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

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Representative site 2z4m:A1592, See in JSmolMgRNA representative site for type PO             Click on the image to toggle views

Site type: Pout

Schematic drawing for

MgRNA type PO
List of all 94 Mg2+ binding sites with the site type Pout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vt2 A2934 Pout A3184, A3185, A3186, A3187, A3188, A3189 C:A965
1vt2 A2995 Pout A3471, A3472, A3473, A3474, A3475 A:A1028
1vt2 A2907 Pout A3050, A3051, A3052, A3053, A3054, A3055 A:A42
1vt2 A2919 Pout A3115, A3116, A3117, A3118, A3119, A3120 C:A1257
2bx2 L1511 Pout L2021, L2022, L2032, L2033, R2002, R2003 U:R12
2c0b L1510 Pout L2023, L2024, L2028, L2029, R2002, R2003 A:R9
2c4r L1511 Pout L2001, L2002, L2003, L2004, L2005, R2001 U:R9
2nug A506 Pout C520, C521, A526, A527, A528, A529 C:C7
2nug B512 Pout D518, D519, D563, B527, B528, B529 C:D7
2qam B3194 Pout B3769, B3770, B3771, B3772, B3773, B3774 G:B649
2qbd A2136 Pout A2137, A2138, A2139, A2140, A2141, A2142 G:A727
2qbd A2219 Pout A2220, A2221, A2222, A2223, A2224, A2225 U:A916
2qou A1565 Pout A2005, A2006, A2007, A2008, A2009, A2010 U:A854
2qoy A1600 Pout A2176, A2177, A2178, A2179, A2180, A2181 G:A258
2qp1 B2962 Pout B3797, B3798, B3799, B3800, B3801, B3802 G:B2819
2z4m A1592 Pout A1842, A1843, A1844, A1845, A1846, A1847 A:A553
3df3 A2134 Pout A4135, A4136, A4137, A4138, A4139, A4140 U:A1205
3i1p A2906 Pout A3051, A3052, A3053, A3054, A3055, A3056 C:A41
3i1r A2933 Pout A3179, A3180, A3181, A3182, A3183, A3184 G:A822
3i1t A2906 Pout A3050, A3051, A3052, A3053, A3054, A3055 C:A41
3i20 A2933 Pout A3180, A3181, A3182, A3183, A3184, A3185 G:A822
3i22 A2906 Pout A3049, A3050, A3051, A3052, A3053, A3054 A:A42
3i22 A2933 Pout A3184, A3185, A3186, A3187, A3188, A3189 C:A965
3i22 A3035 Pout A3630, A3631, A3632, A3633, A3634, N772 G:A2004
3oar A1552 Pout A1660, A1661, A1662, A1663, A1664, A1665 G:A1079

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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/)
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