eF-site ID 6k3j_4-AB
PDB Code 6k3j
Model 4
Chain A, B

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Title Solution structure of APOBEC3G-CD2 with ssDNA, Product A
Classification HYDROLASE/DNA
Compound DNA dC->dU-editing enzyme APOBEC-3G
Source (6K3J)
Sequence A:  MDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVLLN
QRRGFLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLDQD
YRVTCFTSWSPCFSCAQEMAKFISKNKHVSLCIFTARIYD
DQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGC
PFQPWDGLDEHSQDLSGRLRAILQNQEN
B:  ATTCXXAATT
Description (1)  DNA dC->dU-editing enzyme APOBEC-3G/DNA Complex


Functional site

1) chain A
residue 257
type
ligand
sequence H
description binding site for residue ZN A 401
source : AC1

2) chain A
residue 288
type
ligand
sequence C
description binding site for residue ZN A 401
source : AC1

3) chain A
residue 291
type
ligand
sequence C
description binding site for residue ZN A 401
source : AC1

4) chain A
residue 215-220
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence RHETYL
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

5) chain A
residue 243-246
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence CNQA
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

6) chain A
residue 253-261
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence LEGRHAELC
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

7) chain B
residue 388-389
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence CX
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

8) chain B
residue 391-392
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence AA
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

9) chain A
residue 247
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence P
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

10) chain A
residue 264
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence D
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

11) chain A
residue 287-288
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence PC
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

12) chain A
residue 291
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence C
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

13) chain A
residue 242
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence L
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

14) chain A
residue 250
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence H
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

15) chain A
residue 262
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence F
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

16) chain A
residue 248
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence H
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

17) chain B
residue 393
type binding
ligand 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
sequence T
description 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE binding site
source pdb_hetatom : 5IU_6k3j_B_390

18) chain A
residue 256-260
type binding
ligand ZN: ZINC ION
sequence RHAEL
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

19) chain A
residue 287-292
type binding
ligand ZN: ZINC ION
sequence PCFSCA
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

20) chain A
residue 286
type binding
ligand ZN: ZINC ION
sequence S
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

21) chain B
residue 389
type binding
ligand ZN: ZINC ION
sequence X
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

22) chain A
residue 317
type binding
ligand ZN: ZINC ION
sequence D
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

23) chain A
residue 294-295
type binding
ligand ZN: ZINC ION
sequence EM
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

24) chain A
residue 255
type binding
ligand ZN: ZINC ION
sequence G
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

25) chain A
residue 261
type binding
ligand ZN: ZINC ION
sequence C
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401

26) chain B
residue 388
type binding
ligand ZN: ZINC ION
sequence C
description ZINC ION binding site
source pdb_hetatom : ZN_6k3j_A_401


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