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- PDB-8vq7: hCA-II-apo structure -

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Basic information

Entry
Database: PDB / ID: 8vq7
TitlehCA-II-apo structure
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / Carbonic Anhydrase II / human Carbonic anhydrase II / carbon anhydrase / Two pockets bound / binding pocket / binding pockets / active site / small molecule / bivalent / complex / protein ligand complex / protein inhibition / inhibitor / binder / nano molar binder / nano molar inhibitor / PROTEIN BINDING / 4-(2-Aminoethyl)benzenesulfonamide / secondary binding site / ZYX / 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 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.409 Å
AuthorsIsmail, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: SBDD of Carbonic Anhydrase II Inhibitors
Authors: Ismail, M.M.
History
DepositionJan 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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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)29,3542
Polymers29,2891
Non-polymers651
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.431, 41.283, 72.758
Angle α, β, γ (deg.)90.000, 104.378, 90.000
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 BL21(DE3) (bacteria) / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.1 M Malonate, Tris, pH 8.5 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.409→41.28 Å / Num. obs: 46783 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.948 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.103 / Rrim(I) all: 0.206 / Net I/σ(I): 9.3
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2175 / CC1/2: 0.18 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.409→41.136 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.128 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1724 2280 4.888 %
Rwork0.1334 44361 -
all0.135 --
obs-46641 98.465 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.543 Å2
Baniso -1Baniso -2Baniso -3
1--1.227 Å2-0 Å20.466 Å2
2---0.64 Å2-0 Å2
3---1.439 Å2
Refinement stepCycle: LAST / Resolution: 1.409→41.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 1 307 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161998
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.6512947
X-RAY DIFFRACTIONr_angle_other_deg0.591.5884649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.85857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4410364
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.64910103
X-RAY DIFFRACTIONr_chiral_restr0.0940.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined0.1940.2365
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21754
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2976
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2171
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1850.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.214
X-RAY DIFFRACTIONr_nbd_other0.1580.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.238
X-RAY DIFFRACTIONr_mcbond_it1.1091.2681041
X-RAY DIFFRACTIONr_mcbond_other1.1081.2671041
X-RAY DIFFRACTIONr_mcangle_it1.642.291303
X-RAY DIFFRACTIONr_mcangle_other1.6392.2921304
X-RAY DIFFRACTIONr_scbond_it1.3631.4981120
X-RAY DIFFRACTIONr_scbond_other1.3631.5021121
X-RAY DIFFRACTIONr_scangle_it1.8442.6271637
X-RAY DIFFRACTIONr_scangle_other1.8442.631638
X-RAY DIFFRACTIONr_lrange_it3.67518.6952442
X-RAY DIFFRACTIONr_lrange_other2.91415.6962358
X-RAY DIFFRACTIONr_rigid_bond_restr3.5234159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.409-1.4460.2251670.16930680.17234620.9720.98593.44310.15
1.446-1.4850.2341670.1431020.14433780.9680.98996.77320.126
1.485-1.5280.1771510.12130840.12333050.9830.99297.8820.11
1.528-1.5750.1831560.12330020.12632040.9770.9998.56430.114
1.575-1.6270.1521560.10128970.10430900.9870.99298.80260.095
1.627-1.6840.1621370.10328540.10630150.9810.99199.2040.098
1.684-1.7470.1681400.11127170.11329000.9830.9998.51720.108
1.747-1.8190.1671190.11326550.11628060.9730.9998.85960.115
1.819-1.8990.1561090.11725270.11826690.9780.9998.76360.122
1.899-1.9920.1511150.12424120.12525720.9780.98898.25040.131
1.992-2.0990.1451460.11422880.11624370.9870.9999.87690.123
2.099-2.2260.1441160.10621910.10823110.9870.99399.82690.12
2.226-2.3790.1531050.11320920.11521980.9870.99299.95450.132
2.379-2.5690.1661060.13219300.13420410.9820.98899.7550.156
2.569-2.8130.197680.13517980.13718720.9750.98799.67950.162
2.813-3.1440.154840.15316030.15317000.9840.98599.23530.189
3.144-3.6260.259690.15914240.16415010.9220.9899.4670.191
3.626-4.4330.163780.14312080.14412930.9830.98499.45860.176
4.433-6.2330.179580.1779520.17810110.9850.97899.90110.216
6.233-41.1360.163330.2115570.2085920.9820.96899.66220.258

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