SMTL ID : 6iq4.1

Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-2-1-2-2-1-mer

Ligands

1 x AU: GOLD ION(Non-covalent)

AU.1: 2 residues within 4Å: Chain A: H.76 Ligands: XIS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76

1 x XIS: 4-diphenylphosphanylbenzoic acid(Non-covalent)

XIS.2: 7 residues within 4Å: Chain A: L.72, I.75 Chain E: K.85, Q.88, R.92, R.97 Ligands: AU.1 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:L.72, A:I.75, E:K.85, E:K.85 Salt bridges: E:R.92, E:R.97

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain C: E.51 Chain D: V.18 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:V.18, H2O.1 MG.5: 1 residues within 4Å: Chain I: G.133 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain I: A.76 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain J: G.133 No protein-ligand interaction detected (PLIP)

1 x D0X: [Ru(eta(6)-p-cymene)Cl-2(pta)(Non-covalent)

D0X.4: 5 residues within 4Å: Chain G: Y.44, E.48, E.51 Chain H: E.75, H.79 7 PLIP interactions: 1 interactions with chain H, 6 interactions with chain G Hydrophobic interactions: H:E.75 Salt bridges: G:E.48, G:E.48, G:E.51, G:E.51 Metal complexes: G:E.48, G:E.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batchelor, L.K. et al., Crosslinking Allosteric Sites on the Nucleosome. Angew.Chem.Int.Ed.Engl. (2019)

Release Date

2019-10-30

Peptides

Histone H3.1: AE
Histone H4: B
Histone H2A type 1-B/E: CG
Histone H2B type 1-J: DH
Histone H4: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

C
C

G
G

D
D

H
H

F
F

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

Histone H4

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