1W2Z | pdb_00001w2z

PSAO and Xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.224 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 Biology 344: 599

  • DOI: https://doi.org/10.1016/j.jmb.2004.09.075
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 320.83 kDa 
  • Atom Count: 21,691 
  • Modeled Residue Count: 2,568 
  • Deposited Residue Count: 2,596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AMINE OXIDASE, COPPER CONTAINING
A, B, C, D
649Lathyrus oleraceusMutation(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
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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 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
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