- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.1: 3 residues within 4Å:- Chain A: M.124, P.125, K.126
Ligand excluded by PLIPCL.2: 6 residues within 4Å:- Chain C: G.48, A.49, G.50, A.51
- Chain D: T.94, S.95
Ligand excluded by PLIPCL.4: 3 residues within 4Å:- Chain E: M.124, P.125, K.126
Ligand excluded by PLIPCL.5: 6 residues within 4Å:- Chain G: G.48, A.49, G.50, A.51
- Chain H: T.94, S.95
Ligand excluded by PLIP- 15 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)
MN.3: 1 residues within 4Å:- Chain E: D.81
2 PLIP interactions:1 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.81, H2O.3
MN.6: 1 residues within 4Å:- Chain I: T.135
No protein-ligand interaction detected (PLIP)MN.7: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MN.8: 1 residues within 4Å:- Chain I: G.120
No protein-ligand interaction detected (PLIP)MN.9: 1 residues within 4Å:- Chain I: G.99
No protein-ligand interaction detected (PLIP)MN.10: 3 residues within 4Å:- Chain I: G.96, G.97
- Chain J: C.49
No protein-ligand interaction detected (PLIP)MN.11: 3 residues within 4Å:- Chain I: G.39, G.40
- Chain J: C.106
No protein-ligand interaction detected (PLIP)MN.12: 2 residues within 4Å:- Chain I: A.132, G.133
No protein-ligand interaction detected (PLIP)MN.13: 2 residues within 4Å:- Chain I: G.68
- Chain J: C.78
No protein-ligand interaction detected (PLIP)MN.14: 1 residues within 4Å:- Chain J: G.120
No protein-ligand interaction detected (PLIP)MN.15: 2 residues within 4Å:- Chain J: G.39, G.40
No protein-ligand interaction detected (PLIP)MN.16: 1 residues within 4Å:- Chain J: G.133
No protein-ligand interaction detected (PLIP)MN.17: 1 residues within 4Å:- Chain J: G.99
No protein-ligand interaction detected (PLIP)MN.18: 1 residues within 4Å:- Chain J: G.68
No protein-ligand interaction detected (PLIP)MN.19: 1 residues within 4Å:- Chain J: T.37
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Osakabe, A. et al., Polymorphism of apyrimidinic DNA structures in the nucleosome. Sci Rep (2017)
- Release Date
- 2017-03-08
- Peptides
- Histone H3.1: AE
Histone H4: BF
Histone H2A type 1-B/E: CG
Histone H2B type 1-J: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
CG
GD
DH
H
SMTL ID : 5jrg.1
Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)
Histone H3.1
Histone H4
Histone H2A type 1-B/E
Histone H2B type 1-J
Related Entries With Identical Sequence
3a6n.1 | 3afa.1 | 3an2.1 | 3av1.1 | 3av2.1 | 3ayw.1 | 3aze.1 | 3azf.1 | 3azg.1 | 3azh.1 | 3azi.1 | 3azj.1 | 3azk.1 | 3azl.1 | 3azm.1 | 3azn.1 | 3w96.1 | 3w97.1 | 3w98.1 | 3w99.1 | 3wa9.1 | 3waa.1 | 3wkj.1 | 3wtp.1 | 4ym5.1 | 4ym6.1 | 4z5t.1 | 5av5.1 | 5av6.1 | 5av8.1 more...less...5av9.1 | 5avb.1 | 5avc.1 | 5ay8.1 | 5b0y.1 | 5b0z.1 | 5b1l.1 | 5b1m.1 | 5b24.1 | 5b2i.1 | 5b2j.1 | 5b31.1 | 5b32.1 | 5b33.1 | 5b40.1 | 5cpi.1 | 5cpj.1 | 5cpk.1 | 5gse.1 | 5gtc.1 | 5gxq.1 | 5x7x.1 | 5xm0.1 | 5xm1.1 | 5y0c.1 | 5y0d.1 | 5z23.1 | 5z30.1 | 5zbx.1 | 6a5l.1 | 6a5o.1 | 6a5p.1 | 6a5r.1 | 6a5t.1 | 6a5u.1 | 6hkt.1 | 6inq.1 | 6ir9.1 | 6j4w.1 | 6j4x.1 | 6j4y.1 | 6j4z.1 | 6j50.1 | 6j51.1 | 6jou.1 | 6jr0.1 | 6jr1.1 | 6k1i.1 | 6k1j.1 | 6k1k.1 | 6kvd.1 | 6kxv.1 | 6l49.1 | 6l4a.1 | 6r8y.1 | 6r8z.1 | 6r90.1 | 6r91.1 | 6r92.1 | 6r93.1 | 6r94.1 | 6t90.1 | 6t93.1 | 6usj.1 | 6v2k.1 | 6yov.1 | 7bxt.1 | 7c0m.1 | 7d1z.1 | 7d20.1 | 7dbh.1 | 7scy.1 | 7scz.1 | 7vbm.1 | 7vz4.1 | 7w9v.1 | 7wbv.1 | 7wbw.1 | 7wbx.1 | 7x57.1 | 7x58.1 | 7xse.1 | 7xsx.1 | 7xsz.1 | 7xt7.1 | 7xtd.1 | 7xti.1 | 7xzx.1 | 7xzy.1 | 7xzz.1 | 7y00.1 | 7y7i.1 | 7yoz.1 | 8gui.1 | 8guj.1 | 8guk.1 | 8h0v.1 | 8h0w.1 | 8he5.1 | 8ihl.1 | 8jl9.1 | 8jlb.1 | 8jld.1 | 8jnd.1 | 8jne.1 | 8jnf.1 | 8kb5.1 | 8osj.1 | 8osk.1 | 8osl.1 | 8ots.1 | 8xbt.1 | 8xbu.1 | 8xbw.1 | 8ybj.1 | 8ybk.1