8CGS

Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to antimony oxyanion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism.

Engrola, F.Correia, M.A.S.Watson, C.Romao, C.C.Veiros, L.F.Romao, M.J.Santos-Silva, T.Santini, J.M.

(2023) J Biol Chem 299: 105036-105036

  • DOI: https://doi.org/10.1016/j.jbc.2023.105036
  • Primary Citation of Related Structures:  
    8CCQ, 8CFF, 8CGS

  • PubMed Abstract: 

    Arsenic contamination of groundwater is among one of the biggest health threats affecting millions of people in the world. There is an urgent need for efficient arsenic biosensors where the use of arsenic metabolizing enzymes can be explored. In this work, we have solved four crystal structures of arsenite oxidase (Aio) in complex with arsenic and antimony oxyanions and the structures determined correspond to intermediate states of the enzymatic mechanism. These structural data were complemented with density-functional theory calculations providing a unique view of the molybdenum active site at different time points that, together with mutagenesis data, enabled to clarify the enzymatic mechanism and the molecular determinants for the oxidation of As(III) to the less toxic As(V) species.


  • Organizational Affiliation

    UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arsenite oxidase subunit AioA
A, C, E, G
822Alcaligenes faecalisMutation(s): 0 
Gene Names: aioAaoxBasoA
EC: 1.20.9.1
UniProt
Find proteins for Q7SIF4 (Alcaligenes faecalis)
Explore Q7SIF4 
Go to UniProtKB:  Q7SIF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AioB
B, D, F, H
133Alcaligenes faecalisMutation(s): 0 
EC: 1.20.9.1
UniProt
Find proteins for Q7SIF3 (Alcaligenes faecalis)
Explore Q7SIF3 
Go to UniProtKB:  Q7SIF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DB [auth G]
EB [auth G]
I [auth A]
AA [auth C],
BA [auth C],
DB [auth G],
EB [auth G],
I [auth A],
J [auth A],
NA [auth E],
OA [auth E]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
F3S (Subject of Investigation/LOI)
Query on F3S

Download Ideal Coordinates CCD File 
EA [auth C],
HB [auth G],
M [auth A],
RA [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
UJI (Subject of Investigation/LOI)
Query on UJI

Download Ideal Coordinates CCD File 
IA [auth C],
MB [auth G],
R [auth A],
VA [auth E]
tetrakis(oxidanyl)antimony
H4 O4 Sb
JMPYBWKBSUDWDS-UHFFFAOYSA-J
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
CB [auth F],
MA [auth D],
PB [auth H],
Z [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
IB [auth G],
LA [auth C],
Y [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
FA [auth C]
JB [auth G]
N [auth A]
S [auth A]
SA [auth E]
FA [auth C],
JB [auth G],
N [auth A],
S [auth A],
SA [auth E],
T [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BB [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
4MO (Subject of Investigation/LOI)
Query on 4MO

Download Ideal Coordinates CCD File 
DA [auth C],
GB [auth G],
L [auth A],
QA [auth E]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth C]
JA [auth C]
KB [auth G]
P [auth A]
TA [auth E]
GA [auth C],
JA [auth C],
KB [auth G],
P [auth A],
TA [auth E],
XA [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth C],
UA [auth E],
W [auth A],
X [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
WA [auth E],
YA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
LB [auth G],
NB [auth G],
O [auth A],
Q [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth E],
KA [auth C],
U [auth A],
V [auth A],
ZA [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
OB [auth G]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
O
Query on O

Download Ideal Coordinates CCD File 
CA [auth C],
FB [auth G],
K [auth A],
PA [auth E]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.378α = 97.71
b = 109.21β = 90.06
c = 117.342γ = 96.28
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-20
    Changes: Structure summary