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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 1vq7:08033, See in JSmolMgRNA representative site for type fac-3OP-OB     Click on the image to toggle views


Site type: fac-3Oph·Ob

Schematic drawing for
fac-3Oph·Ob

MgRNA type fac-3OP-OB
List of all 138 Mg2+ binding sites with the site type fac-3Oph·Ob in RNA crystal structures 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 #", "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
1jj2 08033 fac-3Oph·Ob 6  0.86  0.87  0.80yes
1k73 A8033 fac-3Oph·Ob 6  0.94  0.89  0.87yes
1k8a A8033 fac-3Oph·Ob 6  0.97  0.80  0.49no
1k9m A8033 fac-3Oph·Ob 6  0.92  0.59  0.71no
1kc8 A8033 fac-3Oph·Ob 6  0.93  0.87  0.69yes
1kd1 A8033 fac-3Oph·Ob 6  0.93  0.79  0.77yes
1kqs 08033 fac-3Oph·Ob 6  0.94  0.92  0.74yes
1m1k A8033 fac-3Oph·Ob 6  0.78  0.71  0.94yes
1m90 A8033 fac-3Oph·Ob 6  0.83  0.86  0.82yes
1n8r A8033 fac-3Oph·Ob 6  0.66  0.64  0.94yes
1nji A8033 fac-3Oph·Ob 6  0.83  0.85  0.99yes
1q7y A8033 fac-3Oph·Ob 6  0.76  0.87  0.98yes
1q81 A8033 fac-3Oph·Ob 6  0.96  0.78  0.69yes
1q82 A8033 fac-3Oph·Ob 6  0.95  0.78  0.82yes
1q86 A8033 fac-3Oph·Ob 6  0.94  0.83  0.67yes
1qvf 08033 fac-3Oph·Ob 6  0.94  0.91  0.66yes
1qvg 08033 fac-3Oph·Ob 6  0.96  0.92  0.38no
1s72 08033 fac-3Oph·Ob 6  0.88  0.89  0.79yes
1vq4 08033 fac-3Oph·Ob 6  0.97  0.85  0.79yes
1vq5 08033 fac-3Oph·Ob 6  0.97  0.95  0.93yes
1vq6 08033 fac-3Oph·Ob 6  0.95  0.90  0.91yes
1vq7 08033 fac-3Oph·Ob 6  0.97  0.94  0.99yes
1vq9 08002 fac-3Oph·Ob 6  0.63  0.88  0.77yes
1vqk 08002 fac-3Oph·Ob 6  0.63  0.89  0.55yes
1vqo 08002 fac-3Oph·Ob 6  0.55  0.77  0.69yes

# 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>