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

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Representative site 3df3:A2016, See in JSmolMgRNA representative site for type 2PO-3BO        Click on the image to toggle views


Site type: 2Pout·3Bout

Schematic drawing for
2Pout·3Bout

MgRNA type 2PO-3BO
List of all 277 Mg2+ binding sites with the site type 2Pout·3Bout 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 08071 2Pout·3Bout 6  0.99  0.84  0.57yes
1k73 A8071 2Pout·3Bout 6  0.98  0.91  0.59yes
1k8a A8071 2Pout·3Bout 6  0.81  0.81  0.78yes
1k9m A8071 2Pout·3Bout 6  0.63  0.79  0.54yes
1kc8 A8071 2Pout·3Bout 6  0.83  0.84  0.60yes
1kd1 A8071 2Pout·3Bout 6  0.64  0.71  0.58yes
1kqs 08071 2Pout·3Bout 6  0.90  0.97  0.46no
1m1k A8071 2Pout·3Bout 6  0.69  0.72  0.66yes
1m90 A8071 2Pout·3Bout 6  0.88  0.96  0.69yes
1mms D397 2Pout·3Bout 5  0.42  0.65  0.81no
1n78 C700 2Pout·3Bout 6  0.91  0.86  0.91yes
1n78 D701 2Pout·3Bout 6  0.80  0.90  0.96yes
1n8r A8071 2Pout·3Bout 6  0.74  0.88  0.40no
1nji A8071 2Pout·3Bout 6  0.67  0.91  0.67yes
1nuj B419 2Pout·3Bout 6  0.72  0.88  0.82yes
1nuj H422 2Pout·3Bout 6  0.70  0.89  0.93yes
1nuv B412 2Pout·3Bout 6  0.70  0.80  0.93yes
1nuv H415 2Pout·3Bout 6  0.80  0.89  0.84yes
1q7y A8071 2Pout·3Bout 6  0.98  0.82  0.82yes
1q81 A8071 2Pout·3Bout 6  0.95  0.90  0.73yes
1q82 A8071 2Pout·3Bout 6  0.68  0.76  0.53yes
1q86 A8071 2Pout·3Bout 6  0.82  0.88  0.76yes
1qvf 08071 2Pout·3Bout 6  0.84  0.82  0.61yes
1qvg 08071 2Pout·3Bout 6  0.93  0.86  0.49no
1s72 08071 2Pout·3Bout 6  0.94  0.86  0.60yes

# 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>