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Chlorine in PDB 3eck: Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations

Enzymatic activity of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations

All present enzymatic activity of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations:
1.13.11.15;

Protein crystallography data

The structure of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations, PDB code: 3eck 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) 24.20 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.735, 163.176, 101.373, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.8

Other elements in 3eck:

The structure of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations 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 E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations (pdb code 3eck). 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 E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations, PDB code: 3eck:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3eck

Go back to Chlorine Binding Sites List in 3eck
Chlorine binding site 1 out of 4 in the Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:18.4
occ:1.00
 O A:HOH836 3.1 31.5 1.0
NH1 A:ARG243 3.2 14.9 1.0
NH1 A:ARG293 3.3 14.4 1.0
NH2 A:ARG243 3.3 13.2 1.0
CE1 A:HIS248 3.3 15.5 1.0
ND1 A:HIS248 3.4 14.5 1.0
CB A:ARG293 3.5 13.3 1.0
CG A:ARG293 3.5 13.2 1.0
CD A:ARG293 3.6 16.0 1.0
CZ A:ARG243 3.7 14.1 1.0
O A:ARG293 3.8 14.1 1.0
CA A:ARG293 3.8 12.7 1.0
OH A:TYR257 3.9 14.0 1.0
CH2 A:TRP304 4.1 17.4 1.0
C A:ARG293 4.1 12.7 1.0
CZ2 A:TRP304 4.2 16.5 1.0
CZ A:ARG293 4.3 14.9 1.0
NE A:ARG293 4.4 14.5 1.0
NE2 A:HIS248 4.4 14.2 1.0
CG A:HIS248 4.6 13.2 1.0
O A:HOH828 4.7 17.5 1.0
CZ3 A:TRP304 4.7 17.3 1.0
CE2 A:TRP304 4.9 15.8 1.0
CZ A:TYR257 4.9 11.7 1.0

Chlorine binding site 2 out of 4 in 3eck

Go back to Chlorine Binding Sites List in 3eck
Chlorine binding site 2 out of 4 in the Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:18.8
occ:1.00
 O B:HOH854 3.1 29.6 1.0
NH1 B:ARG243 3.2 14.0 1.0
NH2 B:ARG243 3.2 12.6 1.0
NH1 B:ARG293 3.3 14.4 1.0
CE1 B:HIS248 3.3 14.2 1.0
ND1 B:HIS248 3.4 13.3 1.0
CB B:ARG293 3.5 11.5 1.0
CG B:ARG293 3.5 12.5 1.0
CD B:ARG293 3.6 12.9 1.0
CZ B:ARG243 3.7 13.8 1.0
O B:ARG293 3.8 12.8 1.0
CA B:ARG293 3.8 11.3 1.0
OH B:TYR257 4.0 13.0 1.0
CH2 B:TRP304 4.1 16.0 1.0
C B:ARG293 4.2 11.3 1.0
CZ2 B:TRP304 4.2 15.2 1.0
CZ B:ARG293 4.3 16.2 1.0
NE B:ARG293 4.4 12.9 1.0
NE2 B:HIS248 4.5 11.6 1.0
CG B:HIS248 4.6 12.6 1.0
O B:HOH851 4.7 16.0 1.0
CZ3 B:TRP304 4.8 14.6 1.0
CE2 B:TRP304 4.9 14.5 1.0
CZ B:TYR257 5.0 13.0 1.0

