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Iron in PDB 3a18: Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal)

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

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

Protein crystallography data

The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal), PDB code: 3a18 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) 19.93 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.118, 148.569, 79.113, 90.00, 90.30, 90.00
R / Rfree (%) 24.7 / 28

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal) (pdb code 3a18). 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 Butyraldoxime (Soaked Crystal), PDB code: 3a18:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3a18

Go back to Iron Binding Sites List in 3a18
Iron binding site 1 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal)


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 Butyraldoxime (Soaked Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe354

b:10.1
occ:1.00
FE A:HEM354 0.0 10.1 1.0
NA A:HEM354 2.0 8.0 1.0
NC A:HEM354 2.0 8.3 1.0
NB A:HEM354 2.1 8.1 1.0
ND A:HEM354 2.1 8.0 1.0
NE2 A:HIS299 2.2 11.4 1.0
N1 A:BXO355 2.2 9.5 1.0
C1A A:HEM354 3.0 9.9 1.0
C1C A:HEM354 3.0 8.1 1.0
O1 A:BXO355 3.0 8.5 1.0
C1 A:BXO355 3.0 11.8 1.0
C4D A:HEM354 3.1 7.4 1.0
C4A A:HEM354 3.1 9.3 1.0
C4B A:HEM354 3.1 8.1 1.0
C4C A:HEM354 3.1 7.7 1.0
C1B A:HEM354 3.1 8.1 1.0
C1D A:HEM354 3.1 7.5 1.0
CE1 A:HIS299 3.1 11.8 1.0
CD2 A:HIS299 3.2 12.7 1.0
CHA A:HEM354 3.4 7.7 1.0
CHC A:HEM354 3.4 8.2 1.0
CHB A:HEM354 3.4 8.6 1.0
CHD A:HEM354 3.5 7.3 1.0
ND1 A:HIS299 4.2 12.5 1.0
C2A A:HEM354 4.3 9.6 1.0
C3A A:HEM354 4.3 9.3 1.0
C2C A:HEM354 4.3 7.4 1.0
C3C A:HEM354 4.3 6.8 1.0
C3D A:HEM354 4.3 7.5 1.0
C3B A:HEM354 4.3 7.0 1.0
C2B A:HEM354 4.3 7.7 1.0
CG A:HIS299 4.3 13.8 1.0
C2D A:HEM354 4.3 7.9 1.0
C2 A:BXO355 4.5 13.8 1.0
OG A:SER219 4.8 6.3 1.0

Iron binding site 2 out of 4 in 3a18

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Iron binding site 2 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal)


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 Butyraldoxime (Soaked Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe354

b:9.1
occ:1.00
FE B:HEM354 0.0 9.1 1.0
NB B:HEM354 2.0 7.6 1.0
ND B:HEM354 2.0 7.0 1.0
NC B:HEM354 2.0 7.2 1.0
NA B:HEM354 2.1 8.3 1.0
NE2 B:HIS299 2.1 10.6 1.0
N1 B:BXO355 2.2 12.9 1.0
C1 B:BXO355 3.0 14.9 1.0
C4B B:HEM354 3.0 8.1 1.0
C4D B:HEM354 3.0 6.6 1.0
C1C B:HEM354 3.0 8.9 1.0
C1D B:HEM354 3.1 6.6 1.0
C1A B:HEM354 3.1 7.9 1.0
C1B B:HEM354 3.1 8.5 1.0
CD2 B:HIS299 3.1 11.0 1.0
C4C B:HEM354 3.1 7.5 1.0
C4A B:HEM354 3.1 8.4 1.0
O1 B:BXO355 3.1 13.3 1.0
CE1 B:HIS299 3.2 9.5 1.0
CHC B:HEM354 3.4 7.5 1.0
CHA B:HEM354 3.4 7.6 1.0
CHD B:HEM354 3.5 8.0 1.0
CHB B:HEM354 3.5 8.8 1.0
CG B:HIS299 4.2 11.9 1.0
ND1 B:HIS299 4.2 9.7 1.0
C3B B:HEM354 4.3 8.0 1.0
C2C B:HEM354 4.3 7.5 1.0
C2B B:HEM354 4.3 7.6 1.0
C3D B:HEM354 4.3 6.2 1.0
C2D B:HEM354 4.3 6.6 1.0
C2A B:HEM354 4.3 7.8 1.0
C3C B:HEM354 4.3 7.4 1.0
C3A B:HEM354 4.3 8.4 1.0
C2 B:BXO355 4.5 16.5 1.0
OG B:SER219 4.8 8.2 1.0
CD1 B:ILE302 4.9 21.5 1.0

