1LPI | pdb_00001lpi

HEW LYSOZYME: TRP...NA CATION-PI INTERACTION

• PDB DOI: https://doi.org/10.2210/pdb1LPI/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 1998-04-15 Released: 1998-06-17 
• Deposition Author(s): Wouters, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.269 (Depositor) 
• R-Value Work: 
  0.163 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Cation-pi (Na+-Trp) interactions in the crystal structure of tetragonal lysozyme.

Wouters, J.

(1998) Protein Sci 7: 2472-2475

• PubMed: 9828016 
• DOI: https://doi.org/10.1002/pro.5560071127
• Primary Citation Related Structures: 
  1LPI


• PubMed Abstract: 
  

  Experimental evidence of a cation-pi interaction between a sodium cation (Na+) and the indole ring of residue Trp123 in a structure (2.0 A) of hen egg-white lysozyme is presented. The geometry of the metal ion-pi interaction observed in the protein structure (distance between the aromatic plane and the cation approximately 4 A) is consistent with geometries observed among small molecules crystal structures and quantum chemistry ab initio calculations. The present crystal structure of lysozyme provides unique structural information about the geometry of binding of cations to pi systems in proteins. It shows that the metal ion-pi interaction within proteins is not significantly different from similar bindings found in small molecules and that it can be modeled by theoretical methods.

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Organizational Affiliation: 
• Facultés Universitaires N.-D. de la Paix, Namur, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.35 kDa 
• Atom Count: 1,091 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.269 (Depositor) 
• R-Value Work:  0.163 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 79.1	β = 90
c = 37.9	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
SHELXL-96	model building
SHELXL-96	refinement
SHELXL-96	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Wouters, J.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary