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DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site

X-ray diffraction
2.246Å resolution
PDB entry 4ny8 coloured by chain, front view.
PDB entry 4ny8 coloured by chain, side view.
PDB entry 4ny8 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA polymerase beta and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 20596.45 Å2
Buried surface area: 4863.18 Å2
Dissociation area: 607.36 Å2
Dissociation energy (ΔGdiss): 14.01 kcal/mol
Dissociation entropy (TΔSdiss): 8.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117892

Macromolecules

DNA polymerase beta
Chain: A
Length: 326 amino acids
Theoretical weight: 37.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 10-335; Coverage: 97%)
Gene name: POLB
Pfam:
InterPro:
CATH:
DNA polymerase beta in PDB entry 4ny8, assembly 1, front view.
DNA polymerase beta in PDB entry 4ny8, assembly 1, side view.
DNA polymerase beta in PDB entry 4ny8, assembly 1, top view.
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DNA chain T
Name: 5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
Representative chains: T
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 16 nucleotides
Theoretical weight: 4.86 KDa
5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' in PDB entry 4ny8, assembly 1, front view.
5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' in PDB entry 4ny8, assembly 1, side view.
5'-D(*CP*CP*GP*AP*CP*(6OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' in PDB entry 4ny8, assembly 1, top view.
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DNA chain P
Name: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'
Representative chains: P
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3' in PDB entry 4ny8, assembly 1, front view.
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3' in PDB entry 4ny8, assembly 1, side view.
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3' in PDB entry 4ny8, assembly 1, top view.
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DNA chain D
Name: 5'-D(P*GP*TP*CP*GP*G)-3'
Representative chains: D
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
5'-D(P*GP*TP*CP*GP*G)-3' in PDB entry 4ny8, assembly 1, front view.
5'-D(P*GP*TP*CP*GP*G)-3' in PDB entry 4ny8, assembly 1, side view.
5'-D(P*GP*TP*CP*GP*G)-3' in PDB entry 4ny8, assembly 1, top view.
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