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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4nvv



4NVV (3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic dityromycin bound to 70s ribosome
List of all 75 Mg2+ binding sites in the PDB structure 4nvv in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4nvv A3522 Ob U:A959(O4) A4630, A4631, A4632, A4633, A4634 U:A907, A:A956, A:A957, A:A908
4nvv A3487 Ob C:A1020(O2) A4549, A4550, A4551, A4552 A:A595 A:A595
4nvv A3442 Ob U:A2431(O4) A4436, A4437, A4438, 85101, 85102 C:A2429
4nvv A3400 Ob G:A1232(O6) A4305, A4306, A4307, A4308 G:A865, G:A1231, C:A864 G:A865, G:A1231
4nvv A3348 Nb G:A2024(N7) A4180, A4181, A4182, A4183, A4184 G:A2024 G:A2025
4nvv A3309 Nb G:A322(N7) A4080, A4081, A4082, A4083, A4084 C:A321, G:A322, G:A362
4nvv A3316 2Nb G:A780(N7), A:A808(N7) A4100, A4101, A4102, A4103 C:A779, G:A780, G:A807, A:A808
4nvv A3435 Oph A:A2610(OP1) A4419, A4420, D402, D403, D404
4nvv A3351 Oph C:A597(OP1) A4193, A4194, A4195, A4196, A4197 A:A2076 G:A2057, U:A2056
4nvv A3550 Oph G:A2057(OP1) A4705, A4706, A4707, A4708 G:A2059, G:A2060
4nvv A3427 Oph·Pout A:A1992(OP2) A4400, A4401, A4402, A4403 A:A1922 U:A1865 G:A1866
4nvv A3425 Oph·Pout A:A1723(OP2) A4391, A4392, A4393, A4394, A4395 C:A1722 G:A1721 A:A1723, A:A1724
4nvv A3367 Oph·Pout G:A1254(OP2) A4238, A4239, A4240, A4241 A:A1255 A:A355
4nvv A3457 Oph·Pout A:A1711(OP2) A4482, A4483, A4484, A4485, A4486 G:A2014 G:A2014, A:A1712, G:A1713, G:A1714, A:A1711
4nvv A3459 Oph·Pout A:A990(OP2) A4488, A4489, A4490, A4491 G:A878 G:A989, G:A878
4nvv B3011 Oph·Pout G:B101(OP2) B4012, B4013, B4014, B4015 A:B102 A:B102
4nvv A3588 Oph·Pout U:A988(OP2) A4802, A4803, A4804, P305, P306 G:A879 G:A989
4nvv A3575 Oph·Pout G:A2019(OP2) A4764, A4765, A4766, E404 U:A2017
4nvv A3350 Oph·Pout U:A1398(OP1) A4188, A4189, A4190, A4191, A4192 C:A1421 A:A1618
4nvv A3325 Oph·2Pout G:A1807(OP2) A4125, A4126, A4127, A4128, A4129 U:A1806, A:A2003 G:A1807

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>