SMTL ID : 4ki4.1

Ternary complex of rb69 mutant L415F with ribonucleotides at 0 and -1 position

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 18 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, F.415, Y.416, P.417, R.482, K.486, K.560, N.564, Y.567, T.622, D.623 Chain B: A.3, G.4 Chain C: C.14 Ligands: CA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:S.414, A:F.415, A:Y.416, A:N.564 Water bridges: A:R.482, A:K.486, A:K.486 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: TTP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.411, A:D.411, A:L.412, A:D.623 CA.3: 1 residues within 4Å: Chain A: E.716 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.716 CA.4: 2 residues within 4Å: Chain A: E.660, D.684 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.660, A:D.684 CA.6: 2 residues within 4Å: Chain A: D.192, E.196 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:E.196, A:E.196, H2O.7

6 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: E.172, E.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.172 NA.7: 4 residues within 4Å: Chain A: N.505, N.507, K.531, K.532 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.507, A:K.531 NA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.9: 2 residues within 4Å: Chain A: E.686, E.716 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.686 Water bridges: A:E.686 NA.10: 1 residues within 4Å: Chain A: N.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.232, A:N.232 NA.11: 3 residues within 4Å: Chain A: D.114, I.115, E.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.116 Water bridges: A:I.115

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain B: A.8, G.9 Chain C: T.7, G.8, C.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clausen, A.R. et al., Structure-function analysis of ribonucleotide bypass by B family DNA replicases. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-10-09

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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