eF-site ID 2nvy-ABCEFHIJKL PDB Code 2nvy Chain A, B, C, E, F, H, I, J, K, L Title RNA Polymerase II form II in 150 mM Mn+2 Classification TRANSCRIPTION Compound DNA-directed RNA polymerase II largest subunit Source ORGANISM_COMMON: baker's yeast; ORGANISM_SCIENTIFIC: Saccharomyces cerevisiae; Sequence A:  VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETM DETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHF GHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNEL MRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQL VSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRV LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPV PPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEH NGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRP VKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLEL DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG AKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDP VLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNAD FDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCM GIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIP TPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQV CAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITE TIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRF LNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQM SACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVE NSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRL VKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQ SLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILG DLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQA FDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTL KKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQA KLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQ LHFSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFK NDLFVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENI TLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGV NLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKE VYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNR SNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILG QMAPIGTGAFDVMIDEESL B:  FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDY TLQDIICEDSTLIEISFGKIYVTKPMVNESDGVTHALYPQ EARLRNLTYSSGLFVDVKKRTYEKVFIGRLPIMLRSKNCY LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAG NIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYG REGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTA LGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGY MINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL FKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGA GVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVC PAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTL RRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDD ESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEY IDAEEEESILIAMQPEDLEPDVDPAKRIRVSHHATTFTHC EIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVF LTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMD QEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAP GVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLV TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITY RREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKV AALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYN GHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPGLRF GEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMT VIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAM NITPRLYTDRSRDF C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ VVVRGIDTLQKKVASILLALTQMDQD E:  MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLE DFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIR KSETSGRYASYRICM F:  KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDL EGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL IVDL H:  SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLD INVELFPVAAQDSLTVTIASSLTRSWRPPQAGDRSLADDY DYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLN NLKQENAYLLIRR I:  MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS PLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ FS J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG LKRYCCRRMILTHVDLIEKFLRYNP K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTL L:  ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRL VQFEAR Description Functional site 1) chain J residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN J 3001 source : AC1 2) chain J residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN J 3001 source : AC1 3) chain J residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN J 3001 source : AC1 4) chain J residue 46 type sequence C description BINDING SITE FOR RESIDUE ZN J 3001 source : AC1 5) chain C residue 86 type sequence C description BINDING SITE FOR RESIDUE ZN C 3002 source : AC2 6) chain C residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN C 3002 source : AC2 7) chain C residue 92 type sequence C description BINDING SITE FOR RESIDUE ZN C 3002 source : AC2 8) chain C residue 95 type sequence C description BINDING SITE FOR RESIDUE ZN C 3002 source : AC2 9) chain I residue 7 type sequence C description BINDING SITE FOR RESIDUE ZN I 3003 source : AC3 10) chain I residue 10 type sequence C description BINDING SITE FOR RESIDUE ZN I 3003 source : AC3 11) chain I residue 29 type sequence C description BINDING SITE FOR RESIDUE ZN I 3003 source : AC3 12) chain I residue 32 type sequence C description BINDING SITE FOR RESIDUE ZN I 3003 source : AC3 13) chain I residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN I 3004 source : AC4 14) chain I residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN I 3004 source : AC4 15) chain I residue 103 type sequence C description BINDING SITE FOR RESIDUE ZN I 3004 source : AC4 16) chain I residue 106 type sequence C description BINDING SITE FOR RESIDUE ZN I 3004 source : AC4 17) chain I residue 108 type sequence H description BINDING SITE FOR RESIDUE ZN I 3004 source : AC4 18) chain L residue 31 type sequence C description BINDING