Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

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High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.

(2011) Nucleic Acids Res 39

PubMed: 21459852 | PubMedCentral: PMC3152349 | DOI: 10.1093/nar/gkr202

Structures of d(CGCGCG) 2 available in the PDB and NDB (code in italics) Data Base Code Resolution (Å) R (%) i/a a SF b Crystal form a (Å) b (Å) c (Å) Amine Metal ions ... eference 2DCG 0.90 14.0 i n A 17.87 31.55 44.58 Spermine Mg 2+ ( 1 ) 1DCG 1.00 17.5 i n A 18.01 31.03 44.80 – Mg 2+ ( 33 ) ZDF013 c 1.00 19.5 i n A 17.45 31.63 45.56 – – ( 34 ) 292D 1.00 16.1 i n A 17.94 31.23 44.55 Polyamine Mg 2+ , Na + ( 35 ) 293D 1.00 19.1 i n A 17.93 31.23 44.64 Spermidine Mg 2+ , Na + ( 36 ) 336D 1.00 19.0 i n A 17.98 31.51 44.38 Thermospermine Mg 2+ ( 37 ) 1ICK 0.95 8.6 a y A 17.87 31.55 44.58 Spermine Mg 2+ ( 4 ) 1DJ6 1.00 16.9 i y A 17.93 31.36 44.62 Polyamine Mg 2+ ( 38 ) 2ELG 1.00 23.2 i y A 17.85 30.99 44.02 Spermidine Mg 2+ , Na + ( 39 ) 2IE1 1.60 19.0 i y A 17.64 30.38 43.63 Polyamine – ( 40 ) 3P4J 0.55 7.77 a y A 17.88 31.42 43.90 Spermine – This work 1D48 1.00 18.5 i n B 18.41 30.77 43.15 Spermine – ( 14 ) 131D 1.00 18.0 i n B 18.27 30.69 42.46 Spermine Na + ( 41 ) 1I0T 0.60 16.0 i n B 18.32 30.68 42.49 Spermine – ( 5 ) 1V9G 1.80N d 22.2 i y B 18.46 30.76 43.18 Spermine(D) e – ( 42 ) 1WOE 1.50N d 17.6 i y B 18.46 30.76 43.18 Spermine – ( 42 ) a Model refined isotropically (i) or anisotropically (a).

ACCESSION NUMBER PDB: 3P4J.

of parameters 3740     wR2 (%) 20.19      R factor , F o >4σ( F o ) (%) 6.77     Reflections, F o >4σ( F o ) 112 143      R factor , all reflections (%) 7.77     All reflections 130 650      R free F o >4 σ ( F o ) (%) 7.47     Free reflections, F o >4 σ ( F o ) 1470      R free , all reflections (%) 8.47     All free reflections 1724 Asymmetric unit contents     DNA nucleotides 12 a     DNA atoms 240     Average B-factor of DNA atoms (Å 2 ) 2.69     Spermine atomic sites b 22     Average B-factor of spermine atoms (Å 2 ) 9.80     Fully occupied water sites 22     Alternative pairs of water sites 13     Partially occupied water sites 93     Total occupancy of all water sites 78.6     Average B-factor of all water sites (Å 2 ) 8.48 PDB code 3P4J Values corresponding to the highest resolution range are given in parentheses.

This refinement was accepted as final and the resulting atomic parameters and structure factors have been deposited in the PDB with the ID code 3P4J.

Publication Year: 2011


Structural fluctuation observed in Z-DNA d(CGCGCG)? in the absence of divalent metal cations and polyamines.

(2013) J Synchrotron Radiat 20

PubMed: 24121329 | PubMedCentral: PMC3795545 | DOI: 10.1107/S0909049513020773

Recently, the 0.55 Å resolution crystal structure of the binary complex of Z-DNA d(CGCGCG) 2 and spermine in the absence of divalent metal cations was reported [Protein Data Bank (PDB)... ID 3p4j ; Brzezinski et al. , 2011 ▶ ].

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4381091

However, the target values for the C4–N9–C1′ [129.0(7)°] and C8–N9–C1′ [124.5(7)°] exocyclic angles in syn purines, which seem to be ina... equate in the above dictionaries, were taken from the ultrahigh-resolution Z-DNA–Spm structure (0.55 Å; PDB 3p4j) reported by Brzezinski et al. [ 29 ].

For the previously described d(CGCGCG) 2 –Spk–Mn 2+ (PDB 4hig), d(CGCGCG) 2 –Spk–Zn 2+ (4hif), d(CGCGCG) 2 –Put 2+ –K + [ 39 ] and d(CGCGCG) 2 –Spm (3p4j) complexes, the analogous values of the overlap area for the same bases were 4.36, 5.24, 4.76, and 4.76 Å 2 , respectively.

In view of the accumulated facts, it seems that the rigidity observed in that ultrahigh-resolution structure (PDB 3p4j) was a fortuitous exception rather than a rule.

Publication Year: 2015