8I7Q

Cobalt and Calcium coordinated Concanavalin A at pH 7.4 from Canavalia ensiformis

• PDB DOI: https://doi.org/10.2210/pdb8I7Q/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Canavalia ensiformis
• Mutation(s): No 


• Deposited: 2023-02-01 Released: 2023-12-27 
• Deposition Author(s): Hwang, Y., Jeong, J.H., Lee, S.J.
• Funding Organization(s): National Research Foundation (NRF, Korea), Ministry of Education (MoE, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Selective interactions of Co 2+ -Ca 2+ -concanavalin A with high mannose N -glycans.

Hwang, Y., Jeong, J.H., Lee, D.H., Lee, S.J.

(2024) Dalton Trans 53: 428-433

• PubMed: 38086668 
• DOI: https://doi.org/10.1039/d3dt03575a
• Primary Citation of Related Structures:  
  8I7Q


• PubMed Abstract: 
  

  Concanavalin A (ConA) has an intrinsic binding affinity to carbohydrates. Here, we obtained Co ²⁺ -Ca ²⁺ -ConA (2.83 Å, PDB: 8I7Q) via X-ray crystallography by substituting native ConA (Mn ²⁺ -Ca ²⁺ ); it has binding selectivity for high-mannose N -glycan similar to native ConA. Our findings may thus inform antiviral reagent design.

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Organizational Affiliation: 

Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.69 kDa 
• Atom Count: 1,828 
• Modelled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin A	A	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866  Go to UniProtKB:  P02866

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO (Subject of Investigation/LOI)	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.82	α = 90
b = 86.05	β = 90
c = 88.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Hwang, Y., Jeong, J.H., Lee, S.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2015M3D3A1A01064876
Ministry of Education (MoE, Korea)	Korea, Republic Of	2017R1A6A1A03015876

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Database references