SITE FOR RESIDUE ZN L 3005 source : AC5 19) chain L residue 34 type sequence C description BINDING SITE FOR RESIDUE ZN L 3005 source : AC5 20) chain L residue 48 type sequence C description BINDING SITE FOR RESIDUE ZN L 3005 source : AC5 21) chain L residue 51 type sequence C description BINDING SITE FOR RESIDUE ZN L 3005 source : AC5 22) chain L residue 53 type sequence H description BINDING SITE FOR RESIDUE ZN L 3005 source : AC5 23) chain A residue 107 type sequence C description BINDING SITE FOR RESIDUE ZN A 3006 source : AC6 24) chain A residue 110 type sequence C description BINDING SITE FOR RESIDUE ZN A 3006 source : AC6 25) chain A residue 148 type sequence C description BINDING SITE FOR RESIDUE ZN A 3006 source : AC6 26) chain A residue 167 type sequence C description BINDING SITE FOR RESIDUE ZN A 3006 source : AC6 27) chain B residue 1163 type sequence C description BINDING SITE FOR RESIDUE ZN B 3007 source : AC7 28) chain B residue 1166 type sequence C description BINDING SITE FOR RESIDUE ZN B 3007 source : AC7 29) chain B residue 1182 type sequence C description BINDING SITE FOR RESIDUE ZN B 3007 source : AC7 30) chain B residue 1185 type sequence C description BINDING SITE FOR RESIDUE ZN B 3007 source : AC7 31) chain A residue 67 type sequence C description BINDING SITE FOR RESIDUE ZN A 3008 source : AC8 32) chain A residue 70 type sequence C description BINDING SITE FOR RESIDUE ZN A 3008 source : AC8 33) chain A residue 77 type sequence C description BINDING SITE FOR RESIDUE ZN A 3008 source : AC8 34) chain A residue 80 type sequence H description BINDING SITE FOR RESIDUE ZN A 3008 source : AC8 35) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE MN A 3009 source : AC9 36) chain A residue 483 type sequence D description BINDING SITE FOR RESIDUE MN A 3009 source : AC9 37) chain A residue 485 type sequence D description BINDING SITE FOR RESIDUE MN A 3009 source : AC9 38) chain A residue 481 type sequence D description BINDING SITE FOR RESIDUE MN A 3010 source : BC1 39) chain B residue 836 type sequence E description BINDING SITE FOR RESIDUE MN A 3010 source : BC1 40) chain J residue 10 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 41) chain L residue 31-51 type ZN_FING sequence CAECSSKLSLSRTDAVRCKDC description C4-type source Swiss-Prot : SWS_FT_FI1 42) chain J residue 45 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 43) chain J residue 46 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 44) chain A residue 483 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 45) chain A residue 485 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 46) chain A residue 107 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 47) chain A residue 110 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 48) chain A residue 148 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 49) chain A residue 167 type ZN_FING sequence C description C4-type source Swiss-Prot : SWS_FT_FI1 50) chain A residue 481 type ZN_FING sequence D description C4-type source Swiss-Prot : SWS_FT_FI1 51) chain I residue 7 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 52) chain I residue 10 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 53) chain I residue 29 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 54) chain I residue 32 type BINDING sequence C description BINDING => ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI3 55) chain I residue 40 type MOD_RES sequence S description Phosphoserine => ECO:0007744|PubMed:18407956 source Swiss-Prot : SWS_FT_FI5 56) chain B residue 977-989 type prosite sequence GDKFASRHGQKGT description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT source prosite : PS01166 57) chain E residue 147-160 type prosite sequence HELVPKHIRLSSDE description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE source prosite : PS01110 58) chain J residue 2-11 type prosite sequence IVPVRCFSCG description RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG source prosite : PS01112 59) chain K residue 35-66 type prosite sequence FEKEDHTLGNLIRAELLNDRKVLFAAYKVEHP description RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP source prosite : PS01154 60) chain C residue 31-71 type prosite sequence NSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLI P description RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP source prosite : PS00446 61) chain F residue 86-100 type prosite sequence TKYERARILGTRALQ description RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ source prosite : PS01111 62) chain I residue 75-110 type prosite sequence CPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIF description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF source prosite : PS00466 63) chain I residue 6-32 type prosite sequence FCRDCNNMLYPREDKENNRLLFECRTC description RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCrDCNNMLypredkennrllfeCrtC source prosite : PS01030 64) chain B residue 837 type catalytic sequence D description 788 source MCSA : MCSA1 65) chain A residue 483 type catalytic sequence D description 788 source MCSA : MCSA1 66) chain A residue 485 type catalytic sequence D description 788 source MCSA : MCSA1 67) chain I residue 75 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 68) chain I residue 78 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 69) chain I residue 103 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 70) chain I residue 106 type BINDING sequence C description BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:11313498, ECO:0000269|PubMed:11805306, ECO:0000269|PubMed:15537538, ECO:0000305|PubMed:11313499 source Swiss-Prot : SWS_FT_FI4 71) chain L residue 51 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 72) chain B residue 1185 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 73) chain L residue 31 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 74) chain L residue 34 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2 75) chain L residue 48 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI2

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