Primary Citation PubMed: 15989951
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Dissecting protein-RNA recognition sites.
(2008) Nucleic Acids Res 36
PubMed: 18353859 | PubMedCentral: PMC2377425 | DOI: 10.1093/nar/gkn102
The protein–RNA data set A. Complexes with tRNA ( 21 ) 1asy 1c0a 1f7u* 1ffy* 1gax 1h3e 1h4s 1j1u* 1n78* 1qf6 1qtq 1ser 1... tt 1u0b* 1vfg 2azx 2bte 2csx 2drb 2fk6 2fmt B. Ribosomal proteins ( 11 ) 1dfu* 1f7y 1feu* 1g1x 1i6u 1mji 1mms 1mzp 1s03 1sds* 2hw8* C. Duplex RNA ( 17 ) 1di2* 1e7k 1hq1* 1msw* 1ooa 1r3e* 1rpu 1si3 1wne 1yvp* 1zbi* 2az0 2ez6* 2f8s 2gjw 2hvy* 2ipy D. Single-stranded RNA ( 30 ) 1a9n 1av6 1cvj 1g2e* 1jbs* 1jid* 1k8w* 1knz 1kq2 1lng* 1m5o* 1m8v 1m8w* 1n35 1wpu* 1wsu* 1zbh 1zh5* 2a8v 2anr* 2asb* 2b3j* 2bx2 2db3* 2f8k* 2g4b 2gic 2i82* 2ix1 2j0s* E. Miscellaneous ( 2 ) 2bgg* 2bh2* Asterisk indicates PDB entry with resolution better than 2.4 Å.
Publication Year: 2008
Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage.
(2010) Mol Cell 40
PubMed: 21095591 | PubMedCentral: PMC3025331 | DOI: 10.1016/j.molcel.2010.11.001
Figure 6 Comparison of the Active Sites of Type 1 and 2 RNases H Stereoview of the comparison of the active sites of B. halodurans RNase H1 (PDB 1ZBI ) and T. maritima RNase H2.
Publication Year: 2010
PCNA directs type 2 RNase H activity on DNA replication and repair substrates.
(2011) Nucleic Acids Res 39
PubMed: 21245041 | PubMedCentral: PMC3089482 | DOI: 10.1093/nar/gkq980
The rotation and translation matrix generated was applied to the RNA/DNA hybrid (PDB ID: 1ZBI, chains A and B) using PDBSET in the CCP4 package ( 34 ).
The RNA/DNA hybrid from the Escherichia coli RNase HI co-crystal structure (PDB ID: 1ZBI) was docked into the active site of Afu RNase HII based on the conserved metal coordination geometry between the two enzymes.
Publication Year: 2011
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.
(2011) BMC Bioinformatics 12
PubMed: 21851628 | PubMedCentral: PMC3179970 | DOI: 10.1186/1471-2105-12-348
There are 72 protein-RNA complexes in the training set taken from crystal structures of protein-RNA complexes downloaded from the Protein Data Bank (PDB codes: 1a1v , 1a34 , 1b2m , 1c0a , 1d9d , 1dfu ... 1di2 , 1bu1 , 1ec6 , 1f7u , 1feu , 1ffy , 1fxl , 1gtf , 1gtr , 1hq1 , 1j1u , 1jbs , 1jid , 1jj2 - 50S ribosome structure, 1k8w , 1knz , 1lng , 1m8w , 1mji , 1msw , 1n35 , 1n78 , 1ooa , 1qln , 1r3e , 1r9f , 1rc7 , 1sds , 1tfw , 1u0b , 1urn , 1uvj , 1wsu , 1yvp , 1zbi , 1a8v , 2bgg , 2bh2 ) [ 25 ].
Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.
(2012) PLoS Comput Biol 8
PubMed: 23028290 | PubMedCentral: PMC3459882 | DOI: 10.1371/journal.pcbi.1002693
In order to approximate a catalytically competent configuration, two Mg 2+ ions were placed in the active site by analogy with the active site configuration of an RNase H complex bound to a DNAȂ... ;RNA hybrid  (PDB accession number 1ZBI).
Publication Year: 2012
Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger.
(2012) Nucleic Acids Res 40
PubMed: 23042681 | PubMedCentral: PMC3526281 | DOI: 10.1093/nar/gks885
The model of the ZfQQR-nucleic acid complex was combined with the crystal structure of RNase HI from B. halodurans complexed with the DNA–RNA hybrid (PDB code 1zbi) ( 6 ).
Calcium inhibition of ribonuclease H1 two-metal ion catalysis.
(2014) J Am Chem Soc 136
PubMed: 24499076 | PubMedCentral: PMC3985467 | DOI: 10.1021/ja411408x
Methods The QM/MM calculations were initiated from the X-ray crystal structure of the B. halodurans RNase H1 enzyme complexed with a hybrid RNA.DNA duplex substrate, and with both metal sites occupied... by Mg 2+ (PDB code 1ZBI 51 ).
This water molecule (WAT 26 in the 1ZBL structure) is present in most high-resolution structures (e.g., PDB ID: 1ZBL, 1ZBI, 2G8F, or 2QKK).
Publication Year: 2014
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification.
(2014) Nucleic Acids Res 42
PubMed: 24464998 | PubMedCentral: PMC3985635 | DOI: 10.1093/nar/gkt1414
( B ) Superposition of the active sites of RNase H1 (D132N mutant) from B. halodurans (PDB code: 1zbi; shown in green) and RNase T from E. coli (PDB code: 3nh1; shown in magenta), with metal ions and ... ubstrate nucleic acids bound.
Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site.
(2014) F1000Res 3
PubMed: 25075292 | PubMedCentral: PMC4032109 | DOI: 10.12688/f1000research.3605.1
( D ) Structural diversity of RNases H in complex with substrate: Homo sapiens RNase H with Ca 2+ ions (2QKK), brown; Bacillus halodurans RNase H with Mn 2+ ions (1ZBI), dark green.
PubMed ID is not available.
Published in 2015
In addition, the structure of RNase HI from Bacillus halodurans in complex with an RNA/DNA hybrid (PDB code: 1ZBI, Z -score = 4.7, r.m.s.d. = 3.8 Å, sequence identity = 13%) ( 41 ) also showed... similarity to that of PhoExo I.
Publication Year: 2015
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.