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- PDB-6rkn: Human Carbonic Anhydrase II in complex with a fluorinated Benzene... -

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Basic information

Entry
Database: PDB / ID: 6rkn
TitleHuman Carbonic Anhydrase II in complex with a fluorinated Benzenesulfonamide.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 Conversion
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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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 / cytosol / 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-CARBOXYPHENYL)(CHLORO)MERCURY / beta-D-glucopyranose / 4-FLUOROBENZENESULFONAMIDE / alpha-D-glucopyranose / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.959 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II.
Authors: Glockner, S. / Ngo, K. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3219
Polymers29,8071
Non-polymers1,5148
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-63 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.339, 41.555, 72.163
Angle α, β, γ (deg.)90.00, 104.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P00918, carbonic anhydrase

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Sugars , 2 types, 3 molecules

#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 250 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#5: Chemical ChemComp-FBS / 4-FLUOROBENZENESULFONAMIDE


Mass: 175.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6FNO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2018 / Details: Sagitally bended Si(111) crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.959→41.555 Å / Num. obs: 139058 / % possible obs: 93.8 % / Redundancy: 3.71 % / Biso Wilson estimate: 7.5 Å2 / CC1/2: 0.998 / Rsym value: 0.053 / Net I/σ(I): 13.32
Reflection shellResolution: 0.96→1.02 Å / Redundancy: 3.53 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 21525 / CC1/2: 0.934 / Rsym value: 0.239 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 0.959→40.977 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 8.63
RfactorNum. reflection% reflectionSelection details
Rfree0.1242 6952 5 %Random selection of 5 %
Rwork0.1084 ---
obs0.1092 139048 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.959→40.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 70 245 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072637
X-RAY DIFFRACTIONf_angle_d1.0673641
X-RAY DIFFRACTIONf_dihedral_angle_d15.4871000
X-RAY DIFFRACTIONf_chiral_restr0.086381
X-RAY DIFFRACTIONf_plane_restr0.008503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9595-0.97040.15772140.1444069X-RAY DIFFRACTION87
0.9704-0.98180.14382230.13234233X-RAY DIFFRACTION91
0.9818-0.99380.14932220.12764229X-RAY DIFFRACTION91
0.9938-1.00630.13982250.11954264X-RAY DIFFRACTION91
1.0063-1.01960.13442240.11814262X-RAY DIFFRACTION91
1.0196-1.03360.12072250.10934266X-RAY DIFFRACTION91
1.0336-1.04830.11652210.09664199X-RAY DIFFRACTION90
1.0483-1.0640.10232280.08514338X-RAY DIFFRACTION92
1.064-1.08060.09182280.08314327X-RAY DIFFRACTION93
1.0806-1.09830.08512290.07914351X-RAY DIFFRACTION93
1.0983-1.11730.09422290.08014354X-RAY DIFFRACTION93
1.1173-1.13760.09242300.07824362X-RAY DIFFRACTION94
1.1376-1.15950.09572290.07834356X-RAY DIFFRACTION93
1.1595-1.18310.08452240.07924258X-RAY DIFFRACTION91
1.1831-1.20890.092340.08054436X-RAY DIFFRACTION94
1.2089-1.2370.09872290.08044362X-RAY DIFFRACTION94
1.237-1.26790.10222320.08474409X-RAY DIFFRACTION94
1.2679-1.30220.09182350.08254456X-RAY DIFFRACTION95
1.3022-1.34050.10322350.08614470X-RAY DIFFRACTION95
1.3405-1.38380.10662350.08894475X-RAY DIFFRACTION95
1.3838-1.43320.1052310.09214372X-RAY DIFFRACTION93
1.4332-1.49060.09882370.09024511X-RAY DIFFRACTION96
1.4906-1.55850.10522380.09134529X-RAY DIFFRACTION97
1.5585-1.64060.09342400.0974554X-RAY DIFFRACTION97
1.6406-1.74340.11372400.10064550X-RAY DIFFRACTION97
1.7434-1.87810.12452390.1064541X-RAY DIFFRACTION97
1.8781-2.0670.11992370.11284506X-RAY DIFFRACTION95
2.067-2.36610.12252450.11914664X-RAY DIFFRACTION98
2.3661-2.98090.15482460.13484680X-RAY DIFFRACTION98
2.9809-41.01480.17032480.13774713X-RAY DIFFRACTION97

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