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Chlorine in PDB 4ghe: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution, PDB code: 4ghe was solved by E.G.Kovaleva, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.30 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.513, 150.116, 96.169, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.6

Other elements in 4ghe:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution (pdb code 4ghe). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution, PDB code: 4ghe:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4ghe

Go back to Chlorine Binding Sites List in 4ghe
Chlorine binding site 1 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:24.4
occ:1.00
 NH1 A:ARG243 3.0 21.2 1.0
NH2 A:ARG243 3.2 19.1 1.0
CE1 A:HIS248 3.2 16.9 1.0
O A:HOH847 3.2 38.3 1.0
NH1 A:ARG293 3.3 18.9 1.0
ND1 A:HIS248 3.4 16.2 1.0
CB A:ARG293 3.5 15.2 1.0
CZ A:ARG243 3.6 20.0 1.0
CD A:ARG293 3.7 16.9 1.0
CG A:ARG293 3.7 16.3 1.0
O A:ARG293 3.8 16.1 1.0
CA A:ARG293 3.9 14.9 1.0
CZ2 A:TRP304 3.9 20.0 1.0
CH2 A:TRP304 3.9 20.7 1.0
C A:ARG293 4.2 14.4 1.0
CZ A:ARG293 4.2 18.1 1.0
O A:HOH846 4.4 30.5 1.0
NE A:ARG293 4.4 17.0 1.0
NE2 A:HIS248 4.4 16.7 1.0
CG A:HIS248 4.7 15.4 1.0
CE2 A:TRP304 4.7 19.6 1.0
CZ3 A:TRP304 4.7 21.2 1.0
CE2 A:PHE257 4.7 16.8 1.0
CZ A:PHE257 4.8 17.4 1.0
NE A:ARG243 4.9 19.5 1.0

Chlorine binding site 2 out of 4 in 4ghe

Go back to Chlorine Binding Sites List in 4ghe
Chlorine binding site 2 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:21.6
occ:1.00
 NH1 B:ARG293 3.1 16.6 1.0
NH1 B:ARG243 3.2 18.0 1.0
NH2 B:ARG243 3.3 16.4 1.0
CE1 B:HIS248 3.3 15.9 1.0
O B:HOH909 3.4 30.0 1.0
ND1 B:HIS248 3.5 15.7 1.0
CB B:ARG293 3.5 15.5 1.0
CD B:ARG293 3.6 16.5 1.0
CG B:ARG293 3.6 15.9 1.0
CZ B:ARG243 3.7 16.8 1.0
O B:ARG293 3.9 15.5 1.0
CA B:ARG293 3.9 15.2 1.0
CH2 B:TRP304 4.0 19.4 1.0
CZ2 B:TRP304 4.0 18.7 1.0
CZ B:ARG293 4.2 16.2 1.0
C B:ARG293 4.3 14.6 1.0
NE B:ARG293 4.3 16.4 1.0
O B:HOH906 4.4 31.8 1.0
NE2 B:HIS248 4.5 16.0 1.0
CG B:HIS248 4.7 15.0 1.0
CZ3 B:TRP304 4.7 19.3 1.0
CE2 B:TRP304 4.7 17.8 1.0
CE2 B:PHE257 4.9 14.1 1.0
CZ B:PHE257 4.9 14.2 1.0

Chlorine binding site 3 out of 4 in 4ghe

Go back to Chlorine Binding Sites List in 4ghe
Chlorine binding site 3 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:7.4
occ:0.20
 O10 C:4NC403 0.6 20.6 0.8
N9 C:4NC403 2.1 23.2 0.8
C3 C:4NC403 2.8 19.8 0.8
C4 C:4NC403 2.8 20.1 0.8
NH1 C:ARG243 2.9 21.5 1.0
O11 C:4NC403 3.1 24.6 0.8
NH1 C:ARG293 3.2 18.3 1.0
NH2 C:ARG243 3.2 22.3 1.0
CE1 C:HIS248 3.5 15.7 1.0
CZ C:ARG243 3.5 20.8 1.0
ND1 C:HIS248 3.7 15.3 1.0
CH2 C:TRP304 3.7 18.7 1.0
CD C:ARG293 3.7 18.4 1.0
CZ2 C:TRP304 3.7 18.2 1.0
CG C:ARG293 3.7 18.3 1.0
CB C:ARG293 3.8 18.0 1.0
C2 C:4NC403 4.0 19.0 0.8
C5 C:4NC403 4.1 17.8 0.8
O C:ARG293 4.2 16.9 1.0
CZ C:ARG293 4.2 18.3 1.0
CA C:ARG293 4.2 17.2 1.0
NE C:ARG293 4.4 18.5 1.0
CZ3 C:TRP304 4.5 19.1 1.0
CE2 C:TRP304 4.5 17.4 1.0
C C:ARG293 4.5 17.1 1.0
O8 C:4NC403 4.6 18.5 0.8
NE2 C:HIS248 4.7 14.7 1.0
CE2 C:PHE257 4.7 13.1 1.0
CZ C:PHE257 4.7 13.2 1.0
NE C:ARG243 4.8 20.0 1.0
CG C:HIS248 4.9 14.3 1.0

Chlorine binding site 4 out of 4 in 4ghe

Go back to Chlorine Binding Sites List in 4ghe
Chlorine binding site 4 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:21.7
occ:1.00
 NH1 D:ARG243 3.2 17.5 1.0
NH1 D:ARG293 3.2 13.6 1.0
CE1 D:HIS248 3.3 12.1 1.0
NH2 D:ARG243 3.3 16.0 1.0
ND1 D:HIS248 3.4 11.9 1.0
CB D:ARG293 3.6 13.2 1.0
CG D:ARG293 3.6 13.7 1.0
CD D:ARG293 3.7 14.2 1.0
CZ D:ARG243 3.7 16.8 1.0
CZ2 D:TRP304 4.0 16.5 1.0
O D:ARG293 4.0 12.6 1.0
CH2 D:TRP304 4.0 16.9 1.0
CA D:ARG293 4.0 12.4 1.0
CZ D:ARG293 4.2 14.2 1.0
C D:ARG293 4.4 12.9 1.0
NE D:ARG293 4.4 14.3 1.0
NE2 D:HIS248 4.4 12.3 1.0
O D:HOH909 4.6 24.8 1.0
CG D:HIS248 4.7 11.8 1.0
CE2 D:TRP304 4.7 15.2 1.0
CZ3 D:TRP304 4.7 18.3 1.0
CE2 D:PHE257 4.7 12.0 1.0
CZ D:PHE257 4.8 11.9 1.0

Reference:

E.G.Kovaleva, J.D.Lipscomb. Structural Basis For the Role of Tyrosine 257 of Homoprotocatechuate 2,3-Dioxygenase in Substrate and Oxygen Activation. Biochemistry V. 51 8755 2012.
ISSN: ISSN 0006-2960
PubMed: 23066739
DOI: 10.1021/BI301115C
Page generated: Sun Jul 21 14:38:38 2024

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