn Z4099 4Pout·Bout 4   0.18   0.55   0.16 no 2vhn Z4102 2Pout 5   0.33   0.61   0.22 no 2vhn Z4002 3Pout·2Bout 4   0.22   0.63   0.21 no 2vhn Z4015 Pout·Rout·Bout 3   0.15   0.19   0.49 no 2vhn Z4027 3Pout·4Bout 4   0.17   0.61   0.78 no 2vhn Z4041 4Pout·Bout 3   0.13   0.49   0.35 no 2vhn Z4043 trans,cis-4Oph 4   0.14   0.35   0.86 no 2vhn Z4062 2Pout 3   0.10   0.41   0.24 no 2vhn Z4096 Mg2+ bound by non-RNA 4   0.18   0.36   0.83 no 2vhn Z4103 Bout 2   0.19   0.16   0.69 no 2vhn Z4104 2Pout·Bout 3   0.10   0.30   0.29 no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e 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].

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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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