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Iron in PDB 2iga: Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.

Enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.

All present enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.:
1.13.11.15;

Protein crystallography data

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations., PDB code: 2iga 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) 52.70 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.678, 153.022, 96.389, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 24.5

Other elements in 2iga:

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. (pdb code 2iga). 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 Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations., PDB code: 2iga:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2iga

Go back to Iron Binding Sites List in 2iga
Iron binding site 1 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:31.8
occ:1.00
O13 A:XXP600 2.0 21.6 0.6
OE1 A:GLU267 2.1 28.2 1.0
NE2 A:HIS155 2.2 26.6 1.0
O A:HOH1042 2.2 25.4 1.0
O11 A:XXP600 2.2 15.4 0.6
NE2 A:HIS214 2.3 22.2 1.0
C1 A:XXP600 2.3 26.4 0.6
C2 A:XXP600 2.6 26.1 0.6
CE1 A:HIS155 2.9 23.8 1.0
CD A:GLU267 3.1 29.6 1.0
CD2 A:HIS214 3.2 25.2 1.0
CE1 A:HIS214 3.3 27.9 1.0
O12 A:XXP600 3.3 28.0 0.6
CD2 A:HIS155 3.3 27.5 1.0
OE2 A:GLU267 3.6 27.7 1.0
NE2 A:HIS200 3.8 31.4 1.0
O10 A:XXP600 3.8 45.3 0.6
C3 A:XXP600 4.1 27.2 0.6
ND1 A:HIS155 4.1 26.2 1.0
OH A:TYR257 4.2 24.1 1.0
CG A:HIS155 4.3 31.1 1.0
ND1 A:HIS214 4.4 24.2 1.0
CG A:HIS214 4.4 27.3 1.0
CG A:GLU267 4.4 25.8 1.0
CE1 A:HIS200 4.4 32.0 1.0
ND2 A:ASN157 4.5 28.9 1.0
CB A:ALA216 4.6 26.4 1.0
CB A:GLU267 4.6 26.2 1.0
CE1 A:TYR257 4.7 21.1 1.0
CB A:ASN157 4.7 27.8 1.0
C6 A:XXP600 4.9 44.7 0.6
CD1 A:TYR269 4.9 26.6 1.0
CZ A:TYR257 5.0 22.5 1.0
CD2 A:HIS200 5.0 31.8 1.0
CE1 A:TYR269 5.0 28.4 1.0

Iron binding site 2 out of 4 in 2iga

Go back to Iron Binding Sites List in 2iga
Iron binding site 2 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:29.0
occ:1.00
OE1 B:GLU267 2.0 22.2 1.0
O7 B:XX3600 2.2 28.4 0.8
O13 B:XX3600 2.2 28.1 0.8
NE2 B:HIS155 2.2 22.2 1.0
O8 B:XX3600 2.3 34.5 0.8
NE2 B:HIS214 2.3 22.1 1.0
C2 B:XX3600 2.7 36.9 0.8
C1 B:XX3600 2.7 37.2 0.8
O12 B:XX3600 2.8 39.6 0.8
CD B:GLU267 3.1 24.5 1.0
CE1 B:HIS214 3.1 24.6 1.0
CD2 B:HIS155 3.2 21.1 1.0
CE1 B:HIS155 3.2 26.4 1.0
CD2 B:HIS214 3.3 26.0 1.0
OE2 B:GLU267 3.5 26.1 1.0
NE2 B:HIS200 3.8 35.1 1.0
C3 B:XX3600 4.0 38.9 0.8
C6 B:XX3600 4.1 33.4 0.8
OH B:TYR257 4.2 23.7 1.0
ND1 B:HIS214 4.3 21.6 1.0
ND1 B:HIS155 4.3 22.0 1.0
ND2 B:ASN157 4.3 21.3 1.0
CG B:HIS155 4.3 22.2 1.0
CG B:GLU267 4.4 19.1 1.0
CG B:HIS214 4.4 24.2 1.0
CE1 B:HIS200 4.5 33.1 1.0
CB B:GLU267 4.6 26.8 1.0
CE1 B:TYR257 4.6 21.6 1.0
CB B:ALA216 4.7 25.9 1.0
CB B:ASN157 4.7 26.1 1.0
CD2 B:HIS200 4.9 31.4 1.0
CZ B:TYR257 4.9 25.0 1.0
C4 B:XX3600 5.0 41.4 0.8

