7Y2N | pdb_00007y2n

apo-Carbonic Anhydrase II soaked in 3NPA after UV at 160 K

• PDB DOI: https://doi.org/10.2210/pdb7Y2N/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-09 Released: 2023-12-20 
• Deposition Author(s): Kim, C.U., Kim, J.K.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.118 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Fast product release requires active-site water dynamics in carbonic anhydrase.

Kim, J.K., Lim, S.W., Jeong, H., Lee, C., Kim, S., Son, D.W., Kumar, R., Andring, J.T., Lomelino, C., Wierman, J.L., Cohen, A.E., Shin, T.J., Ghim, C.M., McKenna, R., Jo, B.H., Min, D., Choi, J.M., Kim, C.U.

(2025) Nat Commun 16: 4404-4404

• PubMed: 40355440 
• DOI: https://doi.org/10.1038/s41467-025-59645-x
• Primary Citation Related Structures: 
  7Y2A, 7Y2C, 7Y2E, 7Y2F, 7Y2G, 7Y2H, 7Y2I, 7Y2J, 7Y2K, 7Y2L, 7Y2M, 7Y2N, 7Y2O, 7Y2Q, 8WEP, 8WER, 8WES, 9L2X, 9L2Y, 9L2Z, 9L30, 9L31, 9L32, 9L33, 9LDO, 9LDP, 9LR6


• PubMed Abstract: 
  

  Water plays an essential role in enzyme structure, stability, and the substantial rate enhancement of enzyme catalysis. However, direct observations linking enzyme catalysis and active-site water dynamics pose a significant challenge due to experimental difficulties. By integrating an ultraviolet (UV) photolysis technique with temperature-controlled X-ray crystallography, we track the catalytic pathway of carbonic anhydrase II (CAII) at 1.2 Å resolution. This approach enables us to construct molecular movies of CAII catalysis, encompassing substrate (CO ₂ ) binding, conversion from substrate to product (bicarbonate), and product release. In the catalytic pathway, we identify an unexpected configuration in product binding and correlate it with sub-nanosecond rearrangement of active-site water. Based on these experimental observations, we propose a comprehensive mechanism of CAII and describe the detailed structure and dynamics of active-site water in CAII. Our findings suggest that CAII has evolved to utilize the structure and fast dynamics of the active-site waters for its diffusion-limited catalytic efficiency.

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Organizational Affiliation: 
• Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Frontier of Extreme Physics, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea.
Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, 52828, Republic of Korea.
Anti-Aging Bio Cell Factory Regional Leading Research Center (ABC-RLRC), Gyeongsang National University, Jinju, 52828, Republic of Korea.
Department of Chemistry, Pusan National University, Busan, 46241, Republic of Korea.
Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea.
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA.
Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York, 14853, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, 94025, USA.
Graduate School of Semiconductor Materials and Devices Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.33 kDa 
• Atom Count: 2,521 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO2 (Subject of Investigation/LOI)	B [auth A]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.118 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.148	α = 90
b = 41.407	β = 104.43
c = 72.407	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Kim, C.U., Kim, J.K.

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Funding Organization	Location	Grant Number
Other private	Korea, Republic Of	SSTF-BA1702-04 (Samsung Science and Technology Foundation)

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references, Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description