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- PDB-23on: Crystal Structure Analysis of Bovine Carbonic Anhydrase II to 4-2... -

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Basic information

Entry
Database: PDB / ID: 23on
TitleCrystal Structure Analysis of Bovine Carbonic Anhydrase II to 4-2-methyl-1,3-oxazol-5-ylbenzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase / CARBOHYDRATE
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / apical part of cell ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / apical part of cell / zinc ion binding / plasma membrane / cytoplasm
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
4-(2-methyl-1,3-oxazol-5-yl)benzenesulfonamide / ACETATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsStoliarskaia, M.Y. / Nikonov, O.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Not funded Russian Federation
CitationJournal: To Be Published
Title: X ray structures of bovine CA2 bound to 4-2-methyl-1,3-oxazol-5-ylbenzenesulfonamide
Authors: Stoliarskaia, M.Y. / Nikonov, O.S.
History
DepositionFeb 12, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,37815
Polymers58,0412
Non-polymers1,33713
Water7,692427
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6607
Polymers29,0211
Non-polymers6396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11530 Å2
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7198
Polymers29,0211
Non-polymers6987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.773, 80.163, 61.771
Angle α, β, γ (deg.)90.000, 106.940, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29020.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CA2 / Production host: Escherichia coli (E. coli)
References: UniProt: P00921, carbonic anhydrase, cyanamide hydratase

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Non-polymers , 5 types, 440 molecules

#2: Chemical ChemComp-8V8 / 4-(2-methyl-1,3-oxazol-5-yl)benzenesulfonamide


Mass: 238.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2M ammonium sulfate, 0.1M Tris-base Buffer

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→24.35 Å / Num. obs: 89053 / % possible obs: 99.91 % / Redundancy: 4.4 % / Biso Wilson estimate: 8.28 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 12.93
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 89053

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.35 Å / SU ML: 0.1556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 4520 5.08 %
Rwork0.1552 84487 -
obs0.1575 89007 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 82 427 4585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614421
X-RAY DIFFRACTIONf_angle_d0.88766038
X-RAY DIFFRACTIONf_chiral_restr0.0576629
X-RAY DIFFRACTIONf_plane_restr0.0076791
X-RAY DIFFRACTIONf_dihedral_angle_d7.7735603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.29171460.24262789X-RAY DIFFRACTION99.9
1.52-1.530.26771520.23052835X-RAY DIFFRACTION99.93
1.53-1.550.25651490.2112753X-RAY DIFFRACTION99.97
1.55-1.570.30571310.20842874X-RAY DIFFRACTION100
1.57-1.590.29471470.19692760X-RAY DIFFRACTION99.93
1.59-1.620.23541630.18932841X-RAY DIFFRACTION99.9
1.62-1.640.25471470.17332800X-RAY DIFFRACTION100
1.64-1.660.23641520.17672815X-RAY DIFFRACTION99.97
1.66-1.690.21571290.16462820X-RAY DIFFRACTION100
1.69-1.720.2311450.16522809X-RAY DIFFRACTION100
1.72-1.750.22971370.16312834X-RAY DIFFRACTION100
1.75-1.780.2071590.15362798X-RAY DIFFRACTION100
1.78-1.810.20211600.15312811X-RAY DIFFRACTION100
1.81-1.850.20981370.14772788X-RAY DIFFRACTION99.97
1.85-1.890.23341620.14862811X-RAY DIFFRACTION99.97
1.89-1.930.20451610.14452801X-RAY DIFFRACTION100
1.93-1.980.20821520.14092791X-RAY DIFFRACTION100
1.98-2.040.20581430.13752839X-RAY DIFFRACTION100
2.04-2.10.17971560.13472800X-RAY DIFFRACTION100
2.1-2.160.18841720.14582807X-RAY DIFFRACTION99.9
2.16-2.240.1991740.14562772X-RAY DIFFRACTION100
2.24-2.330.18171300.1432860X-RAY DIFFRACTION99.93
2.33-2.440.21261670.15162794X-RAY DIFFRACTION99.83
2.44-2.560.20931670.15312808X-RAY DIFFRACTION99.83
2.56-2.720.17551300.15442853X-RAY DIFFRACTION99.9
2.72-2.930.21721540.16512827X-RAY DIFFRACTION99.97
2.93-3.230.16491560.15882804X-RAY DIFFRACTION99.9
3.23-3.70.1811370.14362857X-RAY DIFFRACTION99.93
3.7-4.650.14781450.12612849X-RAY DIFFRACTION99.8
4.65-24.350.15821600.14872887X-RAY DIFFRACTION99.61

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