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Iron in PDB 3zds: Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.

Enzymatic activity of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.

All present enzymatic activity of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.:
1.13.11.5;

Protein crystallography data

The structure of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen., PDB code: 3zds was solved by J.-H.Jeoung, M.Bommer, T.-Y.Lin, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.37 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 93.737, 93.857, 163.438, 87.62, 80.39, 68.29
R / Rfree (%) 20.3 / 25.2

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. (pdb code 3zds). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen., PDB code: 3zds:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3zds

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Iron binding site 1 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2000

b:11.0
occ:1.00
 NE2 A:HIS367 2.0 13.3 1.0
OE2 A:GLU337 2.2 14.2 1.0
O2 A:M8O2001 2.2 7.9 0.8
ND1 A:HIS331 2.2 14.4 1.0
O A:HOH3450 2.3 14.2 1.0
OE1 A:GLU337 2.3 11.8 1.0
CD A:GLU337 2.6 21.2 1.0
CE1 A:HIS367 3.0 12.8 1.0
C3 A:M8O2001 3.1 18.6 0.8
CD2 A:HIS367 3.1 14.6 1.0
CE1 A:HIS331 3.1 12.9 1.0
CG A:HIS331 3.3 13.0 1.0
CB A:HIS331 3.6 10.2 1.0
C1 A:M8O2001 3.9 20.3 0.8
O4 A:M8O2001 3.9 18.9 0.8
O5 A:M8O2001 4.0 30.9 0.8
CG A:GLU337 4.1 11.3 1.0
ND1 A:HIS367 4.2 13.6 1.0
CG A:HIS367 4.2 12.4 1.0
C5 A:M8O2001 4.2 25.9 0.8
NE2 A:HIS331 4.3 13.2 1.0
O A:HOH3458 4.3 4.5 0.6
O A:HOH3503 4.3 12.1 0.7
C7 A:M8O2001 4.4 18.1 0.8
CD2 A:HIS331 4.4 13.7 1.0
ND2 A:ASN333 4.4 10.6 1.0
C4 A:M8O2001 4.5 20.2 0.8
O1 A:M8O2001 4.6 20.1 0.8
C2 A:M8O2001 4.9 21.2 0.8
CB A:ASN333 4.9 10.6 1.0
CB A:GLU337 4.9 5.5 1.0

Iron binding site 2 out of 12 in 3zds

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Iron binding site 2 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2000

b:8.6
occ:0.80
 NE2 B:HIS367 2.0 13.3 1.0
OE2 B:GLU337 2.2 7.6 1.0
ND1 B:HIS331 2.2 8.3 1.0
O6' B:OMD2001 2.3 15.4 0.9
O B:HOH3421 2.3 13.3 0.8
OE1 B:GLU337 2.4 7.7 1.0
CD B:GLU337 2.6 21.3 1.0
CE1 B:HIS367 2.9 13.6 1.0
CE1 B:HIS331 3.1 8.8 1.0
CD2 B:HIS367 3.1 13.2 1.0
C6' B:OMD2001 3.3 15.6 0.9
CG B:HIS331 3.3 7.9 1.0
CB B:HIS331 3.7 6.3 1.0
C5' B:OMD2001 4.0 17.6 0.9
C1' B:OMD2001 4.0 16.8 0.9
ND1 B:HIS367 4.1 15.2 1.0
CG B:GLU337 4.1 10.4 1.0
CG B:HIS367 4.2 13.6 1.0
C2 B:OMD2001 4.2 19.9 0.9
O B:HOH3419 4.2 3.1 0.6
O B:HOH3430 4.2 9.4 0.6
NE2 B:HIS331 4.3 9.2 1.0
CD2 B:HIS331 4.4 9.9 1.0
ND2 B:ASN333 4.4 8.3 1.0
O B:HOH3429 4.7 5.3 0.6
O1 B:OMD2001 4.8 16.1 0.9
CB B:ASN333 4.8 6.2 1.0
C1 B:OMD2001 4.9 20.3 0.9
CE B:MET394 4.9 11.0 1.0

