Zinc in PDB 3tio: Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations

The structure of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations, PDB code: 3tio was solved by H.M.Park, J.W.Choi, J.E.Lee, C.H.Jung, B.Y.Kim, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.976, 84.384, 97.758, 90.00, 93.18, 90.00
R / Rfree (%)	19.3 / 21

The binding sites of Zinc atom in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations (pdb code 3tio). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations, PDB code: 3tio:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:11.2 occ:1.00 NE2 A:HIS96 2.0 9.4 1.0 NE2 C:HIS91 2.1 8.2 1.0 ND1 A:HIS67 2.1 10.5 1.0 NE2 A:HIS70 2.1 11.9 1.0 CE1 A:HIS67 3.0 10.1 1.0 CD2 A:HIS70 3.0 14.2 1.0 CD2 A:HIS96 3.0 9.4 1.0 CE1 A:HIS96 3.0 10.1 1.0 CE1 C:HIS91 3.0 9.3 1.0 CD2 C:HIS91 3.1 8.6 1.0 CE1 A:HIS70 3.1 14.2 1.0 CG A:HIS67 3.1 9.6 1.0 CB A:HIS67 3.5 8.9 1.0 O A:VAL68 3.8 13.7 1.0 NE2 A:HIS67 4.1 9.7 1.0 ND1 A:HIS96 4.1 10.5 1.0 ND1 C:HIS91 4.1 8.0 1.0 OE1 C:GLN61 4.2 10.1 1.0 CG A:HIS96 4.2 9.6 1.0 ND1 A:HIS70 4.2 15.3 1.0 CG A:HIS70 4.2 15.2 1.0 CG C:HIS91 4.2 7.9 1.0 CD2 A:HIS67 4.2 10.3 1.0 OH C:TYR168 4.3 11.2 1.0 O C:HOH191 4.5 14.6 1.0 CA A:HIS67 4.9 9.4 1.0 NH2 A:ARG46 4.9 9.9 1.0 N A:VAL68 5.0 11.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn185 b:11.5 occ:1.00 ND1 B:HIS67 2.0 13.1 1.0 NE2 A:HIS91 2.1 8.9 1.0 NE2 B:HIS96 2.1 11.6 1.0 NE2 B:HIS70 2.2 16.3 1.0 CE1 B:HIS67 3.0 11.5 1.0 CD2 B:HIS70 3.0 22.9 1.0 CD2 B:HIS96 3.0 11.6 1.0 CE1 A:HIS91 3.0 9.2 1.0 CD2 A:HIS91 3.1 9.3 1.0 CE1 B:HIS96 3.1 13.1 1.0 CG B:HIS67 3.1 9.4 1.0 CE1 B:HIS70 3.2 20.7 1.0 CB B:HIS67 3.5 11.1 1.0 O B:VAL68 3.7 17.0 1.0 OE1 A:GLN61 4.0 14.6 1.0 NE2 B:HIS67 4.1 12.0 1.0 CG B:HIS70 4.1 22.0 1.0 OH A:TYR168 4.1 13.3 1.0 ND1 A:HIS91 4.2 8.2 1.0 ND1 B:HIS70 4.2 22.0 1.0 ND1 B:HIS96 4.2 13.1 1.0 CG B:HIS96 4.2 10.3 1.0 CD2 B:HIS67 4.2 10.2 1.0 CG A:HIS91 4.2 8.3 1.0 O A:HOH192 4.4 14.9 1.0 N B:VAL68 4.8 14.9 1.0 NH2 B:ARG46 4.8 11.0 1.0 C B:VAL68 4.8 17.2 1.0 CA B:HIS67 4.8 10.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn185 b:10.2 occ:1.00 NE2 C:HIS96 2.0 9.5 1.0 NE2 B:HIS91 2.1 8.0 1.0 NE2 C:HIS70 2.1 11.7 1.0 ND1 C:HIS67 2.1 9.1 1.0 CE1 C:HIS67 3.0 8.9 1.0 CD2 C:HIS96 3.0 8.8 1.0 CE1 C:HIS96 3.0 10.7 1.0 CE1 B:HIS91 3.0 8.5 1.0 CD2 C:HIS70 3.0 12.5 1.0 CE1 C:HIS70 3.0 12.1 1.0 CD2 B:HIS91 3.1 8.4 1.0 CG C:HIS67 3.1 8.0 1.0 CB C:HIS67 3.5 9.3 1.0 O C:VAL68 3.8 13.6 1.0 OE1 B:GLN61 4.1 11.7 1.0 ND1 C:HIS96 4.1 9.9 1.0 ND1 C:HIS70 4.1 13.0 1.0 ND1 B:HIS91 4.1 9.3 1.0 NE2 C:HIS67 4.1 9.5 1.0 CG C:HIS96 4.2 8.5 1.0 CG C:HIS70 4.2 14.0 1.0 CG B:HIS91 4.2 7.7 1.0 CD2 C:HIS67 4.2 7.5 1.0 OH B:TYR168 4.2 11.9 1.0 O B:HOH187 4.4 12.3 1.0 NH2 C:ARG46 4.9 10.7 1.0 CA C:HIS67 4.9 8.6 1.0 N C:VAL68 4.9 10.8 1.0 C C:VAL68 5.0 12.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn185 b:9.2 occ:1.00 NE2 D:HIS96 2.1 7.7 1.0 NE2 F:HIS91 2.1 7.8 1.0 ND1 D:HIS67 2.1 9.1 1.0 O F:HOH1 2.2 6.8 1.0 CE1 F:HIS91 3.0 7.7 1.0 CD2 D:HIS96 3.0 9.7 1.0 CE1 D:HIS67 3.0 8.4 1.0 CE1 D:HIS96 3.1 9.6 1.0 CG D:HIS67 3.1 8.9 1.0 CD2 F:HIS91 3.1 7.4 1.0 CB D:HIS67 3.5 7.1 1.0 O D:VAL68 3.8 10.5 1.0 OH F:TYR168 4.0 12.3 1.0 ND1 F:HIS91 4.1 6.5 1.0 NE2 D:HIS67 4.1 8.6 1.0 CG D:HIS96 4.2 8.0 1.0 ND1 D:HIS96 4.2 9.9 1.0 OE1 F:GLN61 4.2 10.5 1.0 CD2 D:HIS67 4.2 8.2 1.0 CG F:HIS91 4.2 6.1 1.0 O F:HOH200 4.4 18.9 1.0 N D:VAL68 4.5 9.4 1.0 C D:VAL68 4.7 10.2 1.0 O F:HOH245 4.8 20.4 1.0 CA D:HIS67 4.8 7.8 1.0 NH2 D:ARG46 4.9 8.6 1.0 C D:HIS67 4.9 7.7 1.0

