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Iron in PDB 7cup: Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440

Enzymatic activity of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440

All present enzymatic activity of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440:
1.13.11.9;

Protein crystallography data

The structure of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440, PDB code: 7cup was solved by G.Q.Liu, H.Z.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.41 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.961, 143.750, 118.690, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.3

Iron Binding Sites:

The binding sites of Iron atom in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 (pdb code 7cup). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440, PDB code: 7cup:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7cup

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Iron binding site 1 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:43.7
occ:1.00
 NE2 A:HIS318 2.2 35.4 1.0
NE2 A:HIS265 2.2 40.2 1.0
OD1 A:ASP320 2.3 30.1 1.0
OG A:SER302 2.3 36.5 1.0
O A:HOH632 2.3 30.9 1.0
O A:HOH631 2.4 38.0 1.0
CB A:SER302 2.8 29.6 1.0
CD2 A:HIS265 2.9 36.5 1.0
CD2 A:HIS318 3.2 32.4 1.0
CE1 A:HIS318 3.2 34.4 1.0
CG A:ASP320 3.2 30.0 1.0
CE1 A:HIS265 3.3 40.1 1.0
OD2 A:ASP320 3.5 30.1 1.0
CG A:HIS265 4.1 36.0 1.0
O A:LEU319 4.1 25.4 1.0
CA A:SER302 4.2 30.2 1.0
O A:HOH550 4.2 31.2 1.0
ND1 A:HIS265 4.2 42.9 1.0
ND1 A:HIS318 4.3 34.9 1.0
CG A:HIS318 4.3 32.9 1.0
CB A:ASP320 4.6 25.1 1.0
O A:HOH629 4.6 38.0 1.0
C A:LEU319 4.8 26.4 1.0
CA A:ASP320 4.8 23.9 1.0

Iron binding site 2 out of 6 in 7cup

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Iron binding site 2 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:39.0
occ:1.00
 O B:HOH655 2.1 28.4 1.0
NE2 B:HIS318 2.2 34.5 1.0
NE2 B:HIS265 2.2 37.4 1.0
O B:HOH625 2.3 30.1 1.0
OG B:SER302 2.4 34.0 1.0
OD1 B:ASP320 2.5 27.2 1.0
CB B:SER302 2.9 25.6 1.0
CD2 B:HIS265 3.0 34.5 1.0
CD2 B:HIS318 3.1 30.9 1.0
CE1 B:HIS318 3.2 33.4 1.0
CE1 B:HIS265 3.2 35.9 1.0
CG B:ASP320 3.4 28.5 1.0
OD2 B:ASP320 3.7 32.1 1.0
O B:HOH557 3.9 28.2 1.0
CG B:HIS265 4.1 32.7 1.0
ND1 B:HIS265 4.2 38.7 1.0
O B:LEU319 4.2 23.2 1.0
O B:HOH701 4.3 48.5 1.0
CG B:HIS318 4.3 33.2 1.0
ND1 B:HIS318 4.3 35.8 1.0
CA B:SER302 4.3 25.9 1.0
O B:HOH721 4.4 51.1 1.0
OG B:SER264 4.7 35.5 1.0
CB B:ASP320 4.8 23.7 1.0
C B:LEU319 4.9 22.8 1.0

Iron binding site 3 out of 6 in 7cup

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Iron binding site 3 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:39.6
occ:1.00
 NE2 C:HIS265 2.1 34.2 1.0
O C:HOH528 2.2 28.9 1.0
OD1 C:ASP320 2.2 28.9 1.0
NE2 C:HIS318 2.2 30.4 1.0
OG C:SER302 2.2 32.1 1.0
O C:HOH530 2.2 36.5 1.0
CB C:SER302 2.7 24.3 1.0
CD2 C:HIS265 2.9 31.1 1.0
CE1 C:HIS265 3.1 30.5 1.0
CG C:ASP320 3.2 25.2 1.0
CD2 C:HIS318 3.2 32.8 1.0
CE1 C:HIS318 3.2 33.2 1.0
OD2 C:ASP320 3.5 29.8 1.0
O C:LEU319 4.0 23.0 1.0
CG C:HIS265 4.0 30.1 1.0
ND1 C:HIS265 4.1 33.4 1.0
O C:HOH554 4.1 30.5 1.0
CA C:SER302 4.1 22.7 1.0
ND1 C:HIS318 4.3 34.9 1.0
CG C:HIS318 4.3 31.7 1.0
OG C:SER264 4.4 26.9 1.0
CB C:ASP320 4.5 24.4 1.0
C C:LEU319 4.7 23.2 1.0
CA C:ASP320 4.7 21.9 1.0
C C:SER302 4.9 21.1 1.0
N C:ASP320 5.0 20.8 1.0

