eF-site ID 1e9n-AB PDB Code 1e9n Chain A, B click to enlarge Title A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism Classification DNA REPAIR Compound DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE Source (APE1_HUMAN) Sequence A:  ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLD WVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAP SEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDS FVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKP LVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELL QAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDY FLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL B:  ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLD WVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAP SEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDS FVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKP LVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELL QAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDY FLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL Description Functional site 1) chain A residue 70 type sequence D description BINDING SITE FOR RESIDUE PB A1319 source : AC1 2) chain A residue 96 type sequence E description BINDING SITE FOR RESIDUE PB A1319 source : AC1 3) chain A residue 210 type sequence D description BINDING SITE FOR RESIDUE PB A1320 source : AC2 4) chain A residue 212 type sequence N description BINDING SITE FOR RESIDUE PB A1320 source : AC2 5) chain A residue 309 type sequence H description BINDING SITE FOR RESIDUE PB A1320 source : AC2 6) chain B residue 210 type sequence D description BINDING SITE FOR RESIDUE PB B1319 source : AC3 7) chain B residue 212 type sequence N description BINDING SITE FOR RESIDUE PB B1319 source : AC3 8) chain B residue 282 type sequence L description BINDING SITE FOR RESIDUE PB B1319 source : AC3 9) chain B residue 309 type sequence H description BINDING SITE FOR RESIDUE PB B1319 source : AC3 10) chain B residue 96 type sequence E description BINDING SITE FOR RESIDUE PB B1320 source : AC4 11) chain A residue 71 type catalytic sequence G description 510 source MCSA : MCSA1 12) chain A residue 97 type catalytic sequence T description 510 source MCSA : MCSA1 13) chain A residue 172 type catalytic sequence V description 510 source MCSA : MCSA1 14) chain A residue 211 type catalytic sequence L description 510 source MCSA : MCSA1 15) chain A residue 213 type catalytic sequence V description 510 source MCSA : MCSA1 16) chain A residue 284 type catalytic sequence Y description 510 source MCSA : MCSA1 17) chain A residue 309 type catalytic sequence H description 510 source MCSA : MCSA1 18) chain A residue 310 type catalytic sequence C description 510 source MCSA : MCSA1 19) chain B residue 71 type catalytic sequence G description 510 source MCSA : MCSA2 20) chain B residue 97 type catalytic sequence T description 510 source MCSA : MCSA2 21) chain B residue 172 type catalytic sequence V description 510 source MCSA : MCSA2 22) chain B residue 211 type catalytic sequence L description 510 source MCSA : MCSA2 23) chain B residue 213 type catalytic sequence V description 510 source MCSA : MCSA2 24) chain B residue 284 type catalytic sequence Y description 510 source MCSA : MCSA2 25) chain B residue 309 type catalytic sequence H description 510 source MCSA : MCSA2 26) chain B residue 310 type catalytic sequence C description 510 source MCSA : MCSA2 27) chain A residue 89-98 type prosite sequence PDILCLQETK description AP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK source prosite : PS00726 28) chain A residue 251-267 type prosite sequence DSFRHLYPNTPYAYTFW description AP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW source prosite : PS00727 29) chain A residue 277-288 type prosite sequence NVGWRLDYFLLS description AP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS source prosite : PS00728 30) chain A residue 172 type ACT_SITE sequence V description ACT_SITE => ECO:0000269|PubMed:15380100 source Swiss-Prot : SWS_FT_FI1 31) chain B residue 172 type ACT_SITE sequence V description ACT_SITE => ECO:0000269|PubMed:15380100 source Swiss-Prot : SWS_FT_FI1 32) chain A residue 55 type MOD_RES sequence P description Phosphoserine => ECO:0007744|PubMed:23186163 source Swiss-Prot : SWS_FT_FI11 33) chain B residue 55 type MOD_RES sequence P description Phosphoserine => ECO:0007744|PubMed:23186163 source Swiss-Prot : SWS_FT_FI11 34) chain A residue 66 type MOD_RES sequence S description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694 source Swiss-Prot : SWS_FT_FI12 35) chain A residue 94 type MOD_RES sequence L description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694 source Swiss-Prot : SWS_FT_FI12 36) chain B residue 66 type MOD_RES sequence S description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694 source Swiss-Prot : SWS_FT_FI12 37) chain B residue 94 type MOD_RES sequence L description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694 source Swiss-Prot : SWS_FT_FI12 38) chain A residue 198 type MOD_RES sequence G description N6-acetyllysine => ECO:0007744|PubMed:19608861 source Swiss-Prot : SWS_FT_FI13 39) chain B residue 198 type MOD_RES sequence G description N6-acetyllysine => ECO:0007744|PubMed:19608861 source Swiss-Prot : SWS_FT_FI13 40) chain A residue 234 type MOD_RES sequence P description Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352 source Swiss-Prot : SWS_FT_FI14 41) chain B residue 234 type MOD_RES sequence P description Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352 source Swiss-Prot : SWS_FT_FI14 42) chain A residue 311 type MOD_RES sequence P description S-nitrosocysteine => ECO:0000269|PubMed:17403694 source Swiss-Prot : SWS_FT_FI15 43) chain B residue 311 type MOD_RES sequence P description S-nitrosocysteine => ECO:0000269|PubMed:17403694 source Swiss-Prot : SWS_FT_FI15 44) chain A residue 211 type ACT_SITE sequence L description Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX source Swiss-Prot : SWS_FT_FI2 45) chain B residue 211 type ACT_SITE sequence L description Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX source Swiss-Prot : SWS_FT_FI2 46) chain A residue 310 type ACT_SITE sequence C description Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI3 47) chain B residue 310 type ACT_SITE sequence C description Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI3 48) chain A residue 69 type BINDING sequence V description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 49) chain B residue 213 type BINDING sequence V description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 50) chain B residue 309 type BINDING sequence H description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 51) chain B residue 310 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 52) chain A residue 97 type BINDING sequence T description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 53) chain A residue 211 type BINDING sequence L description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 54) chain A residue 213 type BINDING sequence V description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 55) chain A residue 309 type BINDING sequence H description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 56) chain A residue 310 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 57) chain B residue 69 type BINDING sequence V description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 58) chain B residue 97 type BINDING sequence T description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 59) chain B residue 211 type BINDING sequence L description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 source Swiss-Prot : SWS_FT_FI4 60) chain A residue 213 type SITE sequence V description Transition state stabilizer => ECO:0000269|PubMed:8932375 source Swiss-Prot : SWS_FT_FI6 61) chain B residue 213 type SITE sequence V description Transition state stabilizer => ECO:0000269|PubMed:8932375 source Swiss-Prot : SWS_FT_FI6 62) chain A residue 284 type SITE sequence Y description Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799 source Swiss-Prot : SWS_FT_FI7 63) chain B residue 284 type SITE sequence Y description Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799 source Swiss-Prot : SWS_FT_FI7 64) chain A residue 310 type SITE sequence C description Interaction with DNA substrate source Swiss-Prot : SWS_FT_FI8 65) chain B residue 310 type SITE sequence C description Interaction with DNA substrate source Swiss-Prot : SWS_FT_FI8

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