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Iron 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:

Chlorine (Cl) 4 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3eck

Go back to Iron Binding Sites List in 3eck
Iron 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 Iron with other atoms in the Fe 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:Fe500

b:14.9
occ:1.00
 OE1 A:GLU267 2.1 14.1 1.0
NE2 A:HIS214 2.2 14.8 1.0
O A:HOH826 2.2 14.8 1.0
O A:HOH827 2.2 16.2 1.0
NE2 A:HIS155 2.2 14.4 1.0
O A:HOH828 2.3 17.5 1.0
CE1 A:HIS214 3.1 13.9 1.0
CE1 A:HIS155 3.1 13.4 1.0
CD A:GLU267 3.2 14.8 1.0
CD2 A:HIS214 3.2 14.8 1.0
CD2 A:HIS155 3.3 14.7 1.0
OE2 A:GLU267 3.7 15.9 1.0
NE2 A:HIS200 3.8 15.5 1.0
OH A:TYR257 4.1 14.0 1.0
ND1 A:HIS214 4.2 14.1 1.0
ND1 A:HIS155 4.2 13.0 1.0
CG A:HIS214 4.3 12.4 1.0
CG A:HIS155 4.3 14.5 1.0
ND2 A:ASN157 4.4 17.0 1.0
CG A:GLU267 4.4 12.2 1.0
O A:HOH829 4.5 19.6 1.0
CE1 A:HIS200 4.5 16.4 1.0
CE1 A:TYR257 4.5 13.7 1.0
CB A:GLU267 4.5 13.1 1.0
CB A:ALA216 4.6 13.3 1.0
CB A:ASN157 4.6 14.4 1.0
CZ A:TYR257 4.8 11.7 1.0
CD2 A:HIS200 4.9 16.9 1.0
CD1 A:TYR269 4.9 17.2 1.0
CG A:ASN157 5.0 16.8 1.0

Iron binding site 2 out of 4 in 3eck

Go back to Iron Binding Sites List in 3eck
Iron 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 Iron with other atoms in the Fe 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:Fe500

b:14.1
occ:1.00
 OE1 B:GLU267 2.0 13.9 1.0
O B:HOH849 2.2 14.1 1.0
NE2 B:HIS155 2.2 14.4 1.0
NE2 B:HIS214 2.2 13.4 1.0
O B:HOH850 2.3 16.3 1.0
O B:HOH851 2.3 16.0 1.0
CE1 B:HIS214 3.1 12.2 1.0
CD B:GLU267 3.1 14.1 1.0
CE1 B:HIS155 3.1 12.6 1.0
CD2 B:HIS155 3.2 14.2 1.0
CD2 B:HIS214 3.3 12.6 1.0
OE2 B:GLU267 3.6 12.8 1.0
NE2 B:HIS200 3.8 16.5 1.0
OH B:TYR257 4.1 13.0 1.0
ND1 B:HIS214 4.2 12.9 1.0
ND1 B:HIS155 4.3 12.4 1.0
CG B:HIS155 4.3 13.8 1.0
CG B:HIS214 4.4 12.2 1.0
CG B:GLU267 4.4 12.5 1.0
ND2 B:ASN157 4.4 15.8 1.0
CB B:GLU267 4.5 13.0 1.0
CE1 B:HIS200 4.5 17.1 1.0
CE1 B:TYR257 4.5 12.3 1.0
O B:HOH852 4.5 18.2 1.0
CB B:ALA216 4.6 12.3 1.0
CB B:ASN157 4.7 13.8 1.0
CZ B:TYR257 4.8 13.0 1.0
CD2 B:HIS200 4.9 15.9 1.0
CD1 B:TYR269 5.0 14.1 1.0

