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Iron in PDB 7cn3: 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid

Enzymatic activity of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid

All present enzymatic activity of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid:
1.13.11.9;

Protein crystallography data

The structure of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid, PDB code: 7cn3 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) 27.59 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.673, 145.510, 118.976, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.8

Iron Binding Sites:

The binding sites of Iron atom in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid (pdb code 7cn3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid, PDB code: 7cn3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7cn3

Go back to Iron Binding Sites List in 7cn3
Iron binding site 1 out of 6 in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:36.8
occ:1.00
 OD1 A:ASP320 2.3 32.5 1.0
NE2 A:HIS265 2.3 30.9 1.0
NE2 A:HIS318 2.3 44.6 1.0
O A:HOH676 2.3 32.6 1.0
O A:HOH619 2.4 30.6 1.0
OG A:SER302 2.4 33.2 1.0
CD2 A:HIS265 3.1 25.9 1.0
CG A:ASP320 3.1 34.6 1.0
CE1 A:HIS318 3.2 41.1 1.0
CB A:SER302 3.3 29.2 1.0
CE1 A:HIS265 3.3 29.4 1.0
CD2 A:HIS318 3.3 44.2 1.0
OD2 A:ASP320 3.3 36.3 1.0
O A:LEU319 4.2 32.1 1.0
O A:HOH620 4.2 29.7 1.0
CG A:HIS265 4.3 35.0 1.0
ND1 A:HIS318 4.3 44.3 1.0
ND1 A:HIS265 4.3 33.8 1.0
CG A:HIS318 4.4 43.8 1.0
CB A:ASP320 4.5 31.8 1.0
OB2 A:D6O502 4.6 72.3 1.0
CA A:SER302 4.6 32.1 1.0
OG A:SER264 4.7 36.8 1.0
C A:LEU319 4.8 30.0 1.0
CA A:ASP320 4.8 24.8 1.0
O A:HOH755 4.9 47.7 1.0

Iron binding site 2 out of 6 in 7cn3

Go back to Iron Binding Sites List in 7cn3
Iron binding site 2 out of 6 in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:45.0
occ:1.00
 OD1 B:ASP320 2.3 36.2 1.0
O B:HOH645 2.3 33.7 1.0
OG B:SER302 2.3 38.3 1.0
NE2 B:HIS318 2.3 46.7 1.0
NE2 B:HIS265 2.3 34.6 1.0
O B:HOH643 2.4 33.1 1.0
CD2 B:HIS265 2.9 31.5 1.0
CB B:SER302 3.0 37.6 1.0
CE1 B:HIS318 3.2 45.5 1.0
CG B:ASP320 3.2 36.5 1.0
CD2 B:HIS318 3.3 47.1 1.0
CE1 B:HIS265 3.4 35.5 1.0
OD2 B:ASP320 3.4 43.6 1.0
O B:HOH649 4.1 40.1 1.0
CG B:HIS265 4.1 47.0 1.0
O B:LEU319 4.2 30.5 1.0
ND1 B:HIS318 4.3 48.0 1.0
ND1 B:HIS265 4.3 41.4 1.0
OG B:SER264 4.4 42.5 1.0
CG B:HIS318 4.4 44.7 1.0
CA B:SER302 4.4 35.3 1.0
CB B:ASP320 4.6 30.9 1.0
OB B:D6O502 4.8 68.0 1.0
O B:HOH706 4.8 48.1 1.0
C B:LEU319 4.8 34.2 1.0
CA B:ASP320 4.9 28.6 1.0

Iron binding site 3 out of 6 in 7cn3

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Iron binding site 3 out of 6 in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:43.5
occ:1.00
 OG C:SER302 2.2 52.1 1.0
O C:HOH601 2.2 21.3 1.0
NE2 C:HIS318 2.3 41.8 1.0
O C:HOH602 2.3 45.1 1.0
NE2 C:HIS265 2.3 30.1 1.0
OD1 C:ASP320 2.3 40.2 1.0
CE1 C:HIS318 2.8 31.4 1.0
CD2 C:HIS265 2.9 25.1 1.0
CB C:SER302 2.9 25.1 1.0
CG C:ASP320 3.2 34.8 1.0
CE1 C:HIS265 3.4 31.5 1.0
OD2 C:ASP320 3.5 41.5 1.0
CD2 C:HIS318 3.5 38.8 1.0
OB C:G6C502 3.6 48.3 1.0
CG C:HIS265 4.1 29.7 1.0
ND1 C:HIS318 4.1 40.2 1.0
O C:LEU319 4.1 27.6 1.0
OG C:SER264 4.2 34.6 1.0
CA C:SER302 4.3 22.0 1.0
ND1 C:HIS265 4.3 32.3 1.0
CE1 C:HIS105 4.4 49.6 1.0
NE2 C:HIS105 4.4 46.3 1.0
CG C:HIS318 4.4 35.8 1.0
CB C:ASP320 4.5 20.2 1.0
CA C:ASP320 4.7 19.0 1.0
C C:LEU319 4.7 28.3 1.0
CG C:G6C502 4.8 46.8 1.0
N C:ASP320 5.0 21.3 1.0

