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Chlorine in PDB 4ghf: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 and Dioxygen at 1.67 Ang Resolution, PDB code: 4ghf 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) 89.04 / 1.67
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.519, 150.318, 96.105, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.1

Other elements in 4ghf:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 and Dioxygen at 1.67 Ang Resolution (pdb code 4ghf). 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 and Dioxygen at 1.67 Ang Resolution, PDB code: 4ghf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4ghf

Go back to Chlorine Binding Sites List in 4ghf
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 and Dioxygen at 1.67 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 and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:19.4
occ:0.30
 O10 A:4NC402 0.9 24.9 0.7
N9 A:4NC402 2.4 30.4 0.7
NH1 A:ARG243 2.5 29.4 1.0
NH2 A:ARG243 3.0 28.5 1.0
CZ A:ARG243 3.1 29.1 1.0
C3 A:4NC402 3.2 24.4 0.7
C4 A:4NC402 3.2 25.3 0.7
O11 A:4NC402 3.2 33.3 0.7
CE1 A:HIS248 3.4 21.1 1.0
NH1 A:ARG293 3.4 26.2 1.0
ND1 A:HIS248 3.5 19.0 1.0
CB A:ARG293 3.5 20.7 1.0
CD A:ARG293 3.6 22.6 1.0
CG A:ARG293 3.7 21.8 1.0
CH2 A:TRP304 3.8 28.0 1.0
CZ2 A:TRP304 3.8 25.5 1.0
O A:ARG293 4.0 23.4 1.0
CA A:ARG293 4.1 20.9 1.0
C A:ARG293 4.3 21.2 1.0
CZ A:ARG293 4.3 24.1 1.0
C2 A:4NC402 4.3 22.3 0.7
NE A:ARG293 4.4 22.7 1.0
C5 A:4NC402 4.4 25.4 0.7
CZ3 A:TRP304 4.5 29.1 1.0
NE A:ARG243 4.5 28.3 1.0
CE2 A:TRP304 4.5 24.7 1.0
NE2 A:HIS248 4.6 20.6 1.0
CE2 A:PHE257 4.6 19.8 1.0
CZ A:PHE257 4.8 19.9 1.0
CG A:HIS248 4.8 20.0 1.0
O8 A:4NC402 4.9 21.5 0.7

Chlorine binding site 2 out of 4 in 4ghf

Go back to Chlorine Binding Sites List in 4ghf
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 and Dioxygen at 1.67 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 and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:27.0
occ:1.00
 O B:HOH798 3.1 39.9 1.0
NH1 B:ARG243 3.2 25.3 1.0
NH1 B:ARG293 3.2 21.6 1.0
CE1 B:HIS248 3.3 20.9 1.0
NH2 B:ARG243 3.3 23.5 1.0
ND1 B:HIS248 3.4 20.8 1.0
CB B:ARG293 3.5 18.1 1.0
CG B:ARG293 3.6 18.6 1.0
CD B:ARG293 3.6 20.2 1.0
CZ B:ARG243 3.7 22.5 1.0
O B:ARG293 3.9 20.6 1.0
CA B:ARG293 3.9 17.6 1.0
CH2 B:TRP304 4.0 25.8 1.0
CZ2 B:TRP304 4.1 25.5 1.0
CZ B:ARG293 4.2 19.8 1.0
C B:ARG293 4.3 18.2 1.0
NE B:ARG293 4.4 19.9 1.0
NE2 B:HIS248 4.4 20.1 1.0
CG B:HIS248 4.6 19.5 1.0
O B:HOH795 4.6 26.7 1.0
CZ3 B:TRP304 4.7 27.0 1.0
CE2 B:TRP304 4.7 23.7 1.0
CZ B:PHE257 4.9 18.1 1.0
CE2 B:PHE257 4.9 18.3 1.0
NE B:ARG243 5.0 22.8 1.0

