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Iron in PDB 3a16: Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime

Enzymatic activity of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime

All present enzymatic activity of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime:
4.99.1.5;

Protein crystallography data

The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime, PDB code: 3a16 was solved by H.Sawai, H.Sugimoto, Y.Kato, Y.Asano, Y.Shiro, S.Aono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.710, 147.670, 78.910, 90.00, 90.01, 90.00
R / Rfree (%) 24.8 / 27.4

Other elements in 3a16:

The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime (pdb code 3a16). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime, PDB code: 3a16:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3a16

Go back to Iron Binding Sites List in 3a16
Iron binding site 1 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe354

b:8.3
occ:1.00
FE A:HEM354 0.0 8.3 1.0
NC A:HEM354 2.0 5.5 1.0
ND A:HEM354 2.0 6.9 1.0
NB A:HEM354 2.1 7.3 1.0
NA A:HEM354 2.1 6.8 1.0
NE2 A:HIS299 2.2 8.4 1.0
N1 A:PXO355 2.5 12.1 1.0
C4C A:HEM354 3.0 7.3 1.0
C1D A:HEM354 3.0 6.0 1.0
C1C A:HEM354 3.0 7.8 1.0
C4B A:HEM354 3.1 7.0 1.0
C4D A:HEM354 3.1 6.8 1.0
C4A A:HEM354 3.1 8.8 1.0
C1A A:HEM354 3.1 8.4 1.0
CE1 A:HIS299 3.1 7.3 1.0
C1B A:HEM354 3.1 7.3 1.0
CD2 A:HIS299 3.2 6.5 1.0
O1 A:PXO355 3.2 8.7 1.0
CHD A:HEM354 3.4 6.4 1.0
CHC A:HEM354 3.4 7.8 1.0
C1 A:PXO355 3.4 12.6 1.0
CHA A:HEM354 3.5 7.8 1.0
CHB A:HEM354 3.5 8.3 1.0
C2C A:HEM354 4.2 6.9 1.0
C3C A:HEM354 4.2 6.9 1.0
ND1 A:HIS299 4.2 6.3 1.0
C2D A:HEM354 4.3 6.4 1.0
C3B A:HEM354 4.3 7.7 1.0
C3D A:HEM354 4.3 5.7 1.0
C3A A:HEM354 4.3 8.0 1.0
C2B A:HEM354 4.3 7.6 1.0
C2A A:HEM354 4.3 8.5 1.0
CG A:HIS299 4.3 8.5 1.0
C2 A:PXO355 4.9 13.9 1.0
OG A:SER219 4.9 5.6 1.0

Iron binding site 2 out of 4 in 3a16

Go back to Iron Binding Sites List in 3a16
Iron binding site 2 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe354

b:7.9
occ:1.00
FE B:HEM354 0.0 7.9 1.0
NA B:HEM354 2.0 6.4 1.0
NC B:HEM354 2.0 5.0 1.0
ND B:HEM354 2.0 5.5 1.0
NB B:HEM354 2.1 6.0 1.0
NE2 B:HIS299 2.1 4.1 0.2
N1 B:PXO355 2.1 11.9 1.0
NE2 B:HIS299 2.2 9.1 0.8
CD2 B:HIS299 2.8 3.4 0.2
C1 B:PXO355 3.0 14.3 1.0
CE1 B:HIS299 3.0 7.7 0.8
C1D B:HEM354 3.0 5.9 1.0
C1A B:HEM354 3.0 7.1 1.0
C1C B:HEM354 3.1 6.8 1.0
C4A B:HEM354 3.1 7.9 1.0
C1B B:HEM354 3.1 7.7 1.0
C4B B:HEM354 3.1 6.8 1.0
C4C B:HEM354 3.1 6.8 1.0
C4D B:HEM354 3.1 6.0 1.0
O1 B:PXO355 3.1 8.7 1.0
CD2 B:HIS299 3.2 6.5 0.8
CE1 B:HIS299 3.3 3.5 0.2
CHD B:HEM354 3.4 5.9 1.0
CHC B:HEM354 3.4 6.2 1.0
CHB B:HEM354 3.4 6.9 1.0
CHA B:HEM354 3.4 6.8 1.0
CG B:HIS299 4.1 2.9 0.2
ND1 B:HIS299 4.2 7.7 0.8
ND1 B:HIS299 4.3 2.9 0.2
C3A B:HEM354 4.3 7.2 1.0
C2A B:HEM354 4.3 7.2 1.0
C2C B:HEM354 4.3 4.9 1.0
C2D B:HEM354 4.3 5.2 1.0
C2B B:HEM354 4.3 6.4 1.0
C3D B:HEM354 4.3 6.3 1.0
C3B B:HEM354 4.3 7.4 1.0
C3C B:HEM354 4.3 5.3 1.0
CG B:HIS299 4.3 7.8 0.8
C2 B:PXO355 4.4 16.2 1.0
OG B:SER219 4.9 6.6 1.0

