3HSN

Ternary structure of neuronal nitric oxide synthase with NHA and CO bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Single crystal structural and absorption spectral characterizations of nitric oxide synthase complexed with N(omega)-hydroxy-L-arginine and diatomic ligands.

Doukov, T.Li, H.Soltis, M.Poulos, T.L.

(2009) Biochemistry 48: 10246-10254

  • DOI: https://doi.org/10.1021/bi9009743
  • Primary Citation of Related Structures:  
    3HSN, 3HSO, 3HSP

  • PubMed Abstract: 

    The X-ray structures of neuronal nitric oxide synthase (nNOS) with N(omega)-hydroxy-l-arginine (l-NHA) and CO (or NO) bound have been determined at 1.91-2.2 A resolution. Microspectrophotometric techniques confirmed reduced redox state and the status of diatomic ligand complexes during X-ray diffraction data collection. The structure of nNOS-NHA-NO, a close mimic to the dioxygen complex, provides a picture of the potential interactions between the heme-bound diatomic ligand, substrate l-NHA, and the surrounding protein and solvent structure environment. The OH group of l-NHA in the X-ray structures deviates from the plane of the guanidinium moiety substantially, indicating that the OH-bearing, protonated guanidine N(omega) nitrogen of l-NHA has substantial sp(3) hybridization character. This nitrogen geometry, different from that of the guanidinium N(omega) nitrogen of l-arginine, allows a hydrogen bond to be donated to the proximal oxygen of the heme-bound dioxygen complex, thus preventing cleavage of the O-O bond. Instead, it favors the stabilization of the ferric-hydroperoxy intermediate, Fe(3+)-OOH(-), which serves as the active oxidant in the conversion of l-NHA to NO and citrulline in the second reaction of the NOS.


  • Organizational Affiliation

    Macromolecular Crystallographic Group, The Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Stanford, California 94309, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide synthase, brain
A, B
422Rattus norvegicusMutation(s): 0 
Gene Names: Nos1Bnos
EC: 1.14.13.39
UniProt
Find proteins for P29476 (Rattus norvegicus)
Explore P29476 
Go to UniProtKB:  P29476
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29476
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
H4B
Query on H4B

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E [auth A],
O [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
HAR
Query on HAR

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F [auth A],
P [auth B]
N-OMEGA-HYDROXY-L-ARGININE
C6 H14 N4 O3
FQWRAVYMZULPNK-BYPYZUCNSA-N
GOL
Query on GOL

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I [auth A]
J [auth A]
K [auth A]
L [auth A]
R [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
R [auth B],
S [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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H [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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G [auth A],
Q [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CMO
Query on CMO

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D [auth A],
N [auth B]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.16α = 90
b = 110.847β = 90
c = 165.042γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description