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

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Representative site 2qov:B2933, See in JSmolMgRNA representative site for type OP-3PO         Click on the image to toggle views


Site type: Oph·3Pout

Schematic drawing for
Oph·3Pout

MgRNA type OP-3PO
List of all 867 Mg2+ binding sites with the site type Oph·3Pout 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 7 of 35 | | | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vs6 B2942 Oph·3Pout G:B1455(OP2) B3196, B3197, B3198, B3199, B3200 G:B1456, A:B1453, C:B1454 C:B1454 G:B1456, U:B1457
1vs6 B2933 Oph·3Pout G:B450(OP2) B3153, B3154, B3155, B3156, B3157 U:B451, G:B452, A:B449
1vs6 B2979 Oph·3Pout A:B2062(OP1) B3368, B3369, B3370, B3371, B3372 C:B2443, G:B2061, G:B2444 G:B2445, G:B2444
1vs6 B2920 Oph·3Pout G:B1828(OP1) B3087, B3088, B3089, B3090, B3091 G:B1972, G:B1973, A:B1772
1vs6 B2967 Oph·3Pout A:B2005(OP1) B3311, B3312, B3313, B3314 A:B1268, A:B1269, C:B2006
1vs6 B2999 Oph·3Pout G:B862(OP2) B3446, B3447, B3448, B3449, B3450 A:B861, A:B910, A:B863 G:B862, A:B863
1vs7 A1548 Oph·3Pout A:A560(OP2) A1624, A1625, A1626, A1627, A1628 U:A562, A:A563, G:A557 G:A566
1vs8 B3013 Oph·3Pout U:B963(OP1) B3508, B3509, B3510, B3511, B3512 A:B947, A:B2497, C:B2498 U:B963
1vs8 B2937 Oph·3Pout G:B2447(OP2) B3175, B3176, B3177, B3178, B3179 G:B2446, G:B2502, C:B2501 G:B2502
1vs8 B2952 Oph·3Pout A:B2518(OP2) B3245, B3246, B3247, B3248, B3249 A:B2541, U:B2519, C:B2540 A:B2541
1vs8 B2929 Oph·3Pout A:B2062(OP2) B3134, B3135, B3136, B3137, B3138 G:B2061, C:B2443, G:B2444 G:B2444
1vs8 B2978 Oph·3Pout G:B1828(OP1) B3373, B3374, B3375, B3376, B3377 G:B1972, G:B1973, A:B1772
1vs8 B2992 Oph·3Pout C:B31(OP1) B3428, B3429, B3430, B3431, B3432 G:B1239, U:B1199, C:B1200
1vs8 B2980 Oph·3Pout U:B2074(OP1) B3382, B3383, B3384, B3385, B3386 G:B2239, U:B2240, U:B2075 G:B2238
1vs8 B2953 Oph·3Pout G:B1455(OP2) B3250, B3251, B3252, B3253, B3254 G:B1456, A:B1453, C:B1454 C:B1454 U:B1457
1vs8 B2999 Oph·3Pout G:B862(OP2) B3451, B3452, B3453, B3454, B3455 A:B863, A:B861, A:B910 G:B862, A:B863
1vt2 A3020 Oph·3Pout G:A1828(OP2) A3568, A3569, A3570, A3571, C673 U:A1827, G:A1972, C:A1788 G:A1828
1vt2 A2948 Oph·3Pout G:A1333(OP2) A3244, A3245, A3246, A3247, A3248 C:A1314, G:A1332, G:A1334 G:A1331 G:A1333, C:A1335
1vt2 A2981 Oph·3Pout A:A2518(OP2) A3407, A3408, A3409, A3410, A3411 C:A2540, A:A2541, U:A2519
1vt2 A2986 Oph·3Pout A:A218(OP2) A3430, A3431, A3432, A3433 A:A428, A:A217, U:A427 A:A218, G:A220
1vt2 A2971 Oph·3Pout A:A2062(OP2) A3357, A3358, A3359, A3360, A3361 G:A2061, G:A2444, C:A2443 G:A2445, G:A2444
1vt2 A2966 Oph·3Pout C:A2025(OP2) A3332, A3333, A3334, A3335, A3336 U:A2026, U:A2034, A:A2033 A:A2033 U:A2026
1vt2 A2939 Oph·3Pout U:A963(OP1) A3205, A3206, A3207, A3208, A3209 C:A964, A:A2497, A:A947 A:A2497, C:A2498
1vt2 A2954 Oph·3Pout U:A1647(OP2) A3271, A3272, A3273, A3274, A3275 U:A1325, A:A1272, C:A1617 C:A1646, A:A1616 G:A1271
1vt2 A3018 Oph·3Pout A:A1938(OP2) A3559, A3560, A3561, A3562, A3563 A:A1937, C:A1957, C:A1958 G:A1770

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>