SMTL ID : 4qwb.1

CRYSTAL STRUCTURE of DPO4 LINKER REGION P236A MUTANT WITH AN INCOMING D-dCDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x YYY: DEOXYCYTIDINE DIPHOSPHATE(Non-covalent)

YYY.1: 15 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, R.51, A.57, D.105 Chain B: C.13 Chain C: G.5, G.6 Ligands: CA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.12 Hydrogen bonds: A:Y.10, A:F.11, A:Y.12, A:T.45 Water bridges: A:R.51, A:R.51, A:R.51, A:R.51, A:K.159, A:K.159, A:K.159 Salt bridges: A:R.51, A:K.159

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 4 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: YYY.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:F.8, A:D.105, H2O.1 CA.3: 3 residues within 4Å: Chain A: D.7, E.106 Chain B: C.13 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.7, A:E.106, H2O.1, H2O.1, H2O.10 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.1, H2O.2, H2O.10 CA.11: 2 residues within 4Å: Chain B: G.1, G.2 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: R.77, K.78, E.79, V.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.79, A:V.80 Water bridges: A:K.78 ACT.6: 5 residues within 4Å: Chain A: G.246, R.247, K.275 Chain C: A.7, G.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.275 Salt bridges: A:K.275 ACT.7: 5 residues within 4Å: Chain A: I.99, E.100, I.101, T.239, R.240 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.101, A:T.239 Hydrogen bonds: A:I.101, A:R.240, A:R.240 ACT.8: 4 residues within 4Å: Chain A: K.172, I.175, R.176, V.203 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: C.31, V.32, F.33, P.75, M.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.31, A:F.33, A:M.76 GOL.10: 4 residues within 4Å: Chain A: A.220, K.221, Y.224 Chain C: C.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.221 GOL.12: 2 residues within 4Å: Chain A: G.58 Chain C: G.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gaur, V. et al., Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res. (2014)

Release Date

2014-08-27

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV