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6P09

Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+

Functional Information from GO Data
ChainGOidnamespacecontents
A0003677molecular_functionDNA binding
A0003909molecular_functionDNA ligase activity
A0003910molecular_functionDNA ligase (ATP) activity
A0005524molecular_functionATP binding
A0006281biological_processDNA repair
A0006310biological_processDNA recombination
A0071897biological_processDNA biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue MG A 1001
ChainResidue
AGLU592
AHOH1207
AHOH1285
AHOH1355
BDG11
BHOH119

site_idAC2
Number of Residues6
Detailsbinding site for residue MG A 1002
ChainResidue
AHOH1498
AHOH1509
AHOH1529
AHOH1258
AHOH1308
AHOH1497

site_idAC3
Number of Residues6
Detailsbinding site for residue MG A 1003
ChainResidue
AGLY799
AHOH1192
AHOH1307
AHOH1323
CDG4
CHOH222

site_idAC4
Number of Residues6
Detailsbinding site for residue MG A 1004
ChainResidue
AHOH1216
AHOH1248
AHOH1510
AHOH1526
AHOH1530
AHOH1538

site_idAC5
Number of Residues4
Detailsbinding site for residue PEG A 1005
ChainResidue
AALA483
ALYS487
ATRP495
AHOH1122

site_idAC6
Number of Residues17
Detailsbinding site for residue AMP C 101
ChainResidue
AGLU566
ATYR567
ALYS568
ATYR569
AARG573
AARG589
AGLU621
APHE660
AMET723
ALYS725
ATRP742
ALYS744
AHOH1149
CDG1
CHOH202
CHOH208
CHOH209

site_idAC7
Number of Residues5
Detailsbinding site for residue MG C 102
ChainResidue
AHOH1135
AHOH1146
AHOH1149
AHOH1335
CDG1

Functional Information from PROSITE/UniProt
site_idPS00333
Number of Residues27
DetailsDNA_LIGASE_A2 ATP-dependent DNA ligase signature 2. EGLMVKtldvdat.YEiakrs.Hnwl..KLK
ChainResidueDetails
AGLU720-LYS746

site_idPS00697
Number of Residues9
DetailsDNA_LIGASE_A1 ATP-dependent DNA ligase AMP-binding site. EYKYDGQRA
ChainResidueDetails
AGLU566-ALA574

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues11
DetailsRegion: {"description":"Interaction with target DNA"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsActive site: {"description":"N6-AMP-lysine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10135","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"15565146","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1X9N","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsSite: {"description":"Interaction with target DNA"}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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