SMTL ID : 4gc6.1

Crystal structure of Dpo4 in complex with N-MC-dAMP opposite dT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

monomer

Ligands

1 x 0OH: North-methanocarba-2'-deoxyadenosine triphosphate(Non-covalent)

0OH.1: 14 residues within 4Å: Chain A: Y.16, F.17, Y.18, A.50, T.51, R.57, A.63, I.110, D.111 Chain B: C.14 Chain C: T.4, G.5 Ligands: CA.2, CA.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.18, A:I.110 Hydrogen bonds: A:F.17, A:Y.18, A:T.51 Water bridges: A:D.13, A:Y.54, A:R.57, A:K.165 Salt bridges: A:R.57

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.13, F.14, D.111 Ligands: 0OH.1, CA.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:F.14, A:D.111 CA.3: 6 residues within 4Å: Chain A: D.13, E.112, K.165 Chain B: C.14 Ligands: 0OH.1, CA.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.13 CA.4: 3 residues within 4Å: Chain A: A.187, I.192 Chain B: C.13 No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain A: D.300 Chain B: A.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ketkar, A. et al., Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues. Biochemistry (2012)

Release Date

2012-10-24

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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