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

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Representative site 1vs7:A1593, See in JSmolMgRNA representative site for type 2PO            Click on the image to toggle views

Site type: 2Pout

Schematic drawing for

MgRNA type 2PO
List of all 191 Mg2+ binding sites with the site type 2Pout 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
1jj2 B8055 2Pout 03285, 03321, 05963, 07269, 07439, B8668 U:02721, C:02720
1k73 D8055 2Pout A3752, A3788, A6426, A7732, A7903, D8664 U:A2721, C:A2720
1m1k D8055 2Pout A7307, D8555, D8629, D8669, D8670, V2221 U:A2721, C:A2720
1m90 A8055 2Pout A3286, A3323, A5955, A7251, A7422, D8660 U:A2721, C:A2720
1q86 D8055 2Pout A3284, A3322, A5935, A7223, A7392, D8667 U:A2721, C:A2720
1qvf 08115 2Pout 03795, 03810, 05894, 06084, A8552, A8633 G:01849, G:01848
1qvf B8055 2Pout 03272, 03308, 07174, 07338, B8627, B8668 U:02721, C:02720
1qvg 08055 2Pout 03298, 07106, B8623, B8663, B8664, T2221 U:02721, C:02720
1s72 B8055 2Pout 03280, 05942, 07225, B8556, B8670, B8671 U:02721, C:02720
1vq4 B8055 2Pout 06670, 07890, B9354, B9460, B9461, U2221 C:02720, U:02721
1vq5 B8055 2Pout 04073, 06685, 07934, B9356, B9467 U:02721, C:02720
1vq6 B8055 2Pout 06649, 07897, B9357, B9473, B9474, U2221 C:02720, U:02721
1vq7 B8055 2Pout 06681, 07927, B9356, B9470, U2221 C:02720, U:02721
1vs5 A1567 2Pout A1717, A1718, A1719, A1720, A1721, A1722 A:A1357, G:A1356
1vs6 B2921 2Pout B3092, B3093, B3094, B3095, B3096, B3097 A:B947, G:B822
1vs7 A1593 2Pout A1844, A1845, A1846, A1847, A1848, A1849 U:A552, A:A553
1vt2 A2962 2Pout A3311, A3312, A3313, A3314, A3315, A3316 A:A1916, U:A1915
1vt2 A2932 2Pout A3176, A3177, A3178, A3179, E205 A:A802, A:A675
1vt2 A2915 2Pout A3088, A3089, A3090, A3091, A3092, A3093 C:A560, G:A2038
1vt2 A2947 2Pout A3240, A3241, A3242, A3243, T255 U:A1313, G:A1334
1yhq B8042 2Pout 04253, 06886, 08236, B9021, B9135, B9136 U:02721, C:02720
1yj9 B8055 2Pout 03572, 06227, 07504, B8853, B8965, B8966 U:02721, C:02720
1yjn B8055 2Pout 03772, 03810, 06426, 07702, B8963, B8964 U:02721, C:02720
1yjw B8055 2Pout 09615, 09618, 09620, B4139, B4142, B4143 C:02720, U:02721
2avy A1566 2Pout A1715, A1716, A1717, A1718, A1719, A1720 A:A1357, G:A1356

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/)
For any help please contact <dust@iwonka.med.virginia.edu>