`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 2qoy:A1567, See in JSmolMgRNA representative site for type 2BO            Click on the image to toggle views


Site type: 2Bout

Schematic drawing for
2Bout

MgRNA type 2BO
List of all 1271 Mg2+ binding sites with the site type 2Bout 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"
Page 1 of 51 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
1d4r C301 2Bout 4  0.62  0.43  0.95no
1egk A27 2Bout 6  0.96  0.98  1.00yes
1egk C4 2Bout 6  0.93  0.99  1.00yes
1egk A22 2Bout 6  0.95  0.99  1.00yes
1egk A23 2Bout 6  0.93  0.99  1.00yes
1egk A26 2Bout 6  0.96  0.99  1.00yes
1egk A21 2Bout 6  0.93  0.99  1.00yes
1feu C312 2Bout 3  0.44  0.27  0.96no
1hc8 C1164 2Bout 1  0.06 0  0.68no
1hr2 A18 2Bout 6  0.86  0.96  0.99yes
1hr2 B19 2Bout 6  0.86  0.96  0.99yes
1hr2 A22 2Bout 6  0.86  0.96  0.99yes
1ik5 B99 2Bout 5  0.53  0.65  0.97yes
1jj2 08063 2Bout 6  0.99  0.91  0.52yes
1k73 A8063 2Bout 6  0.95  0.82  0.53yes
1k8a A8063 2Bout 6  0.73  0.76  0.88yes
1k9m A8063 2Bout 6  0.77  0.84  0.74yes
1kc8 A8063 2Bout 6  0.83  0.88  0.83yes
1kd1 A8063 2Bout 6  0.70  0.85  0.75yes
1kqs 08063 2Bout 6  0.91  0.85  0.73yes
1l2x A45 2Bout 7  0.82  0.82  0.67no
1l2x A52 2Bout 6  0.88  0.94  0.55yes
1lnt B101 2Bout 4  0.67  0.54  0.80no
1m1k A8063 2Bout 6  0.72  0.55  0.54no
1m90 A8063 2Bout 6  1.00  0.91  0.54yes

# 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>