SMTL ID : 1d9f.1

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x DT- U31- DT: DNA/RNA (5'-D(*TP*TP)-R(*(U31)P)-D(*T)-3')(Non-covalent)

DT-U31-DT.1: 29 residues within 4Å: Chain A: F.31, D.32, E.34, T.35, S.37, L.38, G.95, Q.96, N.97, L.98, K.99, Y.100, D.101, M.120, D.134, M.135, D.136, T.147, I.148, T.149, F.150, E.151, Y.174, D.178, E.218, S.335, Y.336, H.337 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.96 Hydrogen bonds: A:D.32, A:Q.96, A:D.101, A:D.134, A:M.135, A:Y.174 Water bridges: A:E.151 pi-Stacking: A:Y.174

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.32, E.34, Y.174, D.178 Ligands: DT-U31-DT.1, DT-U31-DT.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.32, A:E.34, A:E.34, A:D.178

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: H.196, K.197, R.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.197, A:R.499 SO4.4: 4 residues within 4Å: Chain A: R.359, H.411, R.431, K.435 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.411 Salt bridges: A:R.359, A:R.431, A:K.435 SO4.5: 3 residues within 4Å: Chain A: R.113, G.114, I.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.114, A:I.115 SO4.6: 3 residues within 4Å: Chain A: K.17, R.77, L.81 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.17, A:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teplova, M. et al., Structural origins of the exonuclease resistance of a zwitterionic RNA. Proc.Natl.Acad.Sci.USA (1999)

Release Date

1999-12-02

Peptides

DNA POLYMERASE I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE I

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