Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

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PDB ID Mentions in PubMed Central

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.

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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 ].

Publication Year: 2011


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 [29] (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 ).

Publication Year: 2012


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.

Publication Year: 2014


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.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4538837

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