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Iron in PDB 7cnt: Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine

Enzymatic activity of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine

All present enzymatic activity of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine:
1.13.11.9;

Protein crystallography data

The structure of Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine, PDB code: 7cnt 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) 30.00 / 2.28
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.885, 125.916, 144.129, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26.7

Iron Binding Sites:

The binding sites of Iron atom in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine (pdb code 7cnt). 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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine, PDB code: 7cnt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7cnt

Go back to Iron Binding Sites List in 7cnt
Iron binding site 1 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine


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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:1.0
occ:1.00
 NE2 A:HIS318 2.0 0.4 1.0
OG A:SER302 2.3 76.6 1.0
OD1 A:ASP320 2.5 76.9 1.0
NE2 A:HIS265 2.6 0.5 1.0
CE1 A:HIS318 2.8 0.8 1.0
CD2 A:HIS318 3.1 0.6 1.0
O A:HOH636 3.1 76.6 1.0
CB A:SER302 3.1 59.1 1.0
CE1 A:HIS265 3.2 87.7 1.0
CG A:ASP320 3.4 61.0 1.0
CD2 A:HIS265 3.4 85.7 1.0
OD2 A:ASP320 3.6 73.1 1.0
ND1 A:HIS318 3.9 0.1 1.0
CG A:HIS318 4.1 95.0 1.0
O A:LEU319 4.2 60.0 1.0
ND1 A:HIS265 4.2 98.3 1.0
CG A:HIS265 4.3 86.7 1.0
CA A:SER302 4.4 50.0 1.0
CB A:ASP320 4.8 58.7 1.0
OG A:SER264 4.8 59.5 1.0
C A:LEU319 4.9 55.7 1.0

Iron binding site 2 out of 6 in 7cnt

Go back to Iron Binding Sites List in 7cnt
Iron binding site 2 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine


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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:0.3
occ:1.00
 NE2 B:HIS318 2.1 0.7 1.0
NE2 B:HIS265 2.5 0.1 1.0
CE1 B:HIS318 2.5 99.8 1.0
OD1 B:ASP320 2.6 76.4 1.0
OG B:SER302 3.1 86.4 1.0
CE1 B:HIS265 3.2 99.7 1.0
OD2 B:ASP320 3.3 83.2 1.0
CG B:ASP320 3.3 54.8 1.0
CD2 B:HIS318 3.4 90.7 1.0
CD2 B:HIS265 3.5 78.5 1.0
CB B:SER302 3.7 58.1 1.0
ND1 B:HIS318 3.8 98.3 1.0
CG B:HIS318 4.3 84.8 1.0
ND1 B:HIS265 4.3 86.5 1.0
CG B:HIS265 4.5 74.4 1.0
CB B:ASP320 4.8 53.4 1.0
O B:LEU319 4.9 57.5 1.0

Iron binding site 3 out of 6 in 7cnt

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Iron binding site 3 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine


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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:0.8
occ:1.00
 NE2 C:HIS318 2.1 0.7 1.0
NE2 C:HIS265 2.3 0.1 1.0
OD1 C:ASP320 2.5 77.3 1.0
OG C:SER302 2.7 76.6 1.0
CE1 C:HIS318 2.8 76.3 1.0
CE1 C:HIS265 3.1 82.7 1.0
CD2 C:HIS265 3.2 80.0 1.0
CD2 C:HIS318 3.2 85.3 1.0
CB C:SER302 3.4 64.4 1.0
CG C:ASP320 3.4 60.2 1.0
OD2 C:ASP320 3.6 72.6 1.0
O C:HOH608 3.9 67.5 1.0
ND1 C:HIS318 4.0 88.3 1.0
ND1 C:HIS265 4.1 82.5 1.0
O C:LEU319 4.2 55.0 1.0
CG C:HIS318 4.2 82.1 1.0
CG C:HIS265 4.2 78.7 1.0
OG C:SER264 4.7 88.5 1.0
CA C:SER302 4.8 64.3 1.0
CB C:ASP320 4.8 65.8 1.0

Iron binding site 4 out of 6 in 7cnt

Go back to Iron Binding Sites List in 7cnt
Iron binding site 4 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine


