SMTL ID : 8vat.1

Structure of the E. coli clamp loader bound to the beta clamp in a Open-RNAp/t conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: C.67, P.75, C.76, C.79, C.82 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.67, B:C.76, B:C.79, B:C.82 ZN.5: 5 residues within 4Å: Chain C: C.67, E.68, C.76, C.79, C.82 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.67, C:C.79, C:C.82 ZN.9: 5 residues within 4Å: Chain D: C.67, C.76, G.77, C.79, C.82 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.67, D:C.76, D:C.79, D:C.82 ZN.13: 5 residues within 4Å: Chain E: C.53, C.62, G.63, C.65, C.68 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.53, E:C.62, E:C.65, E:C.68

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

ADP.2: 21 residues within 4Å: Chain B: A.10, R.11, W.13, R.14, P.15, V.21, V.22, T.49, R.50, G.51, V.52, G.53, K.54, T.55, S.56, L.217, R.218, L.221 Chain C: E.147 Ligands: BEF.3, MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.11, B:R.11, B:W.13, B:V.22, B:G.51, B:V.52, B:V.52, B:G.53, B:K.54, B:T.55, B:T.55, B:S.56 Salt bridges: B:R.14, B:K.54, B:R.218, B:R.218 ADP.6: 20 residues within 4Å: Chain C: L.9, A.10, W.13, R.14, P.15, V.21, V.22, R.50, G.51, V.52, G.53, K.54, T.55, S.56, L.217, R.218, L.221 Chain D: E.147 Ligands: BEF.7, MG.8 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:W.13, C:V.22, C:G.51, C:V.52, C:V.52, C:G.53, C:K.54, C:T.55, C:S.56 Salt bridges: C:R.14, C:K.54, C:R.218, C:R.218 ADP.10: 19 residues within 4Å: Chain D: A.10, W.13, R.14, P.15, V.21, V.22, Q.24, R.50, G.51, V.52, G.53, K.54, T.55, S.56, L.217, R.218 Chain E: E.136 Ligands: BEF.11, MG.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:W.13, D:V.22, D:G.51, D:V.52, D:G.53, D:K.54, D:T.55, D:S.56 Salt bridges: D:R.14, D:K.54, D:R.218, D:R.218

3 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 10 residues within 4Å: Chain B: R.50, G.51, K.54, T.160, R.218 Chain C: E.147, T.168, R.172 Ligands: ADP.2, MG.4 No protein-ligand interaction detected (PLIP) BEF.7: 10 residues within 4Å: Chain C: R.50, G.51, K.54, T.55, E.130, R.218 Chain D: T.168, R.172 Ligands: ADP.6, MG.8 No protein-ligand interaction detected (PLIP) BEF.11: 11 residues within 4Å: Chain D: T.49, R.50, G.51, K.54, E.130, T.160, R.218 Chain E: T.157, R.161 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain B: T.55, D.129, E.130 Chain C: E.147, R.172 Ligands: ADP.2, BEF.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.55 MG.8: 4 residues within 4Å: Chain C: T.55, E.130 Ligands: ADP.6, BEF.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.55 MG.12: 5 residues within 4Å: Chain D: T.55, D.129 Chain E: E.136 Ligands: ADP.10, BEF.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Landeck, J.T. et al., Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. J.Biol.Chem. (2024)

Release Date

2024-03-27

Peptides

DNA polymerase III subunit delta: A
DNA polymerase III subunit tau: BCD
DNA polymerase III subunit delta': E
Beta sliding clamp: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

DNA polymerase III subunit delta

DNA polymerase III subunit tau

DNA polymerase III subunit delta'

Beta sliding clamp

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