SMTL ID : 2kfn.1

KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND MANGANESE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

1 x DT- DA- US1- DG: 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3'(Non-covalent)

DT-DA-US1-DG.1: 24 residues within 4Å: Chain A: D.32, T.33, E.34, T.35, L.38, Q.96, N.97, K.99, Y.100, M.120, R.132, D.134, M.135, F.150, E.151, Q.160, F.163, Y.174, D.178, S.335, Y.336, H.337 Ligands: MN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.38 Hydrogen bonds: A:Q.96, A:N.97, A:M.135

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.32, D.101 Ligands: DT-DA-US1-DG.1, DT-DA-US1-DG.1, ZN.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.32, H2O.1

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.32, E.34, Y.174, D.178 Ligands: DT-DA-US1-DG.1, MN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.32, A:E.34, A:D.178 ZN.4: 2 residues within 4Å: Chain A: H.578, E.582 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.578, A:E.582, H2O.12 ZN.5: 3 residues within 4Å: Chain A: R.345, E.387, D.559 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.387, A:D.559

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: L.400, T.414, N.438, Y.468 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.468

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brautigam, C.A. et al., Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli. Biochemistry (1999)

Release Date

1998-11-11

Peptides

KLENOW FRAGMENT OF DNA POLYMERASE I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

KLENOW FRAGMENT OF DNA POLYMERASE I

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