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- PDB-9l31: Zn-Carbonic Anhydrase II complexed with 3NPA at 160 K -

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Basic information

Entry
Database: PDB / ID: 9l31
TitleZn-Carbonic Anhydrase II complexed with 3NPA at 160 K
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Carbonic Anhydrase / enzyme mechanism / metalloenzymes
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
2-(3-NITROPHENYL)ACETIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Samsung Science and Technology FoundationSSTF-BA1702-04 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Fast product release requires active-site water dynamics in carbonic anhydrase.
Authors: 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. ...Authors: 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.
History
DepositionDec 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5363
Polymers29,2891
Non-polymers2472
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-33 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.948, 41.199, 72.246
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MNP / 2-(3-NITROPHENYL)ACETIC ACID


Mass: 181.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 160 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6D / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 19, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 74716 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3591 / CC1/2: 0.862 / CC star: 0.962 / Rpim(I) all: 0.211 / Rrim(I) all: 0.377 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.326 / SU ML: 0.027 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17805 3690 4.9 %RANDOM
Rwork0.14364 ---
obs0.14528 70925 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-0.23 Å2
2--0.03 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 14 242 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192230
X-RAY DIFFRACTIONr_bond_other_d0.0020.022065
X-RAY DIFFRACTIONr_angle_refined_deg2.6061.9523041
X-RAY DIFFRACTIONr_angle_other_deg1.25634797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2124.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.741157
X-RAY DIFFRACTIONr_chiral_restr0.1780.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212574
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02517
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4741.191079
X-RAY DIFFRACTIONr_mcbond_other2.4771.1861078
X-RAY DIFFRACTIONr_mcangle_it2.7941.7951363
X-RAY DIFFRACTIONr_mcangle_other2.8041.7981364
X-RAY DIFFRACTIONr_scbond_it5.6541.5121151
X-RAY DIFFRACTIONr_scbond_other5.651.5121150
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.592.1361671
X-RAY DIFFRACTIONr_long_range_B_refined6.07211.1272695
X-RAY DIFFRACTIONr_long_range_B_other5.66410.7252604
X-RAY DIFFRACTIONr_rigid_bond_restr5.34334295
X-RAY DIFFRACTIONr_sphericity_free47.95565
X-RAY DIFFRACTIONr_sphericity_bonded15.49154396
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 264 -
Rwork0.18 5076 -
obs--97.39 %

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