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- PDB-3m2n: Crystal structure of human carbonic anhydrase isozyme II with 4-{... -

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Basic information

Entry
Database: PDB / ID: 3m2n
TitleCrystal structure of human carbonic anhydrase isozyme II with 4-{2-[N-(6-chloro-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / sulfonamide / Lyase / Metal-binding / LYASE-LYASE INHIBITOR complex
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-J74 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGrazulis, S. / Manakova, E. / Golovenko, D.
CitationJournal: Eur.J.Med.Chem. / Year: 2012
Title: Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases.
Authors: Capkauskaite, E. / Zubriene, A. / Baranauskiene, L. / Tamulaitiene, G. / Manakova, E. / Kairys, V. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 16, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)30,0326
Polymers29,2891
Non-polymers7435
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.041, 41.253, 71.858
Angle α, β, γ (deg.)90.00, 104.74, 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 / Carbonic anhydrase II / CA-II / Carbonate dehydratase II / Carbonic anhydrase C / CAC


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 375 molecules

#2: Chemical ChemComp-J74 / 4-{2-[(6-chloro-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide


Mass: 357.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12ClN5O4S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMETAL ION NATURALLY OCCURS IN CARBONIC ANHYDRASES.
Sequence details126 IS SKIPPED IN THE NUMBERING.

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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: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na-Bicine pH 9, 2M Na-Malonate pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 20, 2009 / Details: Bent, vertically focussing mirror
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.65→41.24 Å / Num. all: 28936 / Num. obs: 28936 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 26.3
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 8.6 / Num. unique all: 4178 / Rsym value: 0.211 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345v. 0.9.7 on RedHat Linux 8data collection
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NNO

2nno


Resolution: 1.65→39.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.867 / SU ML: 0.066 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20304 2928 10.1 %RANDOM
Rwork0.15453 ---
all0.15951 25992 --
obs0.15951 25992 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.049 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20.13 Å2
2---0.69 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 43 370 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0212341
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.9563200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27424.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34815383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.789157
X-RAY DIFFRACTIONr_chiral_restr0.1630.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021854
X-RAY DIFFRACTIONr_nbd_refined0.2370.21198
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2294
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.2113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.284
X-RAY DIFFRACTIONr_mcbond_it1.5211.51439
X-RAY DIFFRACTIONr_mcangle_it2.15622276
X-RAY DIFFRACTIONr_scbond_it3.47831063
X-RAY DIFFRACTIONr_scangle_it4.794.5919
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 195 -
Rwork0.203 1891 -
obs--100 %

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