SMTL ID : 5hrg.1

The crystal structure of AsfvPolX(D51N mutant):DNA4 binary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x DG- DC- DG- DA- DT- DC- DG- DC: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3')(Non-covalent)

DG-DC-DG-DA-DT-DC-DG-DC.1: 41 residues within 4Å: Chain A: G.42, R.46, D.53, N.55, K.89, Q.102, D.104, F.106, H.119, F.120, T.121, G.122, V.124, L.127 Chain B: V.84, C.85, G.86, E.87, R.88, K.89, H.119, V.124, L.127, I.128, R.131, A.132, K.135, K.140, L.141, N.142, Q.143, Y.144 Ligands: DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2, MN.3 Protein-ligand interaction information (PLIP) not available DG-DC-DG-DA-DT-DC-DG-DC.2: 41 residues within 4Å: Chain A: C.85, G.86, E.87, R.88, K.89, H.119, V.124, L.127, I.128, R.131, A.132, K.135, K.140, L.141, N.142, Q.143, Y.144 Chain B: G.42, R.46, D.53, N.55, K.89, V.91, Q.102, D.104, F.106, H.119, F.120, T.121, G.122, V.124, L.127 Ligands: DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1, MN.6 Protein-ligand interaction information (PLIP) not available

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

MN.3: 5 residues within 4Å: Chain A: D.53, N.55, D.104 Ligands: DG-DC-DG-DA-DT-DC-DG-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.53, A:D.53, A:D.104, H2O.6 MN.6: 5 residues within 4Å: Chain B: D.53, N.55, D.104 Ligands: DG-DC-DG-DA-DT-DC-DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.2 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.53, B:D.53, B:D.104

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

SO4.4: 4 residues within 4Å: Chain A: R.129, F.169, T.170, R.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.170 Water bridges: A:R.172 Salt bridges: A:R.129, A:R.172 SO4.5: 3 residues within 4Å: Chain A: N.16, H.17, R.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:H.17 Salt bridges: A:R.21 SO4.7: 4 residues within 4Å: Chain B: R.129, F.169, T.170, R.172 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.170, B:T.170 Salt bridges: B:R.129, B:R.172 SO4.8: 3 residues within 4Å: Chain B: N.16, H.17, R.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.16 Salt bridges: B:R.21 SO4.9: 5 residues within 4Å: Chain B: Y.26, N.27, K.64, K.67, H.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.64 Salt bridges: B:K.67, B:H.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.Q. et al., The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1. To Be Published

Release Date

2017-01-18

Peptides

DNA polymerase beta-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA polymerase beta-like protein