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PDB ID Mentions in PubMed Central Article count: 2

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Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.

(2013) Nucleic Acids Res 41

PubMed: 23268450 | PubMedCentral: PMC3561991 | DOI: 10.1093/nar/gks1296

ACCESSION NUMBERS The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.rcsb.org , with accession codes 4EYH and 4EYI for APG-dCTP and APG-dATP, respectively.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4018060

Table 1 Structures of Y-Family DNA Polymerases name species state PDB entry Structures of the Catalytic Region Dpo4 a Sulfolobus solfataricus apo 2RDI( 100 )     DNA binary complex 2RD... ( 100 )     ternary complex 1JX4, 2AGO; 95 , 136 2ATL 137     frameshift 3QZ7, 3QZ8( 39 )     CPD bypass 1RYR, 1RYS( 138 )     BPDE bypass 1S0M; 138 2IA6 and 2IBK( 37 )     abasic bypass 1S0N, 1S0O, 1S10( 105 )     [AF]G bypass 3KHG, 3KHH, 3KHL, 3KHR( 139 )     APG bypass 4FBU, 4FBT( 140 )     cisplatin bypass 3M9M, 3M9N, 3M9O( 141 )     DFT bypass 2VA2, 2V9W( 142 )     εdG (ε-G) 2BQR( 143 )     PdG bypass 2R8I( 144 )     8-oxo-G bypass 2ASD, 2ASJ, 2ASL; 137 2C2D, 2C2E( 66 )     8-oxo-G mispair 3GII, 3GIJ, 3GIK, 3GIL, 3GIM( 145 )     8-oxo-G (mutant Dpo4) 2UVR, 2UVU, 2UVV, 2UVW( 146 ) Dbh Sulfolobus acidocaldarius apo 1IM4; 93 1K1S 94     DNA binary complex 3BQ0, 3BQ2( 38 )     ternary complex 3BQ1( 38 ) Dpo4–Dbh chimera ternary 4F4W, 4F4X, 4F4Y, 4F4Z, 4F50( 86 ) pol η yeast apo 1JIH( 85 )   human ternary complex 3MFH( 67 )     CPD bypass 3MFI( 67 )     cisplatin bypass 2R8K( 96 )     8-oxo-G bypass 3OHA( 67 )     DNA binary complex 4J9P, 4J9Q, 4J9R, 4J9S( 99 )     ternary complex 4ED8( 127 )     CPD bypass 3MR2, 3MR3( 97 )     cisplatin bypass 4DL2, 4DL3, 4DL4, 4DL5, 4DL6, 4DL7; 98 4EEY 147     T:G mismatch 4J9K, 4J9L, 4J9M, 4J9N, 4J9O, 4J9P, 4J9Q, 4J9R, 4J9S( 98 ) pol ι human ternary complex 2ALZ; 115 3GV8 116     abasic bypass 3G6Y( 148 )     8-oxo-G bypass 3Q8R( 69 )     APG bypass 4EYI( 149 )     εdA (ε-A) 2DPJ( 150 )     T:G mismatch 3GV5, 3GV8; 116 3H4B, 3H4D( 118 ) pol κ human apo 1T94( 102 )     ternary complex 2OH2( 103 )     CPD (extension) 3PZP( 151 )     8-oxo-G bypass 2W7O, 2W7P; 152 3IN5 153 Rev1 yeast ternary complex 2AQ4( 106 )   human ternary complex 3GQC( 107 )         Structures of Regulatory Domains DinB E. coli (PolIV) LF (DinB) and β-clamp 1UNN( 154 ) Dpo4 S. solfataricus Dpo4 and PCNA 3FDS( 155 ) pol η, ι, and κ human PIP (η, ι, or κ) and PCNA 2ZVK, 2ZVM, 2ZVL( 156 ) pol η human apo-UBZ 2I5O( 157 ) pol ι human apo-UBM2 2KHU; 158 2L0G 159   mouse UBM2–Ub 2KHW; 158 2L0F 159     UBM1/2–Ub 2KWU, 2KWV( 160 ) Rev1 yeast BRCT 4ID3; 161 2M2I 73   mouse apo CTD 2LSG( 162 )   human CTD-κ (RIR) 2LSJ( 162 )     CTD-Rev3/7-κ (RIR) 4FJO( 77 )     apo CTD 2LSY( 163 )     CTD-η (RIR) 2LSK( 163 )     CTD-Rev3/7 3VU7( 76 )     CTD-Rev3/7-κ (RIR) 4GK5( 78 ) a There are additional structures in the PDB of Dpo4 complexed with DNA lesions beyond those listed here.

Publication Year: 2014