SMTL ID : 4n5s.1

Ternary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA and ddCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

6 x MN: MANGANESE (II) ION(Non-functional Binders)(Non-covalent)

MN.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.3: 5 residues within 4Å: Chain C: D.331, Y.332, D.506 Ligands: MG.2, DCT.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.331, C:Y.332, C:D.506 MN.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.5: 1 residues within 4Å: Chain C: H.164 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.164, H2O.17, H2O.17, H2O.17, H2O.17 MN.6: 1 residues within 4Å: Chain C: E.546 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.546, H2O.18, H2O.18 MN.7: 1 residues within 4Å: Chain C: E.442 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.442, H2O.8, H2O.13, H2O.21, H2O.21

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: C.12 Chain C: D.331, D.506 Ligands: MN.3, DCT.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.331, C:D.506, H2O.1, H2O.4

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.8: 18 residues within 4Å: Chain A: C.12 Chain B: G.4, G.5 Chain C: R.294, D.331, Y.332, S.333, Q.334, I.335, E.336, H.360, R.380, K.384, T.385, F.388, D.506 Ligands: MG.2, MN.3 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:I.335, C:E.336, C:F.388 Hydrogen bonds: C:R.294, C:S.333, C:Q.334, C:I.335, C:T.385 Water bridges: C:D.331, C:R.380, C:R.380, C:R.380, C:K.384, C:K.384, C:K.384, C:K.384, C:T.385 Salt bridges: C:H.360, C:R.380, C:K.384, C:K.384, C:K.384

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.9: 5 residues within 4Å: Chain B: G.8, C.9 Chain C: R.284, N.286, S.298 2 PLIP interactions: 2 interactions with chain C Water bridges: C:T.106, C:R.284

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

ACT.10: 6 residues within 4Å: Chain B: G.11, T.12 Chain C: N.206, S.207, R.208, D.209 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.208 Hydrogen bonds: C:N.206, C:R.208 ACT.11: 5 residues within 4Å: Chain C: F.30, V.31, L.32, K.35, R.126 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.30, C:L.32 Hydrogen bonds: C:L.32 Water bridges: C:R.126, C:R.126 Salt bridges: C:R.126

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain C: L.391, Y.392, G.393, F.418, L.428, R.467, F.470 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.392 Water bridges: C:R.467

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, E.Y. et al., A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry (2015)

Release Date

2015-01-21

Peptides

DNA polymerase I, thermostable: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase I, thermostable

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