Iron binding site 3 out of 4 in 3eck

Go back to Iron Binding Sites List in 3eck
Iron 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 Iron with other atoms in the Fe 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:Fe500

b:13.7
occ:1.00
 OE1 C:GLU267 2.0 14.9 1.0
O7 C:XXG502 2.2 18.1 0.8
NE2 C:HIS155 2.2 12.2 1.0
NE2 C:HIS214 2.2 12.7 1.0
O8 C:XXG502 2.2 13.5 0.8
O C:HOH798 2.3 14.0 1.0
C1 C:XXG502 2.9 19.4 0.8
C2 C:XXG502 2.9 18.9 0.8
CE1 C:HIS214 3.1 12.3 1.0
CE1 C:HIS155 3.1 11.9 1.0
CD C:GLU267 3.1 11.0 1.0
CD2 C:HIS155 3.2 12.7 1.0
CD2 C:HIS214 3.2 13.3 1.0
OE2 C:GLU267 3.5 15.2 1.0
O13 C:XXG502 3.6 24.1 0.8
NE2 C:HIS200 3.8 15.2 1.0
OH C:TYR257 4.1 13.1 1.0
ND1 C:HIS214 4.2 11.8 1.0
ND1 C:HIS155 4.2 11.4 1.0
C6 C:XXG502 4.2 15.8 0.8
C3 C:XXG502 4.3 22.3 0.8
CG C:HIS155 4.3 13.4 1.0
CG C:HIS214 4.3 12.9 1.0
CG C:GLU267 4.4 11.6 1.0
CE1 C:HIS200 4.5 16.2 1.0
ND2 C:ASN157 4.5 17.5 1.0
CE1 C:TYR257 4.5 10.7 1.0
CB C:GLU267 4.5 11.3 1.0
CB C:ALA216 4.6 11.5 1.0
CB C:ASN157 4.7 13.1 1.0
CZ C:TYR257 4.8 11.3 1.0
CD1 C:TYR269 4.8 15.7 1.0
CE1 C:TYR269 4.9 15.7 1.0
CD2 C:HIS200 5.0 17.1 1.0

Iron binding site 4 out of 4 in 3eck

Go back to Iron Binding Sites List in 3eck
Iron 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 Iron with other atoms in the Fe 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:Fe500

b:11.5
occ:1.00
 OE1 D:GLU267 2.0 12.7 1.0
O7 D:XXG502 2.2 10.8 0.7
NE2 D:HIS155 2.2 10.2 1.0
O8 D:XXG502 2.2 6.7 0.7
NE2 D:HIS214 2.2 11.4 1.0
O D:HOH820 2.3 13.3 1.0
C1 D:XXG502 2.9 14.6 0.7
C2 D:XXG502 2.9 12.5 0.7
CE1 D:HIS155 3.0 9.8 1.0
CD D:GLU267 3.1 10.5 1.0
CE1 D:HIS214 3.1 9.0 1.0
CD2 D:HIS214 3.2 10.2 1.0
CD2 D:HIS155 3.2 11.7 1.0
O13 D:XXG502 3.5 16.8 0.7
OE2 D:GLU267 3.5 12.5 1.0
NE2 D:HIS200 3.8 13.7 1.0
OH D:TYR257 4.1 10.8 1.0
ND1 D:HIS155 4.2 10.7 1.0
C3 D:XXG502 4.3 15.9 0.7
ND1 D:HIS214 4.3 9.3 1.0
C6 D:XXG502 4.3 10.1 0.7
CG D:HIS155 4.3 10.4 1.0
CG D:HIS214 4.3 9.2 1.0
CG D:GLU267 4.4 10.0 1.0
CE1 D:HIS200 4.5 14.1 1.0
CB D:GLU267 4.5 9.9 1.0
ND2 D:ASN157 4.5 13.7 1.0
CE1 D:TYR257 4.6 9.8 1.0
CB D:ALA216 4.6 10.1 1.0
CB D:ASN157 4.7 10.5 1.0
CZ D:TYR257 4.8 9.0 1.0
CD1 D:TYR269 4.8 12.6 1.0
CE1 D:TYR269 4.9 12.3 1.0
CD2 D:HIS200 5.0 13.7 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: Sun Aug 4 09:42:04 2024

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