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SMTL ID : 6jou.1

Crystal structure of the human nucleosome containing H2A.Z.1 S42R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

MN.1:	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.3, H₂O.4
MN.2:	1 residues within 4Å: Chain I: G.121 No protein-ligand interaction detected (PLIP)
MN.3:	1 residues within 4Å: Chain I: G.134 No protein-ligand interaction detected (PLIP)
MN.4:	1 residues within 4Å: Chain I: T.136 No protein-ligand interaction detected (PLIP)
MN.5:	1 residues within 4Å: Chain I: G.68 No protein-ligand interaction detected (PLIP)
MN.6:	1 residues within 4Å: Chain J: G.121 No protein-ligand interaction detected (PLIP)
MN.7:	2 residues within 4Å: Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.8:	1 residues within 4Å: Chain J: G.134 No protein-ligand interaction detected (PLIP)
MN.9:	1 residues within 4Å: Chain J: T.37 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Horikoshi, N. et al., Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo. Biochem.Biophys.Res.Commun. (2019)

Release Date

2020-03-25

Peptides

Histone H3.1: AE
Histone H4: BF
Histone H2A.Z: 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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.1

Histone H4

Histone H2A.Z

Histone H2B type 1-J

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