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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:93.5
occ:1.00
 NE2 D:HIS318 2.0 83.7 1.0
OD1 D:ASP320 2.3 94.9 1.0
NE2 D:HIS265 2.4 0.9 1.0
OG D:SER302 2.8 67.9 1.0
CE1 D:HIS318 2.8 74.1 1.0
CE1 D:HIS265 3.1 99.2 1.0
CG D:ASP320 3.1 63.9 1.0
CD2 D:HIS318 3.2 75.6 1.0
OD2 D:ASP320 3.3 75.4 1.0
CD2 D:HIS265 3.3 87.3 1.0
CB D:SER302 3.4 56.0 1.0
ND1 D:HIS318 4.0 86.0 1.0
O D:LEU319 4.1 60.1 1.0
ND1 D:HIS265 4.1 94.7 1.0
CG D:HIS318 4.2 74.1 1.0
CG D:HIS265 4.3 82.2 1.0
CB D:ASP320 4.6 67.4 1.0
CA D:SER302 4.7 55.3 1.0
OG D:SER264 4.8 95.2 1.0
C D:LEU319 4.8 57.4 1.0
CA D:ASP320 4.9 59.8 1.0

Iron binding site 5 out of 6 in 7cnt

Go back to Iron Binding Sites List in 7cnt
Iron binding site 5 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine


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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:89.8
occ:1.00
 NE2 E:HIS318 1.9 72.5 1.0
OD1 E:ASP320 2.4 76.2 1.0
NE2 E:HIS265 2.5 94.8 1.0
CE1 E:HIS318 2.6 72.4 1.0
O E:HOH619 2.7 75.2 1.0
OG E:SER302 2.8 67.1 1.0
OD2 E:ASP320 2.8 99.5 1.0
CG E:ASP320 2.9 77.3 1.0
CD2 E:HIS318 3.1 63.5 1.0
CD2 E:HIS265 3.3 83.0 1.0
CE1 E:HIS265 3.4 80.7 1.0
CB E:SER302 3.7 72.7 1.0
ND1 E:HIS318 3.8 80.7 1.0
CG E:HIS318 4.1 73.1 1.0
CB E:ASP320 4.4 68.1 1.0
CG E:HIS265 4.5 78.3 1.0
ND1 E:HIS265 4.5 83.8 1.0
O E:LEU319 4.6 64.5 1.0
O E:HOH604 4.7 62.3 1.0
OG E:SER264 4.7 80.9 1.0
CA E:SER302 4.9 71.0 1.0

Iron binding site 6 out of 6 in 7cnt

Go back to Iron Binding Sites List in 7cnt
Iron binding site 6 out of 6 in the Structure of 2,5-Dihydroxypridine Dioxygenase From Pseudomonas Putida KT2440 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine


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 in Complex with Product N-Formylmaleamic Acid Formed Via in Crystallo Reaction with 2,5-Dihydroxypridine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:72.9
occ:1.00
 NE2 F:HIS318 2.1 91.6 1.0
O F:HOH604 2.2 55.1 1.0
OD1 F:ASP320 2.3 63.0 1.0
NE2 F:HIS265 2.4 77.9 1.0
OG F:SER302 2.6 67.5 1.0
CE1 F:HIS318 2.7 85.1 1.0
OD2 F:ASP320 2.9 74.8 1.0
CG F:ASP320 2.9 70.7 1.0
CE1 F:HIS265 3.2 72.1 1.0
CD2 F:HIS318 3.2 65.3 1.0
CD2 F:HIS265 3.4 66.9 1.0
CB F:SER302 3.4 54.5 1.0
ND1 F:HIS318 3.9 84.4 1.0
CG F:HIS318 4.2 82.3 1.0
O F:LEU319 4.3 53.5 1.0
ND1 F:HIS265 4.3 90.0 1.0
CB F:ASP320 4.4 52.9 1.0
CG F:HIS265 4.4 71.2 1.0
CA F:SER302 4.8 60.1 1.0
CA F:ASP320 4.9 52.3 1.0
C F:LEU319 4.9 53.5 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 03:06:49 2024

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