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- PDB-23om: Crystal Structure Analysis of Bovine Carbonic Anhydrase II to 5-(... -

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Basic information

Entry
Database: PDB / ID: 23om
TitleCrystal Structure Analysis of Bovine Carbonic Anhydrase II to 5-(2-morpholin-4-ylcarbonyl-1,3-oxazol-5-yl)thiophene-2-sulfonamide.
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
Chem-8V5 / ACETATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStoliarskaia, M.Y. / Nikonov, O.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Not funded Russian Federation
CitationJournal: To Be Published
Title: The X ray Analysis of the Complexes of Carbonic Anhydrase II in complex with 1,3-Oxazole-Containing Sulfonamide Derivatives Elucidating the Structural Basis for Exceptionally High Inhibitory Potency.
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)60,32819
Polymers58,0412
Non-polymers2,28717
Water3,909217
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,17510
Polymers29,0211
Non-polymers1,1559
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1539
Polymers29,0211
Non-polymers1,1338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.089, 81.043, 61.144
Angle α, β, γ (deg.)90.000, 105.820, 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 / Sugars , 2 types, 4 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
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 232 molecules

#2: Chemical ChemComp-8V5 / 5-(2-morpholin-4-ylcarbonyl-1,3-oxazol-5-yl)thiophene-2-sulfonamide


Mass: 343.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13N3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
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 3, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.7→24.55 Å / Num. obs: 59650 / % possible obs: 97.84 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5210 / CC1/2: 0.568 / Rrim(I) all: 0.788 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.55 Å / SU ML: 0.2257 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2504 3041 5.1 %
Rwork0.1889 56581 -
obs0.192 59622 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 143 217 4456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714407
X-RAY DIFFRACTIONf_angle_d0.92776002
X-RAY DIFFRACTIONf_chiral_restr0.0571625
X-RAY DIFFRACTIONf_plane_restr0.0076780
X-RAY DIFFRACTIONf_dihedral_angle_d10.8822606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.32471110.27272133X-RAY DIFFRACTION81.84
1.73-1.750.30021430.24682314X-RAY DIFFRACTION89.7
1.75-1.790.28631380.22832492X-RAY DIFFRACTION95.46
1.79-1.820.26551690.20812510X-RAY DIFFRACTION97.28
1.82-1.850.3041370.20792589X-RAY DIFFRACTION97.64
1.85-1.890.26161460.20942531X-RAY DIFFRACTION97.81
1.89-1.930.24681410.20352595X-RAY DIFFRACTION98.67
1.93-1.980.24271570.20122581X-RAY DIFFRACTION99.06
1.98-2.030.29881440.19372592X-RAY DIFFRACTION99.13
2.03-2.080.25171360.17872589X-RAY DIFFRACTION99.45
2.08-2.140.28121310.18722628X-RAY DIFFRACTION99.42
2.14-2.210.29231110.19562646X-RAY DIFFRACTION99.64
2.21-2.290.24061270.19282619X-RAY DIFFRACTION99.82
2.29-2.380.28251260.18992635X-RAY DIFFRACTION99.71
2.38-2.490.2631350.20082632X-RAY DIFFRACTION99.93
2.49-2.620.30291330.20572656X-RAY DIFFRACTION99.96
2.62-2.780.24691600.19572621X-RAY DIFFRACTION100
2.78-30.29141490.20412615X-RAY DIFFRACTION99.89
3-3.30.22691350.18862647X-RAY DIFFRACTION99.89
3.3-3.780.2161600.17342615X-RAY DIFFRACTION99.78
3.78-4.750.18421450.14282632X-RAY DIFFRACTION99.25
4.75-24.550.19831070.16312709X-RAY DIFFRACTION98.88

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