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

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Representative site 3r8s:A2932, See in JSmolMgRNA representative site for type OP-NB          Click on the image to toggle views


Site type: Oph·Nb

Schematic drawing for
Oph·Nb

MgRNA type OP-NB
List of all 134 Mg2+ binding sites with the site type Oph·Nb 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 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3oas A2974 Oph·Nb G:A2269(OP1) A:A2267(N7) A3373, A3374, A3375, A3376 A:A2268 G:A2271
3ofd A2912 Oph·Nb A:A453(OP1) G:A450(N7) A3075, A3076, A3077, A3078 A:A449 A:A449
3ofd A2974 Oph·Nb G:A2269(OP1) A:A2267(N7) A3372, A3373, A3374, A3375 G:A2271
3ofq A2912 Oph·Nb A:A453(OP1) G:A450(N7) A3075, A3076, A3077, A3078 A:A449 A:A449
3ofr A2932 Oph·Nb U:A810(OP1) A:A1253(N7) A3172, A3173, A3174, A3175 U:A811 C:A565
3ofz A2930 Oph·Nb U:A810(OP1) A:A1253(N7) A3167, A3168, A3169, A3170 U:A811 C:A565
3og0 A2911 Oph·Nb A:A453(OP1) G:A450(N7) A3073, A3074, A3075, A3076 A:A449 A:A449
3orb A2931 Oph·Nb U:A810(OP1) A:A1253(N7) A3172, A3173, A3174, A3175 U:A811 C:A565
3q3z A3 Oph·Nb G:A56(OP1) G:A38(N7) A91, A92, A94, A132 G:A56, G:A38 U:A37 G:A39, A:A70
3q3z A86 Oph·Nb G:A67(OP2) A:A61(N7) A166, A168, A170 A:A61 U:A66 G:A62
3q3z V82 Oph·Nb G:V56(OP1) G:V38(N7) V88, V90, V93, V94 G:V38 U:V37 G:V38, G:V39, A:V70
3r8s A2932 Oph·Nb U:A810(OP1) A:A1253(N7) A3232, A3233, A3234, A3235 U:A811 C:A565
3r8t A2931 Oph·Nb U:A810(OP1) A:A1253(N7) A3204, A3205, A3206, A3207 U:A811 C:A565, G:A1252
3v23 A3416 Oph·Nb A:A1189(OP2) G:A1190(N7) A4328, A4329, A4330, A4331 G:A1190, U:A1188
3v23 A3352 Oph·Nb A:A981(OP1) G:A979(N7) A4083, A4084, A4085, A4086 C:A982, G:A978, G:A979
3v23 A3336 Oph·Nb A:A2639(OP2) G:A2640(N7) A4024, A4025, A4026, A4027 G:A2640 G:A2641
3v23 A3400 Oph·Nb U:A810(OP1) A:A1253(N7) A4270, A4271, A4272, A4273 U:A811
3v25 A3328 Oph·Nb A:A1189(OP2) G:A1190(N7) A3849, A3850, A3851, P304 G:A1190
3v27 A3314 Oph·Nb U:A511(OP2) G:A512(N7) A3876, A3877, A3878, A3879 C:A510
3v29 A3500 Oph·Nb A:A1189(OP2) G:A1190(N7) A4390, A4391, A4392, P307 G:A1190
3v29 A3464 Oph·Nb A:A2639(OP2) G:A2640(N7) A4271, A4272, A4273, A4274 G:A2640 G:A2638 G:A2641
3v2f A3473 Oph·Nb A:A1189(OP2) G:A1190(N7) A4763, A4764, A4765, P306 G:A1190, U:A1188
3v2f A3418 Oph·Nb A:A2639(OP2) G:A2640(N7) A4611, A4612, A4613, A4614 G:A2640 G:A2638 G:A2641
462d A507 Oph·Nb A:A8(OP2) G:A9(N7) A509, A583, A608, A623 G:A9 G:A7, G:A10
462d B506 Oph·Nb A:B8(OP2) G:B9(N7) B507, B509, B511, B566 G:B9 G:B10

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>