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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
2Pout

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"
Page 4 of 8 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1n A2951 2Pout A3260, A3261, A3262, A3263, A3264 G:A1455, A:A1453
3i1n A2933 2Pout A3182, A3183, A3184, A3185, A3186, A3187 G:A822, A:A947
3i1p A2914 2Pout A3090, A3091, A3092, A3093, A3094, A3095 C:A560, G:A2038
3i1p A2934 2Pout A3183, A3184, A3185, A3186, A3187, A3188 C:A965, G:A822
3i1p A2947 2Pout A3239, A3240, A3241, T348, T350 U:A1313, G:A1334
3i1p A2962 2Pout A3308, A3309, A3310, A3311, A3312, A3313 A:A1916, U:A1915
3i1t A3037 2Pout A3636, A3637, A3638, A3639, A3640, N780 G:A2838, G:A2819
3i1t A2934 2Pout A3185, A3186, A3187, A3188, A3189, A3190 C:A965, G:A822
3i1t A2962 2Pout A3311, A3312, A3313, A3314, A3315, A3316 A:A1916, U:A1915
3i22 A2961 2Pout A3310, A3311, A3312, A3313, A3314, A3315 A:A1916, U:A1915
3i22 A2914 2Pout A3088, A3089, A3090, A3091, A3092, A3093 C:A560, G:A2038
3oas A2914 2Pout A3087, A3088, A3089, A3090, A3091, A3092 C:A560, G:A2038
3oas A2933 2Pout A3183, A3184, A3185, A3186, A3187, A3188 C:A965, A:A947
3oas A2961 2Pout A3309, A3310, A3311, A3312, A3313, A3314 A:A1916, U:A1915
3oas A2906 2Pout A3049, A3050, A3051, A3052, A3053, A3054 C:A41, A:A42
3oat A2932 2Pout A3171, A3172, A3173, A3174, A3175, A3176 G:A822, A:A947
3ofc A2931 2Pout A3173, A3174, A3175, A3176, A3177, A3178 G:A822, A:A947
3ofd A3028 2Pout A3600, A3601, A3602, A3603 U:A1188, A:A1189
3ofd A2907 2Pout A3050, A3051, A3052, A3053, A3054, A3055 C:A41, A:A42
3ofp A1 2Pout A2, A3, A4, A1576, A1577, T87 G:A259, G:A258
3ofq A2937 2Pout A3199, A3200, A3201, A3202 G:A822, A:A945
3ofq A2962 2Pout A3310, A3311, A3312, A3313, A3314, A3315 A:A1916, U:A1915
3ofz A2931 2Pout A3171, A3172, A3173, A3174, A3175, A3176 G:A822, A:A947
3og0 E202 2Pout A3106, A3107, A3108, A3109, A3110, A3111 U:A2016, G:A1256
3og0 A3027 2Pout A3599, A3600, A3601, A3602 U:A1188, A:A1189

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>