1W2Z

PSAO and Xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Using Xenon as a Probe for Dioxygen-Binding Sites in Copper Amine Oxidases.

Duff, A.P.Trambaiolo, D.M.Cohen, A.E.Ellis, P.J.Juda, G.A.Shepard, E.M.Langley, D.B.Dooley, D.M.Freeman, H.C.Guss, J.M.

(2004) J Mol Biol 344: 599

  • DOI: https://doi.org/10.1016/j.jmb.2004.09.075
  • Primary Citation of Related Structures:  
    1RJO, 1RKY, 1W2Z

  • PubMed Abstract: 

    Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site.


  • Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMINE OXIDASE, COPPER CONTAINING
A, B, C, D
649Pisum sativumMutation(s): 0 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for Q43077 (Pisum sativum)
Explore Q43077 
Go to UniProtKB:  Q43077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43077
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EF [auth D]
FF [auth D]
I [auth A]
IB [auth B]
J [auth A]
EF [auth D],
FF [auth D],
I [auth A],
IB [auth B],
J [auth A],
JB [auth B],
KD [auth C],
LD [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
XE
Query on XE

Download Ideal Coordinates CCD File 
CF [auth D]
DF [auth D]
G [auth A]
GB [auth B]
H [auth A]
CF [auth D],
DF [auth D],
G [auth A],
GB [auth B],
H [auth A],
HB [auth B],
ID [auth C],
JD [auth C]
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth C]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth C],
AG [auth D],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth C],
BG [auth D],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth C],
CG [auth D],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth C],
DG [auth D],
EA [auth A],
EC [auth B],
ED [auth B],
EE [auth C],
EG [auth D],
FA [auth A],
FC [auth B],
FD [auth B],
FE [auth C],
FG [auth D],
GA [auth A],
GC [auth B],
GE [auth C],
GF [auth D],
GG [auth D],
HA [auth A],
HC [auth B],
HE [auth C],
HF [auth D],
HG [auth D],
IA [auth A],
IC [auth B],
IE [auth C],
IF [auth D],
IG [auth D],
JA [auth A],
JC [auth B],
JE [auth C],
JF [auth D],
JG [auth D],
K [auth A],
KA [auth A],
KB [auth B],
KC [auth B],
KE [auth C],
KF [auth D],
KG [auth D],
L [auth A],
LA [auth A],
LB [auth B],
LC [auth B],
LE [auth C],
LF [auth D],
LG [auth D],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth B],
MD [auth C],
ME [auth C],
MF [auth D],
MG [auth D],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth B],
ND [auth C],
NE [auth C],
NF [auth D],
NG [auth D],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth B],
OD [auth C],
OE [auth C],
OF [auth D],
OG [auth D],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
PD [auth C],
PE [auth C],
PF [auth D],
PG [auth D],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
QD [auth C],
QE [auth C],
QF [auth D],
QG [auth D],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth C],
RE [auth C],
RF [auth D],
RG [auth D],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
SD [auth C],
SE [auth C],
SF [auth D],
SG [auth D],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TD [auth C],
TE [auth C],
TF [auth D],
TG [auth D],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UD [auth C],
UE [auth C],
UF [auth D],
UG [auth D],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth C],
VE [auth C],
VF [auth D],
VG [auth D],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth C],
WE [auth C],
WF [auth D],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XD [auth C],
XE [auth C],
XF [auth D],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth C],
YE [auth C],
YF [auth D],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth C],
ZE [auth C],
ZF [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CU
Query on CU

Download Ideal Coordinates CCD File 
AF [auth D],
E [auth A],
EB [auth B],
GD [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
BF [auth D],
F [auth A],
FB [auth B],
HD [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B, C, D
L-PEPTIDE LINKINGC9 H9 N O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.507α = 90
b = 196.268β = 107.46
c = 89.665γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-03-14
    Changes: Other
  • Version 1.3: 2019-03-06
    Changes: Advisory, Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.6: 2023-12-13
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary