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Iron in PDB 1pby: Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution

Enzymatic activity of Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution

All present enzymatic activity of Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution:
1.4.99.3;

Protein crystallography data

The structure of Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution, PDB code: 1pby was solved by S.Datta, T.Ikeda, K.Kano, F.S.Mathews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.42 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.237, 99.237, 213.056, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.4

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution (pdb code 1pby). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution, PDB code: 1pby:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1pby

Go back to Iron Binding Sites List in 1pby
Iron binding site 1 out of 2 in the Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe991

b:14.8
occ:1.00
 FE A:HEM991 0.0 14.8 1.0
ND A:HEM991 2.0 14.7 1.0
NC A:HEM991 2.0 15.6 1.0
NB A:HEM991 2.0 14.2 1.0
NA A:HEM991 2.0 14.0 1.0
NE2 A:HIS15 2.1 15.5 1.0
SD A:MET43 2.4 14.5 1.0
C4D A:HEM991 3.0 14.7 1.0
C1A A:HEM991 3.0 14.2 1.0
C1C A:HEM991 3.0 16.4 1.0
C1D A:HEM991 3.0 15.4 1.0
C1B A:HEM991 3.0 14.3 1.0
C4C A:HEM991 3.1 15.9 1.0
C4A A:HEM991 3.1 14.2 1.0
C4B A:HEM991 3.1 15.5 1.0
CE1 A:HIS15 3.1 16.1 1.0
CD2 A:HIS15 3.1 17.4 1.0
CHA A:HEM991 3.4 13.7 1.0
CHD A:HEM991 3.4 15.7 1.0
CHB A:HEM991 3.4 14.4 1.0
CHC A:HEM991 3.4 15.3 1.0
CG A:MET43 3.5 14.5 1.0
CE A:MET43 3.6 14.8 1.0
CG A:HIS15 4.2 17.4 1.0
C3D A:HEM991 4.3 14.9 1.0
C2D A:HEM991 4.3 15.2 1.0
C2A A:HEM991 4.3 14.1 1.0
C3A A:HEM991 4.3 14.8 1.0
C3B A:HEM991 4.3 15.2 1.0
C2B A:HEM991 4.3 14.9 1.0
C2C A:HEM991 4.3 17.3 1.0
C3C A:HEM991 4.3 17.4 1.0
ND1 A:HIS15 4.3 17.4 1.0
CB A:MET43 4.6 13.6 1.0
CG2 B:THR108 4.9 18.7 1.0

Iron binding site 2 out of 2 in 1pby

Go back to Iron Binding Sites List in 1pby
Iron binding site 2 out of 2 in the Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe992

b:11.1
occ:1.00
 FE A:HEM992 0.0 11.1 1.0
ND A:HEM992 2.0 11.4 1.0
NC A:HEM992 2.0 10.6 1.0
NB A:HEM992 2.0 12.0 1.0
NE2 A:HIS126 2.0 12.5 1.0
NA A:HEM992 2.0 10.7 1.0
NE2 A:HIS104 2.1 10.8 1.0
C1C A:HEM992 3.0 11.7 1.0
C4D A:HEM992 3.0 10.9 1.0
C1D A:HEM992 3.0 11.1 1.0
C1A A:HEM992 3.1 11.6 1.0
C1B A:HEM992 3.1 12.2 1.0
CD2 A:HIS126 3.1 13.0 1.0
C4C A:HEM992 3.1 11.5 1.0
C4B A:HEM992 3.1 12.2 1.0
CD2 A:HIS104 3.1 11.4 1.0
C4A A:HEM992 3.1 11.7 1.0
CE1 A:HIS126 3.1 13.4 1.0
CE1 A:HIS104 3.1 10.2 1.0
CHD A:HEM992 3.4 10.5 1.0
CHA A:HEM992 3.4 11.2 1.0
CHC A:HEM992 3.4 11.5 1.0
CHB A:HEM992 3.4 11.8 1.0
CG A:HIS126 4.1 12.7 1.0
CG A:HIS104 4.1 11.0 1.0
C2D A:HEM992 4.3 11.3 1.0
C3D A:HEM992 4.3 11.9 1.0
ND1 A:HIS126 4.3 13.4 1.0
C3B A:HEM992 4.3 12.8 1.0
C2C A:HEM992 4.3 11.0 1.0
C3C A:HEM992 4.3 10.5 1.0
C2B A:HEM992 4.3 12.8 1.0
C2A A:HEM992 4.3 11.8 1.0
C3A A:HEM992 4.3 11.0 1.0
ND1 A:HIS104 4.3 12.3 1.0
O A:HOH1996 4.7 11.1 1.0

Reference:

S.Datta, T.Ikeda, K.Kano, F.S.Mathews. Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase From Paracoccus Denitrificans at 1.7 A Resolution. Acta Crystallogr.,Sect.D V. 59 1551 2003.
ISSN: ISSN 0907-4449
PubMed: 12925784
DOI: 10.1107/S090744490301429X
Page generated: Wed Jul 16 19:33:15 2025

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