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- PDB-1cah: STRUCTURE OF COBALT CARBONIC ANHYDRASE COMPLEXED WITH BICARBONATE -

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Basic information

Entry
Database: PDB / ID: 1cah
TitleSTRUCTURE OF COBALT CARBONIC ANHYDRASE COMPLEXED WITH BICARBONATE
ComponentsCARBONIC ANHYDRASE IICarbonic anhydrase
KeywordsLYASE(OXO-ACID)
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 / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
BICARBONATE ION / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.88 Å
AuthorsHakansson, K. / Wehnert, A.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of cobalt carbonic anhydrase complexed with bicarbonate.
Authors: Hakansson, K. / Wehnert, A.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Structure of Native and Apo Carbonic Anhydrase II and Structure of Some of its Anion-Ligand Complexes
Authors: Hakansson, K. / Carlsson, M. / Svensson, L.A. / Liljas, A.
History
DepositionJun 25, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET B1 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET ...SHEET SHEET B1 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS *B1A* AND *B1B* ARE DEFINED. STRANDS 5, 6, 7, 8, 9, AND 10 OF B1A ARE IDENTICAL TO STRANDS 2, 3, 4, 5, 6, AND 7 OF B1B, RESPECTIVELY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2783
Polymers29,1581
Non-polymers1202
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.700, 41.700, 73.000
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 4, 14, 64 AND 136 ARE PRESENTED WITH TWO ALTERNATIVE CONFORMATIONS.
2: RESIDUES 30 AND 202 ARE CIS PROLINES.

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Components

#1: Protein CARBONIC ANHYDRASE II / Carbonic anhydrase


Mass: 29157.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsIN THIS ENZYME CO 262 IS SUBSTITUTED FOR THE ZINC ION FOUND IN NATIVE CARBONIC ANHYDRASE. ...IN THIS ENZYME CO 262 IS SUBSTITUTED FOR THE ZINC ION FOUND IN NATIVE CARBONIC ANHYDRASE. BICARBONATE IS COMPLEXED WITH THE ENZYME.
Sequence detailsRESIDUES 125 AND 127 ARE ADJACENT IN THE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growDetails: CRYSTALLIZED IN 50 MM TRIS-HC1 2.4 M AMMONIUM SULFATE PH 8. 5 AND 1 MM HGC12 AT 4 DEG C (TILANDER, B., STRANDBERG, B. & FRIDBORG, K. (1965). CRYSTAL STRUCTURE ON HUMAN ERYTHROCYTIC CARBONIC ...Details: CRYSTALLIZED IN 50 MM TRIS-HC1 2.4 M AMMONIUM SULFATE PH 8. 5 AND 1 MM HGC12 AT 4 DEG C (TILANDER, B., STRANDBERG, B. & FRIDBORG, K. (1965). CRYSTAL STRUCTURE ON HUMAN ERYTHROCYTIC CARBONIC ANHYDRASE C. J. MOL. BIOL. 12, 740-760). THE MERCURY IS SUBSEQUENTLY REMOVED BY MERCAPTOETHANOL AND THE ZINC ION WITH DIPICOLINATE. AFTER INSERTION OF COBALT (II), THE CRYSTALS ARE SOAKED IN 0.25 M BICARBONATE 3M AMMONIUM SULFATE 50 MM TRIS-HC1 PH 8.1 OVERNIGHT. THE PROCEDURE IS DESCRIBED IN DETAIL IN THE PAPER MENTIONED ABOVE.
Crystal grow
*PLUS
pH: 8.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.4 Mammonium sulfate11
250 mMTris-HCl11
31 mM11HgCl2

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Data collection

Reflection
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 3.42 Å / Num. all: 20352 / Num. obs: 17858 / % possible obs: 87.7 % / Num. measured all: 50143 / Rmerge(I) obs: 0.067

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.88→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.16 17858
Refinement stepCycle: LAST / Resolution: 1.88→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 5 217 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.961
X-RAY DIFFRACTIONp_mcangle_it1.5531.5
X-RAY DIFFRACTIONp_scbond_it1.9641.5
X-RAY DIFFRACTIONp_scangle_it3.0532
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.2290.15
X-RAY DIFFRACTIONp_singtor_nbd0.1610.2
X-RAY DIFFRACTIONp_multtor_nbd0.1590.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1550.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.43
X-RAY DIFFRACTIONp_staggered_tor16.415
X-RAY DIFFRACTIONp_orthonormal_tor30.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 10 Å / Num. reflection all: 17858 / σ(F): 0 / Rfactor all: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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