Iron binding site 3 out of 4 in 3a16

Go back to Iron Binding Sites List in 3a16
Iron binding site 3 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe354

b:9.1
occ:1.00
FE C:HEM354 0.0 9.1 1.0
NA C:HEM354 2.0 6.9 1.0
NB C:HEM354 2.0 6.8 1.0
ND C:HEM354 2.0 7.0 1.0
NC C:HEM354 2.1 5.8 1.0
N1 C:PXO355 2.2 11.1 1.0
NE2 C:HIS299 2.3 10.8 1.0
C1 C:PXO355 3.0 11.4 1.0
C4D C:HEM354 3.0 6.7 1.0
C1A C:HEM354 3.0 8.8 1.0
C4A C:HEM354 3.1 8.9 1.0
C4B C:HEM354 3.1 7.4 1.0
C1C C:HEM354 3.1 7.5 1.0
C1D C:HEM354 3.1 6.4 1.0
C1B C:HEM354 3.1 7.5 1.0
O1 C:PXO355 3.1 10.1 1.0
C4C C:HEM354 3.1 7.5 1.0
CE1 C:HIS299 3.2 8.8 1.0
CD2 C:HIS299 3.3 7.8 1.0
CHA C:HEM354 3.4 7.8 1.0
CHC C:HEM354 3.4 7.9 1.0
CHB C:HEM354 3.4 8.3 1.0
CHD C:HEM354 3.5 6.5 1.0
C3A C:HEM354 4.3 8.2 1.0
C2A C:HEM354 4.3 8.5 1.0
C3D C:HEM354 4.3 6.4 1.0
C2B C:HEM354 4.3 7.6 1.0
C2D C:HEM354 4.3 6.6 1.0
C2C C:HEM354 4.3 7.1 1.0
C3B C:HEM354 4.3 8.0 1.0
ND1 C:HIS299 4.3 7.8 1.0
C3C C:HEM354 4.3 6.5 1.0
CG C:HIS299 4.4 9.1 1.0
C2 C:PXO355 4.5 12.9 1.0
OG C:SER219 4.9 5.3 1.0

Iron binding site 4 out of 4 in 3a16

Go back to Iron Binding Sites List in 3a16
Iron binding site 4 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe354

b:8.5
occ:1.00
FE D:HEM354 0.0 8.5 1.0
NC D:HEM354 2.0 5.0 1.0
ND D:HEM354 2.0 6.0 1.0
NA D:HEM354 2.1 6.1 1.0
NB D:HEM354 2.1 6.0 1.0
NE2 D:HIS299 2.1 4.7 0.2
N1 D:PXO355 2.1 14.1 1.0
NE2 D:HIS299 2.2 9.2 0.8
CD2 D:HIS299 2.8 3.8 0.2
C1 D:PXO355 3.0 14.2 1.0
C1D D:HEM354 3.0 5.7 1.0
CE1 D:HIS299 3.0 8.5 0.8
C1C D:HEM354 3.0 7.0 1.0
O1 D:PXO355 3.0 7.7 1.0
C4C D:HEM354 3.1 6.5 1.0
C4B D:HEM354 3.1 6.9 1.0
C4A D:HEM354 3.1 7.5 1.0
C1A D:HEM354 3.1 7.3 1.0
C1B D:HEM354 3.1 7.7 1.0
C4D D:HEM354 3.1 6.2 1.0
CD2 D:HIS299 3.2 7.4 0.8
CE1 D:HIS299 3.3 4.5 0.2
CHD D:HEM354 3.4 5.9 1.0
CHC D:HEM354 3.4 6.1 1.0
CHB D:HEM354 3.4 6.9 1.0
CHA D:HEM354 3.5 6.8 1.0
CG D:HIS299 4.1 3.1 0.2
ND1 D:HIS299 4.2 7.7 0.8
ND1 D:HIS299 4.3 3.1 0.2
C2C D:HEM354 4.3 4.7 1.0
C2D D:HEM354 4.3 5.3 1.0
C3C D:HEM354 4.3 5.6 1.0
C3B D:HEM354 4.3 7.4 1.0
C3A D:HEM354 4.3 7.3 1.0
C2A D:HEM354 4.3 7.0 1.0
C3D D:HEM354 4.3 6.0 1.0
C2B D:HEM354 4.3 6.1 1.0
CG D:HIS299 4.3 8.4 0.8
C2 D:PXO355 4.4 15.4 1.0
CD1 D:ILE302 4.5 3.5 0.2
OG D:SER219 4.9 6.5 1.0

Reference:

H.Sawai, H.Sugimoto, Y.Kato, Y.Asano, Y.Shiro, S.Aono. X-Ray Crystal Structure of Michaelis Complex of Aldoxime Dehydratase J.Biol.Chem. V. 284 32089 2009.
ISSN: ISSN 0021-9258
PubMed: 19740758
DOI: 10.1074/JBC.M109.018762
Page generated: Sun Dec 13 14:59:47 2020

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