SMTL ID : 7t21.1

E. coli DnaB bound to ssDNA and ADP-AlF4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 21 residues within 4Å: Chain A: Q.441, R.442, G.444, P.445, I.446 Chain B: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, D.280, Q.281, T.282, G.455, Q.456 Ligands: ALF.2, MG.3 15 PLIP interactions: 2 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:G.444, A:I.446, B:S.234, B:S.234, B:M.235, B:G.236, B:K.237, B:T.238, B:T.239, B:T.239, B:R.271, B:D.280, B:T.282 Salt bridges: B:K.237, B:R.271 ADP.4: 21 residues within 4Å: Chain B: K.440, Q.441, R.442, N.443, G.444, P.445 Chain C: R.232, P.233, S.234, M.235, G.236, K.237, T.238, R.271, D.280, Q.281, T.282, G.455, S.458 Ligands: ALF.5, MG.6 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:K.440, C:S.234, C:S.234, C:M.235, C:G.236, C:K.237, C:T.238, C:R.271, C:D.280, C:T.282 Salt bridges: C:R.271 ADP.7: 22 residues within 4Å: Chain C: Q.441, R.442, N.443, G.444, P.445 Chain D: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, D.280, Q.281, T.282, G.455, Q.456, S.458 Ligands: ALF.8, MG.9 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.234, D:S.234, D:M.235, D:G.236, D:K.237, D:T.238, D:T.239, D:T.239, D:D.280, D:T.282, D:S.458 Salt bridges: D:R.271 ADP.10: 22 residues within 4Å: Chain D: K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Chain E: R.232, P.233, S.234, M.235, G.236, K.237, T.238, R.271, D.280, Q.281, T.282, G.455, S.458 Ligands: ALF.11, MG.12 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.234, E:S.234, E:M.235, E:G.236, E:K.237, E:T.238, E:D.280 Salt bridges: E:R.271, D:K.440 ADP.13: 21 residues within 4Å: Chain E: Q.441, R.442, N.443, G.444, P.445, I.446 Chain F: P.233, S.234, M.235, G.236, T.238, E.262, R.271, D.280, Q.281, T.282, F.453, G.455, Q.456 Ligands: ALF.14, MG.15 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.234, F:S.234, F:M.235, F:G.236, F:T.238, F:D.280, E:I.446 Salt bridges: F:R.271, F:R.271, E:K.440

5 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 8 residues within 4Å: Chain A: K.440, R.442 Chain B: P.233, T.238, E.262, Q.384 Ligands: ADP.1, MG.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.262 ALF.5: 10 residues within 4Å: Chain B: Q.410, K.440 Chain C: P.233, T.238, E.262, M.263, D.343, Q.384 Ligands: ADP.4, MG.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.262, C:E.262 ALF.8: 10 residues within 4Å: Chain C: K.440, R.442 Chain D: P.233, S.234, T.238, E.262, R.271, Q.384 Ligands: ADP.7, MG.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.262 ALF.11: 10 residues within 4Å: Chain D: Q.410, K.440, R.442 Chain E: P.233, T.238, E.262, D.343, Q.384 Ligands: ADP.10, MG.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.262 ALF.14: 10 residues within 4Å: Chain E: Q.410, K.440, R.442 Chain F: P.233, K.237, T.238, E.262, Q.384 Ligands: ADP.13, MG.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.262

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain B: T.238, E.262, D.343 Ligands: ADP.1, ALF.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.238 MG.6: 6 residues within 4Å: Chain C: T.238, E.262, M.263, D.343 Ligands: ADP.4, ALF.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.238 MG.9: 4 residues within 4Å: Chain D: T.238, E.262 Ligands: ADP.7, ALF.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.238 MG.12: 5 residues within 4Å: Chain E: T.238, E.262, D.343 Ligands: ADP.10, ALF.11 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.238 MG.15: 5 residues within 4Å: Chain F: T.238, E.262, D.343 Ligands: ADP.13, ALF.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oakley, A.J. et al., Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli. To Be Published

Release Date

2023-01-18

Peptides

Replicative DNA helicase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Replicative DNA helicase

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