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Structure paper

TitleCharacterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
Journal, issue, pagesBiochemistry, Vol. 35, Page 12778-12787, Year 1996
Publish dateApr 19, 1996 (structure data deposition date)
AuthorsPelletier, H. / Sawaya, M.R.
External linksBiochemistry / PubMed:8841120
MethodsX-ray diffraction
Resolution2.3 - 3.7 Å
Structure data

PDB-1nom:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-1zqa:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR) AT PH 7.5
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-1zqb:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF BACL2 (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-1zqc:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-1zqd:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.5 Å

PDB-1zqe:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CRCL3 (SATURATED SOLUTION)
Method: X-RAY DIFFRACTION / Resolution: 3.7 Å

PDB-1zqf:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CSCL (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-1zqg:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF A SODIUM-FREE ARTIFICIAL MOTHER LIQUOR AT PH 6.5
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-1zqh:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF A SODIUM-FREE ARTIFICIAL MOTHER LIQUOR AT PH 7.5
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-1zqi:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-1zqj:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR) AND MGCL2 (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-1zqk:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (75 MILLIMOLAR) AND MGCL2 (75 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-1zql:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (15 MILLIMOLAR) AND MGCL2 (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-1zqm:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-1zqn:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF BACL2 (15 MILLIMOLAR) AND NACL (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-1zqo:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR) AND NACL (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-1zqp:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (75 MILLIMOLAR) AND NACL (75 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-1zqq:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (15 MILLIMOLAR) AND NACL (15 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-1zqr:
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF NICL2
Method: X-RAY DIFFRACTION / Resolution: 3.7 Å

PDB-1zqs:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF TLCL (0.5 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-1zqu:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-1zqv:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF CACL2 (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-1zqw:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF CSCL (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-1zqx:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-1zqy:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MGCL2 (50 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-1zqz:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (50 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-8ica:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-8icb:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-8icc:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA (NO 5'-PHOSPHATE)
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-8ice:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CDCL2 (1 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-8icf:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (10 MILLIMOLAR) AND MGCL2 (50 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-8icg:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-8ich:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-8ici:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DGTP (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-8icz:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF OF DATP (1 MILLIMOLAR), MNCL2 (5 MILLIMOLAR), AND LITHIUM SULFATE (75 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-9ica:
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-O-(1-THIOTRIPHOSPHATE), SOAKED IN THE PRESENCE OF DATP(ALPHA)S AND MNCL2
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-9icb:
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND COCL2
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-9icc:
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND CRCL3
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-9ice:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CUCL2 (0.1 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-9icg:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-9ich:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DGTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-9ici:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DTTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR)
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-9icj:
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-9icl:
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF PYROPHOSPHATE AND MNCL2
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-K:
Unknown entry

ChemComp-BA:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-CR:
CHROMIUM ION

ChemComp-CS:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-NI:
NICKEL (II) ION

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

ChemComp-CD:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-SO4:
SULFATE ION

ChemComp-STP:
2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE)

ChemComp-CO:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

Source
  • rattus norvegicus (Norway rat)
  • homo sapiens (human)
KeywordsNUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR / TRANSFERASE/DNA / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA / TRANSFERASE-DNA complex

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