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1M77

Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA

Summary for 1M77
Entry DOI10.2210/pdb1m77/pdb
Descriptor5'-D(*CP*CP*CP*GP*AP*TP*CP*GP*GP*G)-3', COBALT HEXAMMINE(III) (3 entities in total)
Functional Keywordsa-dna, cobalt hexammine, dna
Total number of polymer chains1
Total formula weight3207.11
Authors
Ramakrishnan, B.,Sekharudu, C.,Pan, B.C.,Sundaralingam, M. (deposition date: 2002-07-18, release date: 2003-01-07, Last modification date: 2024-04-03)
Primary citationRamakrishnan, B.,Sekharudu, C.,Pan, B.,Sundaralingam, M.
Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA.
Acta Crystallogr.,Sect.D, 59:67-72, 2003
Cited by
PubMed Abstract: The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25 A resolution. The decamer crystallized in the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 44.3, c = 24.8 A and one strand in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to R(work) and R(free) values of 16.3 and 18.5%, respectively, for 5969 reflections. The decamer forms the A-form DNA duplex, with the abutting crystal packing typical of A-DNA. The crystal packing interactions seem to distort the local conformation: A5 adopts the trans/trans conformation for the torsion angles alpha and gamma instead of the usual gauche(-)/gauche(+) conformations, yielding G*(G.C) base triplets. The highly hydrated [Co(NH(3))(6)](3+) ion adopts a novel binding mode to the DNA duplex, binding directly to phosphate groups and connecting to N7 and O6 atoms of guanines by water bridges. Analysis of thermal parameters (B factors) shows that the nucleotides involved in abutting crystal packing are thermally more stable than other nucleotides in the duplex.
PubMed: 12499541
DOI: 10.1107/S0907444902018917
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.25 Å)
Structure validation

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数据于2025-07-09公开中

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