Iron binding site 3 out of 4 in 2iga

Go back to Iron Binding Sites List in 2iga
Iron binding site 3 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:32.8
occ:1.00
OE1 C:GLU267 2.1 23.9 1.0
O7 C:XX2601 2.2 30.3 0.8
NE2 C:HIS155 2.2 25.1 1.0
O8 C:XX2601 2.2 19.6 0.8
NE2 C:HIS214 2.3 24.7 1.0
O1 C:OXY600 2.4 39.7 1.0
O2 C:OXY600 2.5 35.9 1.0
C2 C:XX2601 2.8 27.8 0.8
C1 C:XX2601 2.9 30.3 0.8
CE1 C:HIS214 3.1 24.0 1.0
CE1 C:HIS155 3.1 29.6 1.0
CD C:GLU267 3.2 27.0 1.0
CD2 C:HIS155 3.3 27.5 1.0
CD2 C:HIS214 3.4 26.8 1.0
OE2 C:GLU267 3.7 29.0 1.0
NE2 C:HIS200 3.7 39.7 1.0
OH C:TYR257 4.2 28.1 1.0
C6 C:XX2601 4.2 27.0 0.8
ND1 C:HIS214 4.2 23.5 1.0
ND1 C:HIS155 4.2 25.2 1.0
C3 C:XX2601 4.3 32.7 0.8
CG C:HIS155 4.4 27.6 1.0
CE1 C:HIS200 4.4 38.0 1.0
CG C:HIS214 4.4 27.8 1.0
CG C:GLU267 4.4 27.3 1.0
ND2 C:ASN157 4.5 30.1 1.0
CB C:GLU267 4.5 25.6 1.0
CB C:ALA216 4.6 28.9 1.0
CB C:ASN157 4.7 29.7 1.0
CE1 C:TYR257 4.7 24.6 1.0
CD1 C:TYR269 4.8 31.6 1.0
CD2 C:HIS200 4.9 37.6 1.0
CE1 C:TYR269 4.9 31.6 1.0
CZ C:TYR257 4.9 28.0 1.0

Iron binding site 4 out of 4 in 2iga

Go back to Iron Binding Sites List in 2iga
Iron binding site 4 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:32.0
occ:1.00
OE1 D:GLU267 2.0 27.5 1.0
O13 D:XX3600 2.1 20.5 0.8
NE2 D:HIS214 2.2 23.0 1.0
NE2 D:HIS155 2.2 24.8 1.0
O7 D:XX3600 2.2 36.5 0.8
O8 D:XX3600 2.3 25.9 0.8
C2 D:XX3600 2.7 33.4 0.8
O12 D:XX3600 2.8 34.1 0.8
C1 D:XX3600 2.8 36.0 0.8
CE1 D:HIS155 3.0 21.1 1.0
CE1 D:HIS214 3.1 22.1 1.0
CD D:GLU267 3.1 27.7 1.0
CD2 D:HIS214 3.3 23.6 1.0
CD2 D:HIS155 3.4 25.7 1.0
OE2 D:GLU267 3.6 32.2 1.0
NE2 D:HIS200 3.9 36.0 1.0
ND1 D:HIS155 4.1 24.4 1.0
C3 D:XX3600 4.2 36.2 0.8
C6 D:XX3600 4.2 30.5 0.8
OH D:TYR257 4.2 28.0 1.0
ND1 D:HIS214 4.2 25.6 1.0
CG D:GLU267 4.3 26.2 1.0
CG D:HIS214 4.4 23.2 1.0
CG D:HIS155 4.4 25.3 1.0
ND2 D:ASN157 4.4 28.4 1.0
CB D:GLU267 4.6 26.7 1.0
CE1 D:TYR257 4.6 27.8 1.0
CE1 D:HIS200 4.6 34.7 1.0
CB D:ASN157 4.6 27.7 1.0
CB D:ALA216 4.7 25.6 1.0
CZ D:TYR257 4.9 29.2 1.0
CD1 D:TYR269 4.9 31.6 1.0

Reference:

E.G.Kovaleva, J.D.Lipscomb. Crystal Structures of FE2+ Dioxygenase Superoxo, Alkylperoxo, and Bound Product Intermediates Science V. 316 453 2007.
ISSN: ISSN 0036-8075
PubMed: 17446402
DOI: 10.1126/SCIENCE.1134697
Page generated: Sat Aug 3 23:20:28 2024

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