2G6O | pdb_00002g6o

Structure of bovine eNOS heme domain (BH4-free) complexed with CO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.240 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural studies of constitutive nitric oxide synthases with diatomic ligands bound.

Li, H.Igarashi, J.Jamal, J.Yang, W.Poulos, T.L.

(2006) J Biol Inorg Chem 11: 753-768

  • DOI: https://doi.org/10.1007/s00775-006-0123-8
  • Primary Citation Related Structures: 
    2G6H, 2G6I, 2G6J, 2G6K, 2G6L, 2G6M, 2G6N, 2G6O

  • PubMed Abstract: 

    Crystal structures are reported for the endothelial nitric oxide synthase (eNOS)-arginine-CO ternary complex as well as the neuronal nitric oxide synthase (nNOS) heme domain complexed with L: -arginine and diatomic ligands, CO or NO, in the presence of the native cofactor, tetrahydrobiopterin, or its oxidized analogs, dihydrobiopterin and 4-aminobiopterin. The nature of the biopterin has no influence on the diatomic ligand binding. The binding geometries of diatomic ligands to nitric oxide synthase (NOS) follow the {MXY}(n) formalism developed from the inorganic diatomic-metal complexes. The structures reveal some subtle structural differences between eNOS and nNOS when CO is bound to the heme which correlate well with the differences in CO stretching frequencies observed by resonance Raman techniques. The detailed hydrogen-bonding geometries depicted in the active site of nNOS structures indicate that it is the ordered active-site water molecule rather than the substrate itself that would most likely serve as a direct proton donor to the diatomic ligands (CO, NO, as well as O(2)) bound to the heme. This has important implications for the oxygen activation mechanism critical to NOS catalysis.


  • Organizational Affiliation
    • Department of Molecular Biology and Biochemistry, Center in Chemical and Structural Biology, University of California, Irvine, CA 92697-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 96.08 kDa 
  • Atom Count: 7,353 
  • Modeled Residue Count: 830 
  • Deposited Residue Count: 832 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitric-oxide synthase, endothelial
A, B
416Bos taurusMutation(s): 0 
Gene Names: NOS3
EC: 1.14.13.39
UniProt
Find proteins for P29473 (Bos taurus)
Explore P29473 
Go to UniProtKB:  P29473
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29473
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ARG

Query on ARG



Download:Ideal Coordinates CCD File
G [auth A],
N [auth B]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
CAC

Query on CAC



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CMO

Query on CMO



Download:Ideal Coordinates CCD File
H [auth A],
O [auth B]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.240 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.698α = 90
b = 106.382β = 90
c = 155.897γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations