SMTL ID : 8tll.1 (1 other biounit)

CDCA7 (Mouse) Binds Non-B-form 26-mer DNA oligo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: L.39, S.41, T.51, D.52, T.53, K.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.41, A:T.51, A:K.54, A:K.54 EDO.7: 6 residues within 4Å: Chain C: L.39, S.41, T.51, D.52, T.53, K.54 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.41, C:T.51, C:K.54, C:K.54

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: K.33, C.43, C.46, C.70, C.73 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.43, A:C.46, A:C.70, A:C.73 ZN.3: 4 residues within 4Å: Chain A: H.44, C.100, C.102, C.105 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.44, A:C.100, A:C.102, A:C.105 ZN.4: 4 residues within 4Å: Chain A: C.57, C.62, C.93, C.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.62, A:C.93, A:C.96 ZN.8: 5 residues within 4Å: Chain C: K.33, C.43, C.46, C.70, C.73 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.43, C:C.46, C:C.70, C:C.73 ZN.9: 4 residues within 4Å: Chain C: H.44, C.100, C.102, C.105 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.44, C:C.100, C:C.102, C:C.105 ZN.10: 4 residues within 4Å: Chain C: C.57, C.62, C.93, C.96 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.57, C:C.62, C:C.93, C:C.96

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: A.16, G.18, C.19 Chain D: T.12, G.13 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain B: T.12, G.13 Chain D: A.16, G.18, C.19 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: M.6 Chain B: G.15 Chain C: M.6 Chain D: G.15 Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: M.6 Chain B: G.15 Chain C: M.6 Chain D: G.15 Ligands: MG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hardikar, S. et al., The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA. Sci Adv (2024)

Release Date

2024-08-21

Peptides

Cell division cycle-associated protein 7: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Cell division cycle-associated protein 7

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