SMTL ID : 2xy5.1

Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

monomer

Ligands

1 x GLC- Z9N: alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-Z9N.1: 9 residues within 4Å: Chain A: E.30, Y.32, D.77, R.80, L.100, D.113, I.310, N.312, A.314 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.138, A:R.80, A:T.324, A:R.80, A:R.80, A:D.113, A:N.312, A:A.314 Water bridges: A:R.80, A:Q.313

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

SO4.2: 1 residues within 4Å: Chain A: R.484 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.484 SO4.3: 1 residues within 4Å: Chain A: R.382 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.382 SO4.4: 3 residues within 4Å: Chain A: H.387, R.407, K.411 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.361, A:H.387 Salt bridges: A:R.407, A:K.411 SO4.5: 6 residues within 4Å: Chain A: E.26, V.27, R.80, D.130, Y.134, K.155 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.27, A:D.130, A:R.140 Water bridges: A:K.155 Salt bridges: A:R.80, A:K.155

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 3 residues within 4Å: Chain A: W.87, K.88, G.89 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.87 Hydrogen bonds: A:W.87

1 x CU1: COPPER (I) ION(Non-functional Binders)

CU1.7: 5 residues within 4Å: Chain B: X.5 Chain C: A.5, X.6, G.7 Ligands: EDN.8 No protein-ligand interaction detected (PLIP)

1 x EDN: ETHANE-1,2-DIAMINE(Non-functional Binders)

EDN.8: 6 residues within 4Å: Chain B: C.4, X.5 Chain C: A.5, X.6, G.7 Ligands: CU1.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaul, C. et al., Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair. Nature Chem. (2011)

Release Date

2011-07-27

Peptides

DNA POLYMERASE I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE I