eF-site ID 3rh4-A
PDB Code 3rh4
Chain A

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Title DNA Polymerase Beta with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP)
Classification TRANSFERASE/DNA
Compound 5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
Source null (3RH4)
Sequence A:  TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKY
PHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR
QDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNE
DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKV
DSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKE
YPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEK
GFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYRE
PKDRSE
Description


Functional site
1) chain A
residue 190
type
sequence D
description BINDING SITE FOR RESIDUE MN A 339
source : AC3
2) chain A
residue 192
type
sequence D
description BINDING SITE FOR RESIDUE MN A 339
source : AC3
3) chain A
residue 190
type
sequence D
description BINDING SITE FOR RESIDUE MN A 340
source : AC4
4) chain A
residue 192
type
sequence D
description BINDING SITE FOR RESIDUE MN A 340
source : AC4
5) chain A
residue 256
type
sequence D
description BINDING SITE FOR RESIDUE MN A 340
source : AC4
6) chain A
residue 145
type
sequence D
description BINDING SITE FOR RESIDUE MN A 341
source : AC5
7) chain A
residue 252
type
sequence H
description BINDING SITE FOR RESIDUE MN A 341
source : AC5
8) chain A
residue 285
type
sequence H
description BINDING SITE FOR RESIDUE MN A 342
source : AC6
9) chain A
residue 288
type
sequence E
description BINDING SITE FOR RESIDUE MN A 342
source : AC6
10) chain A
residue 101
type
sequence T
description BINDING SITE FOR RESIDUE NA A 351
source : AC9
11) chain A
residue 103
type
sequence V
description BINDING SITE FOR RESIDUE NA A 351
source : AC9
12) chain A
residue 106
type
sequence I
description BINDING SITE FOR RESIDUE NA A 351
source : AC9
13) chain A
residue 60
type
sequence K
description BINDING SITE FOR RESIDUE NA A 352
source : BC1
14) chain A
residue 62
type
sequence L
description BINDING SITE FOR RESIDUE NA A 352
source : BC1
15) chain A
residue 65
type
sequence V
description BINDING SITE FOR RESIDUE NA A 352
source : BC1
16) chain A
residue 294
type
sequence N
description BINDING SITE FOR RESIDUE CL A 353
source : BC2
17) chain A
residue 297
type
sequence T
description BINDING SITE FOR RESIDUE CL A 353
source : BC2
18) chain A
residue 32
type
sequence A
description BINDING SITE FOR RESIDUE CL A 354
source : BC3
19) chain A
residue 33
type
sequence I
description BINDING SITE FOR RESIDUE CL A 354
source : BC3
20) chain A
residue 34
type
sequence H
description BINDING SITE FOR RESIDUE CL A 354
source : BC3
21) chain A
residue 35
type
sequence K
description BINDING SITE FOR RESIDUE CL A 354
source : BC3
22) chain A
residue 82
type
sequence L
description BINDING SITE FOR RESIDUE CL A 355
source : BC4
23) chain A
residue 86
type
sequence E
description BINDING SITE FOR RESIDUE CL A 355
source : BC4
24) chain A
residue 89
type
sequence R
description BINDING SITE FOR RESIDUE CL A 355
source : BC4
25) chain A
residue 330
type
sequence P
description BINDING SITE FOR RESIDUE CL A 356
source : BC5
26) chain A
residue 331
type
sequence K
description BINDING SITE FOR RESIDUE CL A 356
source : BC5
27) chain A
residue 159
type
sequence Q
description BINDING SITE FOR RESIDUE CL A 357
source : BC6
28) chain A
residue 177
type
sequence V
description BINDING SITE FOR RESIDUE CL A 357
source : BC6
29) chain A
residue 84
type
sequence K
description BINDING SITE FOR RESIDUE CL A 358
source : BC7
30) chain A
residue 179
type
sequence G
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
31) chain A
residue 180
type
sequence S
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
32) chain A
residue 183
type
sequence R
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
33) chain A
residue 189
type
sequence G
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
34) chain A
residue 190
type
sequence D
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
35) chain A
residue 192
type
sequence D
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
36) chain A
residue 271
type
sequence Y
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
37) chain A
residue 272
type
sequence F
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
38) chain A
residue 273
type
sequence T
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
39) chain A
residue 274
type
sequence G
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
40) chain A
residue 276
type
sequence D
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
41) chain A
residue 279
type
sequence N
description BINDING SITE FOR RESIDUE CTP A 338
source : BC8
42) chain A
residue 174
type
sequence I
description BINDING SITE FOR RESIDUE CTP A 350
source : BC9
43) chain A
residue 176
type
sequence T
description BINDING SITE FOR RESIDUE CTP A 350
source : BC9
44) chain A
residue 196
type
sequence T
description BINDING SITE FOR RESIDUE CTP A 350
source : BC9
45) chain A
residue 262
type
sequence K
description BINDING SITE FOR RESIDUE CTP A 350
source : BC9
46) chain A
residue 265
type
sequence Y
description BINDING SITE FOR RESIDUE CTP A 350
source : BC9
47) chain A
residue 266
type
sequence Y
description BINDING SITE FOR RESIDUE CTP A 350
source : BC9
48) chain A
residue 179-198
type prosite
sequence GSFRRGAESSGDMDVLLTHP
description DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
source prosite : PS00522
49) chain A
residue 183
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
source Swiss-Prot : SWS_FT_FI4
50) chain A
residue 72
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
source Swiss-Prot : SWS_FT_FI6
51) chain A
residue 83
type MOD_RES
sequence R
description Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
source Swiss-Prot : SWS_FT_FI7
52) chain A
residue 152
type MOD_RES
sequence R
description Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
source Swiss-Prot : SWS_FT_FI7
53) chain A
residue 41
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
source Swiss-Prot : SWS_FT_FI8
54) chain A
residue 61
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
source Swiss-Prot : SWS_FT_FI8
55) chain A
residue 81
type CROSSLNK
sequence K
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
source Swiss-Prot : SWS_FT_FI8
56) chain A
residue 192
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
57) chain A
residue 256
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
58) chain A
residue 190
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
59) chain A
residue 72
type ACT_SITE
sequence K
description Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863
source Swiss-Prot : SWS_FT_FI1
60) chain A
residue 101
type BINDING
sequence T
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2
61) chain A
residue 103
type BINDING
sequence V
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2
62) chain A
residue 106
type BINDING
sequence I
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2
63) chain A
residue 65
type BINDING
sequence V
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2
64) chain A
residue 60
type BINDING
sequence K
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2
65) chain A
residue 62
type BINDING
sequence L
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2
66) chain A
residue 180
type BINDING
sequence S
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3
67) chain A
residue 189
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3
68) chain A
residue 149
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

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