eF-site ID 5j2e-A
PDB Code 5j2e
Chain A

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Title Ternary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus
Classification Transferase/DNA
Compound DNA polymerase beta
Source null (5J2E)
Sequence A:  TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKY
PHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR
QDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNE
DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKV
DSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKE
YPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEK
GFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYRE
PKDRSE
Description


Functional site
1) chain A
residue 179
type
sequence G
description binding site for residue DUP A 401
source : AC1
2) chain A
residue 180
type
sequence S
description binding site for residue DUP A 401
source : AC1
3) chain A
residue 183
type
sequence R
description binding site for residue DUP A 401
source : AC1
4) chain A
residue 189
type
sequence G
description binding site for residue DUP A 401
source : AC1
5) chain A
residue 190
type
sequence D
description binding site for residue DUP A 401
source : AC1
6) chain A
residue 192
type
sequence D
description binding site for residue DUP A 401
source : AC1
7) chain A
residue 271
type
sequence Y
description binding site for residue DUP A 401
source : AC1
8) chain A
residue 272
type
sequence F
description binding site for residue DUP A 401
source : AC1
9) chain A
residue 273
type
sequence T
description binding site for residue DUP A 401
source : AC1
10) chain A
residue 274
type
sequence G
description binding site for residue DUP A 401
source : AC1
11) chain A
residue 279
type
sequence N
description binding site for residue DUP A 401
source : AC1
12) chain A
residue 190
type
sequence D
description binding site for residue MG A 402
source : AC2
13) chain A
residue 192
type
sequence D
description binding site for residue MG A 402
source : AC2
14) chain A
residue 190
type
sequence D
description binding site for residue MG A 403
source : AC3
15) chain A
residue 192
type
sequence D
description binding site for residue MG A 403
source : AC3
16) chain A
residue 256
type
sequence D
description binding site for residue MG A 403
source : AC3
17) chain A
residue 101
type
sequence T
description binding site for residue NA A 404
source : AC4
18) chain A
residue 103
type
sequence V
description binding site for residue NA A 404
source : AC4
19) chain A
residue 106
type
sequence I
description binding site for residue NA A 404
source : AC4
20) chain A
residue 60
type
sequence K
description binding site for residue NA A 405
source : AC5
21) chain A
residue 62
type
sequence L
description binding site for residue NA A 405
source : AC5
22) chain A
residue 65
type
sequence V
description binding site for residue NA A 405
source : AC5
23) chain A
residue 258
type
sequence R
description binding site for residue CL A 406
source : AC6
24) chain A
residue 271
type
sequence Y
description binding site for residue CL A 406
source : AC6
25) chain A
residue 294
type
sequence N
description binding site for residue CL A 407
source : AC7
26) chain A
residue 297
type
sequence T
description binding site for residue CL A 407
source : AC7
27) chain A
residue 299
type
sequence R
description binding site for residue CL A 407
source : AC7
28) chain A
residue 32
type
sequence A
description binding site for residue CL A 408
source : AC8
29) chain A
residue 34
type
sequence H
description binding site for residue CL A 408
source : AC8
30) chain A
residue 35
type
sequence K
description binding site for residue CL A 408
source : AC8
31) chain A
residue 82
type
sequence L
description binding site for residue CL A 409
source : AC9
32) chain A
residue 89
type
sequence R
description binding site for residue CL A 409
source : AC9
33) chain A
residue 264
type
sequence Q
description binding site for residue CL A 410
source : AD1
34) chain A
residue 267
type
sequence C
description binding site for residue CL A 410
source : AD1
35) chain A
residue 313
type
sequence V
description binding site for residue CL A 410
source : AD1
36) chain A
residue 72
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
source Swiss-Prot : SWS_FT_FI6
37) 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
38) 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
39) 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
40) 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
41) 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
42) chain A
residue 183
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
source Swiss-Prot : SWS_FT_FI4
43) chain A
residue 179-198
type prosite
sequence GSFRRGAESSGDMDVLLTHP
description DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
source prosite : PS00522
44) chain A
residue 192
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
45) chain A
residue 190
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
46) chain A
residue 256
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
47) 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
48) 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
49) 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
50) 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
51) 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
52) 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
53) 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
54) 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
55) 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
56) 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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