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Iron in PDB 7d9j: Spdh Spermidine Dehydrogenase Y443A Mutant

Enzymatic activity of Spdh Spermidine Dehydrogenase Y443A Mutant

All present enzymatic activity of Spdh Spermidine Dehydrogenase Y443A Mutant:
1.5.99.6;

Protein crystallography data

The structure of Spdh Spermidine Dehydrogenase Y443A Mutant, PDB code: 7d9j was solved by S.Che, Q.Zhang, M.Bartlam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.96 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.051, 85.501, 101.109, 90, 98.46, 90
R / Rfree (%) 14.7 / 20.3

Iron Binding Sites:

The binding sites of Iron atom in the Spdh Spermidine Dehydrogenase Y443A Mutant (pdb code 7d9j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Spdh Spermidine Dehydrogenase Y443A Mutant, PDB code: 7d9j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 7d9j

Go back to Iron Binding Sites List in 7d9j
Iron binding site 1 out of 2 in the Spdh Spermidine Dehydrogenase Y443A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Spdh Spermidine Dehydrogenase Y443A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:25.9
occ:1.00
FE A:HEM702 0.0 25.9 1.0
NC A:HEM702 2.0 25.4 1.0
ND A:HEM702 2.0 26.5 1.0
NB A:HEM702 2.0 26.9 1.0
NA A:HEM702 2.1 24.1 1.0
NE2 A:HIS54 2.2 26.4 1.0
NE2 A:HIS562 2.4 22.1 1.0
C4C A:HEM702 2.9 24.2 1.0
C1D A:HEM702 3.0 23.1 1.0
C4B A:HEM702 3.0 26.0 1.0
C1C A:HEM702 3.0 25.5 1.0
C4D A:HEM702 3.1 23.2 1.0
CD2 A:HIS562 3.1 21.9 1.0
C1A A:HEM702 3.1 25.8 1.0
C1B A:HEM702 3.1 27.0 1.0
C4A A:HEM702 3.1 26.4 1.0
CD2 A:HIS54 3.2 22.6 1.0
CE1 A:HIS54 3.2 26.8 1.0
CHD A:HEM702 3.3 20.6 1.0
CHC A:HEM702 3.4 23.1 1.0
CE1 A:HIS562 3.5 24.7 1.0
CHA A:HEM702 3.5 24.3 1.0
CHB A:HEM702 3.5 27.2 1.0
C3C A:HEM702 4.2 25.9 1.0
C2D A:HEM702 4.2 22.1 1.0
C3D A:HEM702 4.2 23.9 1.0
C3B A:HEM702 4.2 27.4 1.0
C2C A:HEM702 4.2 25.2 1.0
C2B A:HEM702 4.3 25.0 1.0
ND1 A:HIS54 4.3 27.9 1.0
CG A:HIS562 4.3 24.7 1.0
C2A A:HEM702 4.3 25.2 1.0
C3A A:HEM702 4.3 23.0 1.0
CG A:HIS54 4.4 26.0 1.0
ND1 A:HIS562 4.5 23.3 1.0
CD A:ARG518 4.6 23.2 1.0
CZ2 A:TRP58 4.9 29.1 1.0
NE1 A:TRP58 4.9 28.1 1.0

Iron binding site 2 out of 2 in 7d9j

Go back to Iron Binding Sites List in 7d9j
Iron binding site 2 out of 2 in the Spdh Spermidine Dehydrogenase Y443A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Spdh Spermidine Dehydrogenase Y443A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:25.0
occ:1.00
FE B:HEM702 0.0 25.0 1.0
NB B:HEM702 2.0 28.6 1.0
ND B:HEM702 2.0 27.9 1.0
NC B:HEM702 2.1 31.7 1.0
NA B:HEM702 2.1 26.9 1.0
NE2 B:HIS54 2.3 27.1 1.0
NE2 B:HIS562 2.3 24.6 1.0
C4B B:HEM702 3.0 29.7 1.0
C1B B:HEM702 3.0 27.1 1.0
C1D B:HEM702 3.0 26.7 1.0
C4D B:HEM702 3.0 28.4 1.0
C4C B:HEM702 3.1 30.4 1.0
C1C B:HEM702 3.1 29.9 1.0
C1A B:HEM702 3.1 28.8 1.0
C4A B:HEM702 3.1 29.5 1.0
CD2 B:HIS54 3.1 26.9 1.0
CD2 B:HIS562 3.1 24.5 1.0
CE1 B:HIS54 3.3 25.8 1.0
CHC B:HEM702 3.4 27.7 1.0
CHD B:HEM702 3.4 25.5 1.0
CE1 B:HIS562 3.4 24.6 1.0
CHA B:HEM702 3.4 28.9 1.0
CHB B:HEM702 3.5 26.9 1.0
C3B B:HEM702 4.2 29.0 1.0
C2B B:HEM702 4.2 25.4 1.0
C2D B:HEM702 4.2 27.3 1.0
C3D B:HEM702 4.2 28.9 1.0
C3C B:HEM702 4.3 26.7 1.0
CG B:HIS54 4.3 24.9 1.0
C2C B:HEM702 4.3 28.7 1.0
C2A B:HEM702 4.4 28.7 1.0
C3A B:HEM702 4.4 29.2 1.0
CG B:HIS562 4.4 22.9 1.0
ND1 B:HIS54 4.4 31.7 1.0
CD B:ARG518 4.5 24.6 1.0
ND1 B:HIS562 4.5 25.4 1.0
NE1 B:TRP58 4.7 34.7 1.0
CZ2 B:TRP58 5.0 31.9 1.0

Reference:

S.Che, Y.Liang, Y.Chen, W.Wu, R.Liu, Q.Zhang, M.Bartlam. Structure of Pseudomonas Aeruginosa Spermidine Dehydrogenase: A Polyamine Oxidase with A Novel Heme-Binding Fold. Febs J. 2021.
ISSN: ISSN 1742-464X
PubMed: 34741591
DOI: 10.1111/FEBS.16264
Page generated: Thu Aug 8 03:44:33 2024

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