SMTL ID : 1d9d.1

CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x DA- U31- C31: 5'-D(*TP*CP*GP)-R(AP*(U31)P*(C31))-3'(Non-covalent)

DA-U31-C31.1: 32 residues within 4Å: Chain A: D.32, T.33, E.34, T.35, D.36, S.37, L.38, Q.96, N.97, K.99, Y.100, D.101, M.120, H.133, D.134, M.135, D.136, T.147, I.148, F.150, E.151, L.161, T.162, F.163, Y.174, E.177, D.178, E.218, S.335, Y.336, H.337 Ligands: ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.38, A:F.150, A:M.135 Hydrogen bonds: A:E.34, A:E.34, A:T.35, A:S.37, A:L.161, A:D.178, A:D.32, A:Q.96, A:D.101, A:M.135, A:I.148, A:Y.174, A:E.177 Water bridges: A:Y.174, A:Y.174, A:Q.96, A:R.132, A:I.148, A:I.148, A:F.150, A:F.150 pi-Stacking: A:F.150

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.32, T.33, E.34, D.178 Ligands: DA-U31-C31.1, DA-U31-C31.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.32, A:E.34, A:D.178 ZN.3: 2 residues within 4Å: Chain A: H.578, E.582 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.578, A:E.582 ZN.4: 3 residues within 4Å: Chain A: R.345, E.387, D.559 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.559, H2O.6 ZN.6: 2 residues within 4Å: Chain A: E.560, H.605 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.560, H2O.10

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: M.391, L.400, T.414, N.438, Y.468 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.468

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

SO4.7: 4 residues within 4Å: Chain A: K.195, H.196, K.197, R.499 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.195, A:K.197, A:R.499 Water bridges: A:G.198 Salt bridges: A:H.196, A:K.197 SO4.8: 4 residues within 4Å: Chain A: R.359, H.411, R.431, K.435 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.359, A:H.411, A:R.431, A:K.435 SO4.9: 4 residues within 4Å: Chain A: E.89, R.113, G.114, I.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.114, A:I.115 SO4.10: 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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