`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
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 4 of 35 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1q82 A8040 Oph·3Pout U:A392(OP2) A3299, A4150, A7338, A9202, N8654 U:A391, C:A171, U:A172
1q82 A8032 Oph·3Pout U:A2115(OP1) A3237, A3298, A3699, A9499, C8645 U:A2116, G:A2272, C:A2273
1q82 A8072 Oph·3Pout U:A954(OP1) A3505, A6896, A7309, A7364, A9743 G:A2299, A:A2301, C:A2298
1q82 A8058 Oph·3Pout G:A2013(OP2) A3274, A7296, A7297, C8646, C8648 G:A1884, U:A1883, C:A2626
1q86 A8032 Oph·3Pout U:A2115(OP1) A3316, A3717, A9513, C8548, C8622 U:A2116, G:A2272, C:A2273
1q86 A8045 Oph·3Pout G:A1979(OP2) A7321, A7373, A7374, A7375 G:A1998, C:A1999, A:A1978
1q86 A8021 Oph·3Pout G:A2304(OP2) A3163, A3164, A7273, A7274, A9485 A:A2301, A:A2303, A:A2305 A:A2305, G:A2304, U:A2306
1q86 A8072 Oph·3Pout U:A954(OP1) A3524, A6930, A7339, A7395, A9754 G:A2299, A:A2301, C:A2298
1q86 A8037 Oph·3Pout A:A2553(OP2) A3174, A7368, A8599, A9658, A9733 A:A2576, U:A2554, C:A2575 C:A2552 A:A2576
1q86 A8035 Oph·3Pout G:A1484(OP2) A3242, A7311, A7312, A7366, A7367 C:A1456, A:A1485, C:A1455 G:A1484, U:A1457
1q86 A8017 Oph·3Pout G:A456(OP2) A3147, A3474, A6907, A7267, A8940 A:A455, G:A458, U:A457
1qvf 08091 Oph·3Pout G:0918(OP1) 05964, 07299, 08614, 09068, 09841 C:02294, C:02391, A:02465 A:02465
1qvf 08040 Oph·3Pout U:0392(OP2) 03303, 04144, 07315, 07316, 09213 U:0391, C:0171, U:0172
1qvf 08021 Oph·3Pout G:02304(OP2) 03154, 03155, 07222, 07223, 09482 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1qvf 08032 Oph·3Pout U:02115(OP1) 03241, 03302, 03700, 09506, A8629 U:02116, G:02272, C:02273
1qvf 08017 Oph·3Pout G:0456(OP2) 03456, 07217, 08934, C8357, C8460 G:0458, A:0455, U:0457
1qvf 08035 Oph·3Pout G:01484(OP2) 03231, 07257, 07258, 07311, 07312 C:01456, A:01485, C:01455 G:01484, U:01457
1qvf 08037 Oph·3Pout A:02553(OP2) 03165, 07313, 08599, 09652, 09726 A:02576, U:02554, C:02575 C:02552 A:02576
1qvg 08040 Oph·3Pout U:0392(OP2) 03293, 04123, 07247, 07248, 09208 U:0391, C:0171, U:0172
1qvg 08032 Oph·3Pout U:02115(OP1) 03231, 03292, 03685, 09496, A8621 U:02116, G:02272, C:02273
1qvg 08021 Oph·3Pout G:02304(OP2) 03144, 03145, 07155, 07156, 09469 A:02301, A:02303, A:02305 A:02305, G:02304, U:02306
1qvg 08037 Oph·3Pout A:02553(OP2) 03154, 07245, 08602, 09641, 09716 A:02576, U:02554, C:02575 C:02552 A:02576
1s72 08040 Oph·3Pout U:0392(OP2) 03312, 04168, 07371, 07372, 09213 U:0391, C:0171, U:0172
1s72 08021 Oph·3Pout G:02304(OP2) 03159, 03160, 07274, 07275, 09486 A:02301, A:02305, A:02303 A:02305, G:02304, U:02306
1s72 08072 Oph·3Pout U:0954(OP1) 03519, 06928, 07339, 07397, 09752 G:02299, A:02301, C:02298

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>