SMTL ID : 1m19.1

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-oligomer

Ligands

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

MN.1: 1 residues within 4Å: Chain G: D.77 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:D.77, H2O.251, H2O.281, H2O.282, H2O.360 MN.2: 1 residues within 4Å: Chain B: G.134 No protein-ligand interaction detected (PLIP) MN.3: 1 residues within 4Å: Chain A: G.134 No protein-ligand interaction detected (PLIP) MN.4: 2 residues within 4Å: Chain B: G.71, A.72 No protein-ligand interaction detected (PLIP) MN.5: 2 residues within 4Å: Chain A: G.70, G.71 No protein-ligand interaction detected (PLIP) MN.6: 1 residues within 4Å: Chain B: G.121 No protein-ligand interaction detected (PLIP) MN.7: 1 residues within 4Å: Chain A: C.88 No protein-ligand interaction detected (PLIP) MN.8: 1 residues within 4Å: Chain B: G.100 No protein-ligand interaction detected (PLIP) MN.9: 1 residues within 4Å: Chain A: G.138 No protein-ligand interaction detected (PLIP) MN.10: 2 residues within 4Å: Chain A: T.38, G.39 No protein-ligand interaction detected (PLIP) MN.11: 2 residues within 4Å: Chain A: T.120, G.121 No protein-ligand interaction detected (PLIP)

5 x IMT- PYB- PYB- PYB- ABU- PYB- PYB- PYB- PYB- BAL- DIB: 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID(Non-functional Binders)

IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB.12: 16 residues within 4Å: Chain A: G.31, T.32, G.33, T.34, A.35, T.36 Chain B: T.112, A.113, C.114, A.115, C.116, T.117, T.118, T.119, T.120 Chain E: A.14 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.14 IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB.13: 16 residues within 4Å: Chain A: G.40, A.41, A.42, A.43, C.44, T.45, G.46, C.47, T.48 Chain B: A.102, G.103, T.104, T.105, T.106, C.107, C.108 No protein-ligand interaction detected (PLIP) IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB.14: 16 residues within 4Å: Chain A: G.70, G.71, A.72, A.73, T.74, T.75, C.76 Chain B: A.73, T.74, T.75, C.76, C.77, G.78, C.79, T.80, G.81 No protein-ligand interaction detected (PLIP) IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB.15: 16 residues within 4Å: Chain A: A.102, G.103, T.104, T.105, T.106, C.107, C.108 Chain B: A.41, A.42, A.43, C.44, T.45, G.46, C.47, T.48, C.49 No protein-ligand interaction detected (PLIP) IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB.16: 16 residues within 4Å: Chain A: T.112, A.113, C.114, A.115, C.116, T.117, T.118, T.119 Chain B: A.30, G.31, T.32, G.33, T.34, A.35, T.36, T.37 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Suto, R.K. et al., Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands. J.Mol.Biol. (2003)

Release Date

2003-02-18

Peptides

Histone H3.2: CG
Histone H4: DH
Histone H2A.1: EI
Histone H2B.1: FJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

G
E

D
B

H
F

E
C

I
G

F
D

J
H

Histone H3.2

Histone H4

Histone H2A.1

Histone H2B.1

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