Chlorine binding site 3 out of 4 in 4ghf

Go back to Chlorine Binding Sites List in 4ghf
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 and Dioxygen at 1.67 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 and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl406

b:17.4
occ:0.10
 O10 C:4NC402 1.0 28.2 0.9
N9 C:4NC402 2.4 28.6 0.9
NH1 C:ARG243 2.5 36.0 1.0
C3 C:4NC402 2.9 21.9 0.9
C4 C:4NC402 3.0 23.2 0.9
NH2 C:ARG243 3.1 36.0 1.0
CZ C:ARG243 3.2 33.2 1.0
O11 C:4NC402 3.3 31.5 0.9
NH1 C:ARG293 3.4 24.4 1.0
CH2 C:TRP304 3.5 30.0 1.0
CE1 C:HIS248 3.5 19.1 1.0
CZ2 C:TRP304 3.5 28.8 1.0
CD C:ARG293 3.7 24.6 1.0
ND1 C:HIS248 3.7 19.2 1.0
CB C:ARG293 3.9 22.9 1.0
CG C:ARG293 4.0 24.1 1.0
C2 C:4NC402 4.1 21.9 0.9
CZ3 C:TRP304 4.2 31.3 1.0
CE2 C:TRP304 4.2 25.9 1.0
C5 C:4NC402 4.3 20.7 0.9
O C:ARG293 4.3 24.1 1.0
CZ C:ARG293 4.3 25.0 1.0
CA C:ARG293 4.4 22.9 1.0
NE C:ARG293 4.5 23.4 1.0
NE C:ARG243 4.5 31.2 1.0
CE2 C:PHE257 4.5 19.1 1.0
CZ C:PHE257 4.6 18.2 1.0
C C:ARG293 4.6 23.1 1.0
NE2 C:HIS248 4.7 19.2 1.0
O8 C:4NC402 4.7 21.0 0.9
CE3 C:TRP304 4.8 29.2 1.0
CD2 C:TRP304 4.9 26.9 1.0
CG C:HIS248 5.0 18.7 1.0

Chlorine binding site 4 out of 4 in 4ghf

Go back to Chlorine Binding Sites List in 4ghf
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 and Dioxygen at 1.67 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 and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:19.6
occ:0.30
 O10 D:4NC402 0.7 22.3 0.7
N9 D:4NC402 2.2 26.2 0.7
NH1 D:ARG243 2.7 28.9 1.0
C3 D:4NC402 2.9 22.1 0.7
C4 D:4NC402 3.0 22.0 0.7
NH2 D:ARG243 3.1 23.9 1.0
O11 D:4NC402 3.2 26.8 0.7
CZ D:ARG243 3.3 25.7 1.0
NH1 D:ARG293 3.3 20.5 1.0
CE1 D:HIS248 3.3 19.0 1.0
ND1 D:HIS248 3.5 19.0 1.0
CD D:ARG293 3.6 20.4 1.0
CB D:ARG293 3.6 17.7 1.0
CG D:ARG293 3.8 19.4 1.0
CH2 D:TRP304 3.8 26.3 1.0
CZ2 D:TRP304 3.8 23.2 1.0
O D:ARG293 4.1 19.5 1.0
CA D:ARG293 4.1 17.2 1.0
C2 D:4NC402 4.2 21.0 0.7
C5 D:4NC402 4.2 20.6 0.7
CZ D:ARG293 4.3 21.5 1.0
NE D:ARG293 4.4 20.9 1.0
C D:ARG293 4.4 17.1 1.0
CZ3 D:TRP304 4.4 26.2 1.0
CE2 D:TRP304 4.5 21.0 1.0
NE2 D:HIS248 4.5 18.4 1.0
NE D:ARG243 4.6 25.3 1.0
CE2 D:PHE257 4.7 17.0 1.0
CZ D:PHE257 4.7 17.3 1.0
O8 D:4NC402 4.8 19.6 0.7
CG D:HIS248 4.8 18.3 1.0
CE3 D:TRP304 5.0 25.6 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 14:39:00 2024

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