Chlorine binding site 3 out of 4 in 3eck

Go back to Chlorine Binding Sites List in 3eck
Chlorine binding site 3 out of 4 in the Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:3.9
occ:0.15
 O11 C:XXG502 0.6 16.0 0.8
S9 C:XXG502 2.1 25.6 0.8
C3 C:XXG502 2.8 22.3 0.8
O10 C:XXG502 2.8 23.8 0.8
C4 C:XXG502 2.9 21.9 0.8
NH1 C:ARG243 2.9 19.8 1.0
O12 C:XXG502 3.2 24.3 0.8
NH2 C:ARG243 3.2 17.9 1.0
NH1 C:ARG293 3.3 13.8 1.0
CE1 C:HIS248 3.4 16.9 1.0
CZ C:ARG243 3.5 17.5 1.0
ND1 C:HIS248 3.5 16.0 1.0
CD C:ARG293 3.6 15.4 1.0
CB C:ARG293 3.7 14.0 1.0
CG C:ARG293 3.7 13.2 1.0
CH2 C:TRP304 3.9 17.6 1.0
O C:ARG293 3.9 15.5 1.0
OH C:TYR257 3.9 13.1 1.0
CA C:ARG293 4.0 13.8 1.0
CZ2 C:TRP304 4.0 17.0 1.0
C5 C:XXG502 4.2 20.4 0.8
C2 C:XXG502 4.2 18.9 0.8
C C:ARG293 4.3 14.3 1.0
CZ C:ARG293 4.3 15.8 1.0
NE C:ARG293 4.4 14.4 1.0
NE2 C:HIS248 4.5 13.0 1.0
O13 C:XXG502 4.5 24.1 0.8
CZ3 C:TRP304 4.5 17.6 1.0
O8 C:XXG502 4.7 13.5 0.8
CG C:HIS248 4.7 13.9 1.0
CE2 C:TRP304 4.8 15.4 1.0
NE C:ARG243 4.8 17.5 1.0
CZ C:TYR257 4.9 11.3 1.0

Chlorine binding site 4 out of 4 in 3eck

Go back to Chlorine Binding Sites List in 3eck
Chlorine binding site 4 out of 4 in the Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of E323L Homoprotocatechuate 2,3-Dioxygenase From Brevibacterium Fuscum in Complex with Putative O-O Bond Cleavage Intermediate Formed Via in Crystallo Reaction with 4-Sulfonyl Catechol at Low Oxygen Concentrations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:11.1
occ:0.35
 O11 D:XXG502 0.6 11.4 0.7
S9 D:XXG502 2.1 20.6 0.7
O10 D:XXG502 2.8 19.4 0.7
C3 D:XXG502 2.8 15.9 0.7
C4 D:XXG502 2.9 16.9 0.7
NH1 D:ARG243 2.9 15.2 1.0
O12 D:XXG502 3.1 21.4 0.7
NH1 D:ARG293 3.2 14.2 1.0
NH2 D:ARG243 3.3 13.0 1.0
CE1 D:HIS248 3.4 13.9 1.0
CZ D:ARG243 3.5 13.6 1.0
CD D:ARG293 3.5 12.3 1.0
ND1 D:HIS248 3.5 11.9 1.0
CB D:ARG293 3.6 11.6 1.0
CG D:ARG293 3.7 12.5 1.0
CH2 D:TRP304 3.9 14.3 1.0
OH D:TYR257 3.9 10.8 1.0
O D:ARG293 4.0 14.3 1.0
CA D:ARG293 4.0 12.1 1.0
CZ2 D:TRP304 4.0 15.2 1.0
C5 D:XXG502 4.2 16.4 0.7
C2 D:XXG502 4.2 12.5 0.7
CZ D:ARG293 4.2 13.8 1.0
NE D:ARG293 4.3 12.9 1.0
C D:ARG293 4.3 12.9 1.0
NE2 D:HIS248 4.5 12.3 1.0
CZ3 D:TRP304 4.5 14.8 1.0
O13 D:XXG502 4.6 16.8 0.7
O8 D:XXG502 4.7 6.7 0.7
CE2 D:TRP304 4.7 13.4 1.0
CG D:HIS248 4.8 12.3 1.0
NE D:ARG243 4.8 14.5 1.0
CZ D:TYR257 4.9 9.0 1.0

Reference:

E.G.Kovaleva, J.D.Lipscomb. Intermediate in the O-O Bond Cleavage Reaction of An Extradiol Dioxygenase. Biochemistry V. 47 11168 2008.
ISSN: ISSN 0006-2960
PubMed: 18826259
DOI: 10.1021/BI801459Q
Page generated: Sat Jul 20 18:47:20 2024

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