Zinc binding site 5 out of 6 in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn185 b:9.8 occ:1.00 NE2 E:HIS96 2.1 9.0 1.0 NE2 D:HIS91 2.1 7.2 1.0 ND1 E:HIS67 2.1 9.0 1.0 O D:HOH753 2.3 8.6 1.0 CE1 D:HIS91 3.0 7.6 1.0 CD2 E:HIS96 3.0 8.1 1.0 CE1 E:HIS67 3.0 9.6 1.0 CE1 E:HIS96 3.1 9.9 1.0 CD2 D:HIS91 3.1 6.4 1.0 CG E:HIS67 3.1 7.6 1.0 O E:HOH596 3.2 32.5 1.0 CB E:HIS67 3.5 8.8 1.0 O E:VAL68 3.9 14.3 1.0 OH D:TYR168 4.1 10.1 1.0 ND1 D:HIS91 4.1 6.1 1.0 O D:HOH203 4.1 17.4 1.0 OE1 D:GLN61 4.2 12.8 1.0 NE2 E:HIS67 4.2 8.9 1.0 CG E:HIS96 4.2 8.9 1.0 ND1 E:HIS96 4.2 9.7 1.0 CG D:HIS91 4.2 5.9 1.0 CD2 E:HIS67 4.2 7.9 1.0 O D:HOH783 4.5 33.7 1.0 N E:VAL68 4.7 10.7 1.0 CA E:HIS67 4.9 9.1 1.0 NH2 E:ARG46 4.9 9.5 1.0 O D:HOH211 4.9 17.4 1.0 C E:VAL68 5.0 14.3 1.0

Zinc binding site 6 out of 6 in the Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structures of Yrda From Escherichia Coli, A Homologous Protein of Gamma-Class Carbonic Anhydrase, Show Possible Allosteric Conformations within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn185 b:9.0 occ:1.00 NE2 E:HIS91 2.0 6.9 1.0 NE2 F:HIS96 2.1 9.3 1.0 NE2 F:HIS70 2.1 10.9 1.0 ND1 F:HIS67 2.1 9.8 1.0 CD2 F:HIS70 3.0 12.1 1.0 CD2 F:HIS96 3.0 9.8 1.0 CE1 E:HIS91 3.0 8.5 1.0 CD2 E:HIS91 3.0 7.7 1.0 CE1 F:HIS67 3.0 8.6 1.0 CE1 F:HIS96 3.1 10.3 1.0 CG F:HIS67 3.1 9.8 1.0 CE1 F:HIS70 3.1 9.1 1.0 CB F:HIS67 3.4 9.7 1.0 O F:VAL68 3.6 11.8 1.0 ND1 E:HIS91 4.1 8.9 1.0 OE1 E:GLN61 4.1 11.3 1.0 CG F:HIS70 4.1 12.1 1.0 CG F:HIS96 4.2 9.4 1.0 CG E:HIS91 4.2 6.9 1.0 ND1 F:HIS96 4.2 10.6 1.0 NE2 F:HIS67 4.2 9.4 1.0 ND1 F:HIS70 4.2 13.0 1.0 CD2 F:HIS67 4.2 9.1 1.0 OH E:TYR168 4.2 10.7 1.0 O E:HOH188 4.4 13.0 1.0 N F:VAL68 4.8 11.6 1.0 C F:VAL68 4.8 12.1 1.0 CA F:HIS67 4.8 10.1 1.0 NH2 F:ARG46 4.9 9.1 1.0 C F:HIS67 4.9 10.7 1.0

H.M.Park, J.H.Park, J.W.Choi, J.E.Lee, B.Y.Kim, C.H.Jung, J.S.Kim. Structures of the Gamma-Class Carbonic Anhydrase Homologue Yrda Suggest A Possible Allosteric Switch Acta Crystallogr.,Sect.D V. 68 920 2012.
ISSN: ISSN 0907-4449
PubMed: 22868757
DOI: 10.1107/S0907444912017210