Iron binding site 4 out of 6 in 7cn3

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Iron binding site 4 out of 6 in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:51.8
occ:1.00
 O D:HOH601 2.1 23.7 1.0
NE2 D:HIS318 2.3 39.7 1.0
O D:HOH606 2.3 46.1 1.0
NE2 D:HIS265 2.3 30.9 1.0
OG D:SER302 2.4 46.4 1.0
OD1 D:ASP320 2.5 31.0 1.0
CD2 D:HIS265 2.6 29.1 1.0
CE1 D:HIS318 2.9 39.8 1.0
CB D:SER302 3.1 31.8 1.0
OB D:G6C502 3.1 48.1 1.0
CD2 D:HIS318 3.5 37.4 1.0
CE1 D:HIS265 3.6 30.5 1.0
CG D:ASP320 3.6 33.6 1.0
CG D:HIS265 3.9 32.8 1.0
OD2 D:ASP320 4.0 32.6 1.0
ND1 D:HIS318 4.1 45.7 1.0
CE1 D:HIS105 4.2 56.1 1.0
NE2 D:HIS105 4.3 52.8 1.0
OG D:SER264 4.3 34.1 1.0
ND1 D:HIS265 4.3 33.8 1.0
CG D:G6C502 4.3 47.1 1.0
O D:LEU319 4.4 31.6 1.0
CG D:HIS318 4.5 40.4 1.0
CA D:SER302 4.5 25.8 1.0
CB D:ASP320 4.8 30.5 1.0
CD1 D:G6C502 4.9 39.0 1.0
CA D:ASP320 5.0 27.6 1.0
C D:LEU319 5.0 30.6 1.0

Iron binding site 5 out of 6 in 7cn3

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Iron binding site 5 out of 6 in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:48.1
occ:1.00
 O E:HOH603 2.3 48.1 1.0
OD1 E:ASP320 2.3 39.7 1.0
OG E:SER302 2.3 55.8 1.0
O E:HOH601 2.3 24.0 1.0
NE2 E:HIS318 2.3 50.5 1.0
NE2 E:HIS265 2.4 40.7 1.0
CE1 E:HIS318 2.8 46.2 1.0
CB E:SER302 3.0 40.2 1.0
CD2 E:HIS265 3.0 35.7 1.0
CG E:ASP320 3.2 31.9 1.0
CE1 E:HIS265 3.4 37.6 1.0
OD2 E:ASP320 3.4 37.5 1.0
CD2 E:HIS318 3.6 51.5 1.0
ND1 E:HIS318 4.0 51.6 1.0
O E:LEU319 4.1 31.6 1.0
CG E:HIS265 4.1 39.3 1.0
OB E:G6C502 4.1 61.3 1.0
ND1 E:HIS265 4.3 43.1 1.0
CA E:SER302 4.4 30.5 1.0
CG E:HIS318 4.4 44.7 1.0
OG E:SER264 4.5 50.3 1.0
CB E:ASP320 4.5 28.2 1.0
CE1 E:HIS105 4.6 57.1 1.0
C E:LEU319 4.8 28.3 1.0
CA E:ASP320 4.8 24.6 1.0
NE2 E:HIS105 4.9 57.1 1.0

Iron binding site 6 out of 6 in 7cn3

Go back to Iron Binding Sites List in 7cn3
Iron binding site 6 out of 6 in the 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2,5-Dihydroxypridine Dioxygenase in Complex with 2,5-Dihydroxypridine and Product N-Formylmaleamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:48.6
occ:1.00
 O F:HOH608 2.3 23.9 1.0
O F:HOH607 2.3 43.8 1.0
OD1 F:ASP320 2.3 38.2 1.0
NE2 F:HIS318 2.3 46.1 1.0
NE2 F:HIS265 2.4 39.1 1.0
OG F:SER302 2.5 64.5 1.0
CE1 F:HIS318 2.9 45.0 1.0
CD2 F:HIS265 2.9 36.1 1.0
CB F:SER302 3.0 49.2 1.0
CG F:ASP320 3.2 35.2 1.0
OD2 F:ASP320 3.4 40.8 1.0
CE1 F:HIS265 3.5 37.2 1.0
CD2 F:HIS318 3.5 50.4 1.0
ND1 F:HIS318 4.1 48.7 1.0
CG F:HIS265 4.1 37.3 1.0
O F:LEU319 4.1 28.6 1.0
OB F:G6C502 4.3 68.1 1.0
OG F:SER264 4.3 47.2 1.0
ND1 F:HIS265 4.3 42.0 1.0
CG F:HIS318 4.4 43.4 1.0
CA F:SER302 4.4 37.1 1.0
CB F:ASP320 4.6 33.1 1.0
CE1 F:HIS105 4.6 62.6 1.0
NE2 F:HIS105 4.6 56.3 1.0
C F:LEU319 4.8 27.0 1.0
CA F:ASP320 4.9 30.9 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 03:05:02 2024

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