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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2r8s:R1004, See in JSmolMgRNA representative site for type 2OB Click on the image to toggle views


Site type: 2Ob

Schematic drawing for
2Ob
MgRNA type 2OB
List of all 1662 Mg2+ binding sites with the site type 2Ob 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
4l6j A4998 2Ob 2  0.03  0.18  0.97no
3cc7 08032 2Ob 6  0.22  0.82  0.97no
3kiw A3054 2Ob 2  0.10  0.19  0.97no
4qcp A3496 2Ob 4  0.29  0.49  0.97no
3uzg A1800 2Ob 2  0.03  0.58  0.97no
4b3t A2640 2Ob 2  0.06  0.17  0.97no
4qcx A3368 2Ob 3  0.17  0.33  0.97no
3ivn B101 2Ob 2  0.03  0.21  0.97no
4gkj A1736 2Ob 2  0.05  0.26  0.97no
4nvv A3357 2Ob 4  0.28  0.37  0.97no
4gkj A1773 2Ob 2  0.18  0.03  0.97no
4dv7 A1698 2Ob 3  0.19  0.13  0.97no
1vxj A3208 2Ob 2  0.04  0.11  0.97no
3pyr A3274 2Ob 2  0.03  0.19  0.97no
4qcz A3350 2Ob 3  0.16  0.18  0.97no
4qcn A3047 2Ob 2  0.08  0.14  0.97no
4qco A3029 2Ob 2  0.15  0.30  0.97no
4dhc A3617 2Ob 4  0.27  0.54  0.97no
4ji0 A1768 2Ob 2  0.20  0.09  0.97no
3v23 B213 2Ob 5  0.41  0.57  0.97no
4qcx B3007 2Ob 2  0.03  0.25  0.97no
2qoy A1577 2Ob 4  0.37  0.45  0.97no
3v2d A3175 2Ob 4  0.28  0.47  0.97no
4dv2 A1664 2Ob 2  0.03  0.25  0.97no
3i8g A1708 2Ob 2  0.07  0.18  0.97no

# 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>