SMTL ID : 2imw.1

Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain C: D.7, F.8, D.105 Ligands: DDS.3 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.7, C:F.8, C:D.105, H2O.9 CA.2: 2 residues within 4Å: Chain C: A.181, I.186 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.181, C:I.186, H2O.2, H2O.3, H2O.9

1 x DDS: 2',3'-dideoxyadenosine triphosphate(Non-covalent)

DDS.3: 19 residues within 4Å: Chain A: G.1 Chain B: C.15 Chain C: D.7, F.8, D.9, Y.10, F.11, Y.12, V.43, A.44, T.45, Y.48, R.51, A.57, G.58, M.76, D.105, K.159 Ligands: CA.1 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.12 Hydrogen bonds: C:Y.10, C:F.11 Water bridges: C:Y.12, C:T.45, C:A.57, C:D.105, C:K.159, C:K.159, C:K.159, C:K.159, C:K.159 Salt bridges: C:R.51, C:R.51, C:R.51, C:K.159, C:K.159

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

EDO.4: 3 residues within 4Å: Chain C: E.100, K.148, R.240 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.148, C:R.240 Water bridges: C:K.148 EDO.5: 3 residues within 4Å: Chain A: G.2 Chain C: K.78, R.247 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.78, C:R.247 EDO.6: 3 residues within 4Å: Chain C: A.220, K.223, Y.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.220, C:Y.224 EDO.7: 5 residues within 4Å: Chain C: H.285, V.287, S.297, R.336, K.348 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.297 Water bridges: C:H.285, C:S.338 EDO.8: 1 residues within 4Å: Chain C: Y.122 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain C: R.247, V.249, R.267, E.271 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.247, C:R.267, C:R.267, C:E.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiala, K.A. et al., Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase. J.Mol.Biol. (2007)

Release Date

2007-01-16

Peptides

DNA polymerase IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
P

DNA polymerase IV