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 4 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 Z4012 Oph·Or 4   0.25   0.52   0.24 no 2vhn Z4013 2Pout·Bout 3   0.10   0.40   0.55 no 2vhn Z4016 Nb 3   0.12   0.25   0.35 no 2vhn Z4019 Oph 3   0.12   0.44   0.12 no 2vhn Z4020 Oph 5   0.22   0.80   0.38 no 2vhn Z4021 cis-2Oph 5   0.29   0.58   0.31 no 2vhn Z4022 Oph·2Pout 5   0.26   0.57   0.15 no 2vhn Z4023 Ob 5   0.24   0.73   0.52 no 2vhn Z4030 cis-2Oph 3   0.23   0.39   0.82 no 2vhn Z4032 fac-3Oph 4   0.12   0.67   0.47 no 2vhn Z4037 Oph·Ob·Nb 6   0.19   0.87   0.79 no 2vhn Z4040 Mg2+ not bound by RNA 1   0.02  0   0.57 no 2vhn Z4044 2Bout 2   0.06   0.25   0.82 no 2vhn Z4045 cis-2Oph 4   0.21   0.45   0.33 no 2vhn Z4049 Mg2+ not bound by RNA 0  0  0   0.54 no 2vhn Z4053 Bout 3   0.17   0.32   0.53 no 2vhn Z4054 Ob 4   0.37   0.59   0.12 no 2vhn Z4064 Oph·Ob 4   0.37   0.44   0.42 no 2vhn Z4068 cis-2Oph·Or 4   0.52   0.78   0.15 no 2vhn Z4076 trans,cis-4Oph 5   0.12   0.63   0.95 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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