Iron binding site 3 out of 4 in 3a18

Go back to Iron Binding Sites List in 3a18
Iron binding site 3 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal)


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 Butyraldoxime (Soaked Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe354

b:10.1
occ:1.00
FE C:HEM354 0.0 10.1 1.0
ND C:HEM354 2.0 7.5 1.0
NC C:HEM354 2.0 7.5 1.0
NB C:HEM354 2.1 7.8 1.0
NA C:HEM354 2.1 8.2 1.0
NE2 C:HIS299 2.2 11.8 1.0
N1 C:BXO355 2.2 10.9 1.0
C1 C:BXO355 3.0 12.7 1.0
C4D C:HEM354 3.0 7.7 1.0
C1D C:HEM354 3.0 7.1 1.0
C1A C:HEM354 3.1 8.6 1.0
C4C C:HEM354 3.1 7.2 1.0
C1C C:HEM354 3.1 7.5 1.0
O1 C:BXO355 3.1 9.0 1.0
C1B C:HEM354 3.1 7.7 1.0
C4B C:HEM354 3.1 7.8 1.0
C4A C:HEM354 3.1 9.1 1.0
CE1 C:HIS299 3.1 11.7 1.0
CD2 C:HIS299 3.2 12.6 1.0
CHA C:HEM354 3.4 8.0 1.0
CHD C:HEM354 3.4 7.4 1.0
CHC C:HEM354 3.4 7.2 1.0
CHB C:HEM354 3.5 7.9 1.0
ND1 C:HIS299 4.2 12.7 1.0
C2C C:HEM354 4.3 6.1 1.0
C3D C:HEM354 4.3 6.7 1.0
C2D C:HEM354 4.3 7.9 1.0
C3C C:HEM354 4.3 6.4 1.0
C2A C:HEM354 4.3 9.0 1.0
C2B C:HEM354 4.3 7.3 1.0
C3B C:HEM354 4.3 7.2 1.0
CG C:HIS299 4.3 13.8 1.0
C3A C:HEM354 4.3 9.0 1.0
C2 C:BXO355 4.4 14.4 1.0
OG C:SER219 4.8 6.5 1.0

Iron binding site 4 out of 4 in 3a18

Go back to Iron Binding Sites List in 3a18
Iron binding site 4 out of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Butyraldoxime (Soaked Crystal)


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 Butyraldoxime (Soaked Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe354

b:9.3
occ:1.00
FE D:HEM354 0.0 9.3 1.0
NC D:HEM354 2.0 7.5 1.0
ND D:HEM354 2.0 7.1 1.0
NB D:HEM354 2.1 8.2 1.0
NA D:HEM354 2.1 8.5 1.0
NE2 D:HIS299 2.1 10.6 1.0
N1 D:BXO355 2.2 12.5 1.0
C1C D:HEM354 3.0 8.6 1.0
C4C D:HEM354 3.0 7.0 1.0
C1D D:HEM354 3.0 6.4 1.0
C1 D:BXO355 3.0 14.7 1.0
C4B D:HEM354 3.0 8.3 1.0
CD2 D:HIS299 3.1 10.9 1.0
C4D D:HEM354 3.1 7.4 1.0
C1A D:HEM354 3.1 8.4 1.0
O1 D:BXO355 3.1 13.0 1.0
C1B D:HEM354 3.1 8.3 1.0
C4A D:HEM354 3.1 8.4 1.0
CE1 D:HIS299 3.1 9.5 1.0
CHD D:HEM354 3.4 7.1 1.0
CHC D:HEM354 3.4 7.8 1.0
CHA D:HEM354 3.4 7.4 1.0
CHB D:HEM354 3.5 9.0 1.0
CG D:HIS299 4.2 11.8 1.0
ND1 D:HIS299 4.2 9.9 1.0
C2C D:HEM354 4.2 7.9 1.0
C3C D:HEM354 4.2 7.4 1.0
C2D D:HEM354 4.3 6.8 1.0
C3D D:HEM354 4.3 6.1 1.0
C3B D:HEM354 4.3 8.6 1.0
C2A D:HEM354 4.3 7.8 1.0
C2B D:HEM354 4.3 7.8 1.0
C3A D:HEM354 4.3 8.4 1.0
C2 D:BXO355 4.5 15.7 1.0
OG D:SER219 4.8 8.7 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 Aug 4 06:38:44 2024

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