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3SV3

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP

Functional Information from GO Data
ChainGOidnamespacecontents
A0001882molecular_functionnucleoside binding
A0003676molecular_functionnucleic acid binding
A0003677molecular_functionDNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0006260biological_processDNA replication
A0006261biological_processDNA-templated DNA replication
A0006281biological_processDNA repair
Functional Information from PDB Data
site_idAC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE 5SI A 1
ChainResidue
AHOH153
APRO816
AMG834
AMG842
AHOH901
AHOH905
AHOH906
AHOH154
AHOH170
AGLN633
AARG801
ALYS804
AGLU805
ALEU813
AALA814

site_idAC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE 5SI A 833
ChainResidue
AHOH169
AHOH191
AARG573
AASP610
ATYR611
AGLN613
AILE614
AGLU615
AHIS639
AARG659
ALYS663
ATHR664
APHE667
AASP785
AMG836
AMG837
AHOH893
BHOH49
BDOC112
CDG205

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 834
ChainResidue
A5SI1
AHOH153
AHOH154
AHOH170

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL A 835
ChainResidue
ATHR544
ATYR545
APRO579
AASN580
AASN583
AHOH871
AHOH882
CHOH95
CDC209
CDC210

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 2
ChainResidue
AHOH155
AARG313
ATRP318
AASP551
ALEU552

site_idAC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT A 8
ChainResidue
AGLU337
ALYS340

site_idAC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT A 9
ChainResidue
AHIS443
ATHR447

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 836
ChainResidue
AASP610
ATYR611
AASP785
A5SI833
AMG837

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MG A 837
ChainResidue
AHOH163
AASP610
AASP785
A5SI833
AMG836
AHOH855
BDOC112

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 838
ChainResidue
AILE823
AGLY824
AGLU825
ASER829

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT A 839
ChainResidue
APRO792
ALYS793
AGLU794
AARG795

site_idBC3
Number of Residues1
DetailsBINDING SITE FOR RESIDUE FMT A 840
ChainResidue
AHOH42

site_idBC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT A 841
ChainResidue
ALEU311
AGLU400
AARG405

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 842
ChainResidue
A5SI1
AHOH901
AHOH902
AHOH903
AHOH904
AHOH905

site_idBC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT A 843
ChainResidue
AASP488
ALYS511
AHOH852
BDC106
CDT212
CFMT217

site_idBC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT A 844
ChainResidue
AGLU708
AARG715
AHOH908

site_idBC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FMT A 845
ChainResidue
AHOH106
AASN485
BDG107
AHOH89
AHOH90

site_idBC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE FMT A 846
ChainResidue
AARG746

site_idCC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE FMT A 847
ChainResidue
ATYR455
AARG596

site_idCC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG B 1
ChainResidue
BHOH2
BHOH3
BHOH4
BHOH5
BHOH6
CHOH222

site_idCC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL C 3
ChainResidue
CHOH41
CDG205
CDG206

site_idCC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 4
ChainResidue
AARG728
CDG206
CDC207

site_idCC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 6
ChainResidue
CHOH135
CDC207
CDG208

site_idCC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE FMT C 1
ChainResidue
CHOH35
CDG213
CDG214

site_idCC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FMT C 217
ChainResidue
AHOH90
AHOH121
AARG487
AFMT843
AHOH852
CHOH8
CDG211
CDT212

site_idCC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL C 218
ChainResidue
BDC104
CHOH36
CDC210
CDG211
CDT212

site_idCC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FMT C 219
ChainResidue
AARG556
BDC103
CDT215
CDC216

Functional Information from PROSITE/UniProt
site_idPS00447
Number of Residues20
DetailsDNA_POLYMERASE_A DNA polymerase family A signature. RraAKtinFGvlYgmSahrL
ChainResidueDetails
AARG659-LEU678

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PDB entries from 2024-06-12

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