Iron binding site 4 out of 6 in 7cup

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Iron binding site 4 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:36.5
occ:1.00
 NE2 D:HIS318 2.1 30.2 1.0
OG D:SER302 2.2 28.8 1.0
O D:HOH541 2.2 30.6 1.0
OD1 D:ASP320 2.2 26.4 1.0
O D:HOH528 2.2 26.3 1.0
NE2 D:HIS265 2.3 28.0 1.0
CB D:SER302 2.8 21.6 1.0
CE1 D:HIS318 3.0 32.6 1.0
CD2 D:HIS318 3.1 28.2 1.0
CG D:ASP320 3.1 24.8 1.0
CD2 D:HIS265 3.2 28.9 1.0
CE1 D:HIS265 3.3 29.3 1.0
OD2 D:ASP320 3.4 30.9 1.0
O D:LEU319 4.0 18.5 1.0
ND1 D:HIS318 4.1 35.7 1.0
O D:HOH602 4.1 30.5 1.0
CA D:SER302 4.2 20.8 1.0
CG D:HIS318 4.2 29.6 1.0
CG D:HIS265 4.3 27.1 1.0
ND1 D:HIS265 4.3 29.1 1.0
OG D:SER264 4.4 24.2 1.0
CB D:ASP320 4.5 21.9 1.0
C D:LEU319 4.6 19.6 1.0
CA D:ASP320 4.7 19.1 1.0
N D:ASP320 4.9 18.6 1.0

Iron binding site 5 out of 6 in 7cup

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Iron binding site 5 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:38.9
occ:1.00
 NE2 E:HIS318 2.0 37.9 1.0
O E:HOH539 2.2 24.3 1.0
OD1 E:ASP320 2.2 32.5 1.0
OG E:SER302 2.2 35.3 1.0
O E:HOH614 2.2 32.5 1.0
NE2 E:HIS265 2.4 40.9 1.0
CB E:SER302 2.9 25.8 1.0
CE1 E:HIS318 3.0 41.6 1.0
CD2 E:HIS318 3.0 37.0 1.0
CG E:ASP320 3.1 31.0 1.0
CD2 E:HIS265 3.2 40.2 1.0
OD2 E:ASP320 3.3 31.2 1.0
CE1 E:HIS265 3.4 39.2 1.0
O E:LEU319 3.8 25.7 1.0
O E:HOH544 3.9 31.3 1.0
ND1 E:HIS318 4.1 42.8 1.0
CG E:HIS318 4.1 35.3 1.0
CA E:SER302 4.2 26.2 1.0
CG E:HIS265 4.3 34.8 1.0
ND1 E:HIS265 4.3 37.8 1.0
CB E:ASP320 4.4 25.3 1.0
OG E:SER264 4.5 39.2 1.0
C E:LEU319 4.6 24.1 1.0
CA E:ASP320 4.7 25.2 1.0
N E:ASP320 4.9 22.4 1.0

Iron binding site 6 out of 6 in 7cup

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Iron binding site 6 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:44.2
occ:1.00
 NE2 F:HIS265 2.2 42.6 1.0
O F:HOH544 2.2 24.0 1.0
OG F:SER302 2.2 36.1 1.0
O F:HOH689 2.2 31.3 1.0
OD1 F:ASP320 2.3 30.6 1.0
NE2 F:HIS318 2.3 38.6 1.0
CB F:SER302 2.8 28.3 1.0
CD2 F:HIS265 3.0 41.8 1.0
CD2 F:HIS318 3.1 37.4 1.0
CG F:ASP320 3.2 28.4 1.0
CE1 F:HIS265 3.2 42.7 1.0
CE1 F:HIS318 3.4 43.3 1.0
OD2 F:ASP320 3.5 28.1 1.0
O F:LEU319 3.9 25.1 1.0
O F:HOH520 4.0 29.3 1.0
CG F:HIS265 4.1 37.3 1.0
CA F:SER302 4.2 27.8 1.0
ND1 F:HIS265 4.2 41.9 1.0
CG F:HIS318 4.3 36.2 1.0
OG F:SER264 4.4 37.3 1.0
ND1 F:HIS318 4.4 45.3 1.0
CB F:ASP320 4.5 25.1 1.0
C F:LEU319 4.7 23.9 1.0
CA F:ASP320 4.8 23.6 1.0
C F:SER302 5.0 27.8 1.0

Reference:

G.Q.Liu, H.Z.Tang. 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid Nat Commun 2020.
ISSN: ESSN 2041-1723
Page generated: Thu Aug 8 03:23:10 2024

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