Citations in PubMed

Primary Citation PubMed: 11587646 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

(2007) Nucleic Acids Res 35

PubMed: 17264128 | PubMedCentral: PMC1851644 | DOI: 10.1093/nar/gkl1155

C 2 H 2 ZF-DNA PDB files PDB code Chains Description Res (Å) Topology a 1llm C,D Zif268-GCN4 (dimer) 1.5 2_3:3_2 1aay A Zif268 1.6 3_2_1 1a1f, 1a1g, 1a1h, 1a1i, 1a1j, 1a1k, 1a1l A Zif268 (Fn1 ... utants) 1.6 3_2_1 1jk1, 1jk2 A Zif268 (Fn1 D20A) 1.9 3_2_1 1zaa C Zif268 2.1 3_2_1 1mey C,F Designed 2.2 3_2_1 1g2d, 1g2f C,F Designed 2.2 3_2_1 1p47 A,B Zif268 tandem 2.2 3_2_1 3_2_1 1f2i G,H,I,J,K,L Zif268-extension (dimer) 2.4 2_1:1_2 1ubd C YY1 (Yin Yang 1) 2.5 4_3_2_1 2gli A GLI (glioblastoma) 2.6 5_4_3_2_1 2drp A,D Tramtrack 2.8 2_1 1tf6 A,D TFIIIA n/a (NMR) 6_5_4_3_2_1 a Topology description for the individual ZF domains; 3_2_1 indicates a polydactyl ZF protein with three ZF domains, 1 refers to the N-terminal ZF domain.

Publication Year: 2007

DNA-binding residues and binding mode prediction with binding-mechanism concerned models.

(2009) BMC Genomics 10 Suppl 3

PubMed: 19958487 | PubMedCentral: PMC2788376 | DOI: 10.1186/1471-2164-10-S3-S23

Table 5 Dataset of 253 TF-DNA complexes for DNA-binding residues prediction 253 TF-DNA Complexes 1A02:F 1A02:J 1A0A:A 1A0A:B 1A6Y:A 1A6Y:B 1AKH:A 1AKH:B 1AM9:A 1AM9:B 1AM9:C 1AM9:D 1AN2:A 1AN4:A 1AN4:... 1APL:C 1APL:D 1AU7:A 1AU7:B 1B01:A 1B01:B 1B72:B 1B8I:B 1BDT:A 1BDT:B 1BDT:C 1BDT:D 1BDV:A 1BDV:B 1BDV:C 1BDV:D 1BY4:A 1BY4:B 1BY4:C 1BY4:D 1C0W:A 1C0W:B 1C0W:C 1C0W:D 1CF7:A 1CF7:B 1CGP:A 1CGP:B 1CMA:A 1CMA:B 1CQT:A 1D5Y:A 1D5Y:B 1D5Y:C 1D5Y:D 1D66:A 1D66:B 1DDN:A 1DDN:B 1DDN:C 1DDN:D 1DSZ:A 1DSZ:B 1DU0:A 1DU0:B 1EA4:A 1EA4:B 1EA4:D 1EA4:E 1EA4:F 1EA4:G 1EA4:H 1EA4:J 1EA4:K 1EA4:L 1F2I:G 1F2I:H 1F2I:I 1F2I:J 1F2I:K 1F2I:L 1F5T:A 1F5T:B 1F5T:C 1F5T:D 1FJL:A 1FJL:B 1FJL:C 1FOS:E 1FOS:F 1FOS:G 1FOS:H 1G2D:C 1G2D:F 1G2F:C 1G2F:F 1GDT:A 1GDT:B 1H88:A 1H88:B 1H89:A 1H89:B 1H8A:A 1H8A:B 1H9T:A 1H9T:B 1HCQ:A 1HCQ:B 1HDD:C 1HDD:D 1HF0:A 1HF0:B 1HJB:A 1HJB:B 1HJB:D 1HJB:E 1HLO:A 1HLO:B 1HW2:A 1HW2:B 1HWT:C 1HWT:D 1HWT:G 1HWT:H 1IO4:A 1IO4:B 1JGG:A 1JGG:B 1JNM:A 1JNM:B 1JT0:A 1JT0:B 1JT0:C 1JT0:D 1JWL:A 1JWL:B 1K61:A 1K61:B 1K61:C 1K61:D 1KB2:A 1KB2:B 1KB4:A 1KB4:B 1KB6:A 1KB6:B 1KU7:A 1L3L:A 1L3L:B 1L3L:C 1L3L:D 1LAT:A 1LAT:B 1LB2:A 1LE8:A 1LE8:B 1LLI:A 1LLI:B 1LLM:C 1LMB:3 1LMB:4 1MDY:A 1MDY:C 1MDY:D 1MEY:C 1MEY:F 1MJM:A 1MJM:B 1MJP:A 1MJP:B 1MNM:C 1MNM:D 1NKP:A 1NKP:B 1NKP:D 1NKP:E 1NLW:A 1NLW:B 1NLW:D 1NLW:E 1P47:A 1P47:B 1PAR:A 1PAR:B 1PAR:C 1PAR:D 1PER:L 1PER:R 1PUF:A 1PUF:B 1PYI:A 1PYI:B 1QP9:A 1QP9:B 1QP9:C 1QP9:D 1R0N:A 1RPE:L 1RPE:R 1TF6:A 1TF6:D 1TRO:A 1TRO:C 1TRO:E 1TRO:G 1TRR:A 1TRR:B 1TRR:D 1TRR:E 1TRR:G 1TRR:H 1TRR:J 1TRR:K 1YRN:A 1YRN:B 1YSA:C 1YSA:D 1ZME:C 1ZME:D 2DRP:A 2DRP:D 2HAP:C 2HAP:D 2HDD:A 2HDD:B 2NLL:A 2NLL:B 2OR1:L 2OR1:R 2PRT:A 2QL2:A 2QL2:B 2QL2:C 2QL2:D 2R5Y:A 2R5Y:B 3BPY:A 3CBB:A 3CBB:B 3CO6:C 3COQ:A 3COQ:B 3D0A:A 3D0A:B 3D0A:C 3D0A:D 3DFX:A 3DFX:B 3DZY:A 3DZY:D 3E00:A 3E00:D 3EXJ:A 3EXJ:B 3EXL:A 3HDD:A 3HDD:B 9ANT:A Defining the DNA-binding residue Previous research used various distance cut-offs from 3.5 Å to 6 Å to define DNA-binding residues between proteins and DNA [ 6 - 10 , 14 , 40 , 42 ].

Publication Year: 2009

Bioinformatic analysis of the protein/DNA interface.

(2014) Nucleic Acids Res 42

PubMed: 24335080 | PubMedCentral: PMC3950675 | DOI: 10.1093/nar/gkt1273

All contacts shown are between the guanine atom O6 and the arginine NH observed in crystal structures 3exj ( 65 ), 1nfk ( 66 ), 1bc8 ( 67 ), 1run ( 68 ), 1g2d ( 69 ) and 2i13 ( 70 ).

Publication Year: 2014

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24914984 | PubMedCentral: PMC4051508 | DOI: 10.1107/S1399004714007603

On the other hand, various NCS-related copies of the same structure were left in the library sets as replicates in the case of the zinc-fingers 1f2i , 1llm , 1mey , 1un6 , 2il3 , 1hgh , 3mjh and 1g2d ...

Publication Year: 2014