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

Go back to Iron Binding Sites List in 7cn3
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

Go back to Iron Binding Sites List in 7cn3
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

Go back to Iron Binding Sites List in 7cn3
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 Dec 17 11:41:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy