SMTL ID : 6jr0.1

Crystal structure of the human nucleosome phased with 12 selenium atoms

Coordinates

PDB Format Compare

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 PLIP CL.2: 7 residues within 4Å: Chain C: G.48, A.49, G.50, A.51 Chain D: T.94, S.95 Chain I: A.111 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain E: M.124, P.125, K.126 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain G: G.48, A.49, G.50, A.51 Chain H: T.94, S.95 Chain J: T.112 Ligand excluded by PLIP

8 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 1 residues within 4Å: Chain E: D.81 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.81, H2O.5, H2O.5 MN.6: 1 residues within 4Å: Chain I: G.100 No protein-ligand interaction detected (PLIP) MN.7: 1 residues within 4Å: Chain I: G.134 No protein-ligand interaction detected (PLIP) MN.8: 1 residues within 4Å: Chain I: G.121 No protein-ligand interaction detected (PLIP) MN.9: 1 residues within 4Å: Chain J: G.134 No protein-ligand interaction detected (PLIP) MN.10: 1 residues within 4Å: Chain J: G.121 No protein-ligand interaction detected (PLIP) MN.11: 2 residues within 4Å: Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP) MN.12: 2 residues within 4Å: Chain J: G.71, A.72 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saotome, M. et al., Structure determination of the nucleosome core particle by selenium SAD phasing. Acta Crystallogr.,Sect.D (2019)

Release Date

2019-10-02

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
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

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