Iron binding site 3 out of 12 in 3zds

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Iron binding site 3 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2000

b:10.3
occ:1.00
 O6' C:HQ92001 2.2 10.2 0.8
ND1 C:HIS331 2.2 10.4 1.0
NE2 C:HIS367 2.3 9.1 1.0
OE2 C:GLU337 2.3 3.9 1.0
O1 C:OXY1999 2.3 7.9 0.8
OE1 C:GLU337 2.4 7.3 1.0
O2 C:OXY1999 2.5 14.6 0.8
CD C:GLU337 2.7 8.0 1.0
C6' C:HQ92001 3.0 17.0 0.8
CE1 C:HIS331 3.1 8.8 1.0
CD2 C:HIS367 3.2 9.8 1.0
CE1 C:HIS367 3.3 8.9 1.0
CG C:HIS331 3.3 8.5 1.0
CB C:HIS331 3.7 7.4 1.0
C5' C:HQ92001 3.9 16.8 0.8
C1' C:HQ92001 4.1 18.6 0.8
C2 C:HQ92001 4.2 18.5 0.8
CG C:GLU337 4.2 14.6 1.0
O C:HOH3414 4.3 8.3 0.6
NE2 C:HIS331 4.3 9.1 1.0
O C:HOH3412 4.3 7.8 1.0
CG C:HIS367 4.4 10.0 1.0
ND1 C:HIS367 4.4 10.7 1.0
CD2 C:HIS331 4.4 9.8 1.0
ND2 C:ASN333 4.5 11.1 1.0
O C:HOH3419 4.6 5.3 0.6
C1 C:HQ92001 4.8 18.0 0.8

Iron binding site 4 out of 12 in 3zds

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Iron binding site 4 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe2000

b:11.5
occ:1.00
 NE2 D:HIS367 2.0 8.7 1.0
OE2 D:GLU337 2.2 9.9 1.0
ND1 D:HIS331 2.2 11.3 1.0
O6' D:OMD2001 2.2 13.7 0.9
O D:HOH3440 2.3 7.4 1.0
OE1 D:GLU337 2.4 11.7 1.0
CD D:GLU337 2.6 6.3 1.0
CE1 D:HIS367 3.0 8.9 1.0
CD2 D:HIS367 3.0 9.7 1.0
CE1 D:HIS331 3.1 10.6 1.0
C6' D:OMD2001 3.3 19.3 0.9
CG D:HIS331 3.3 10.2 1.0
CB D:HIS331 3.7 7.9 1.0
C5' D:OMD2001 3.9 19.5 0.9
CG D:GLU337 4.1 10.4 1.0
CG D:HIS367 4.2 9.3 1.0
ND1 D:HIS367 4.2 9.1 1.0
C1' D:OMD2001 4.2 20.4 0.9
O D:HOH3438 4.2 6.5 0.7
NE2 D:HIS331 4.3 11.2 1.0
C2 D:OMD2001 4.3 17.4 0.9
CD2 D:HIS331 4.4 12.6 1.0
O1 D:OMD2001 4.5 16.3 0.9
O D:HOH3448 4.5 8.4 1.0
O D:HOH3449 4.5 9.2 0.6
ND2 D:ASN333 4.5 6.2 1.0
C1 D:OMD2001 4.7 19.5 0.9
CB D:ASN333 4.9 7.2 1.0
CB D:GLU337 5.0 6.3 1.0

Iron binding site 5 out of 12 in 3zds

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Iron binding site 5 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe2000

b:12.8
occ:1.00
 O6' E:OMD2001 2.1 12.3 0.8
NE2 E:HIS367 2.1 11.3 1.0
OE2 E:GLU337 2.2 7.1 1.0
ND1 E:HIS331 2.2 8.3 1.0
O E:HOH3390 2.2 9.8 1.0
OE1 E:GLU337 2.4 12.8 1.0
CD E:GLU337 2.6 14.8 1.0
CE1 E:HIS331 3.1 7.5 1.0
CE1 E:HIS367 3.1 11.0 1.0
C6' E:OMD2001 3.1 18.3 0.8
CD2 E:HIS367 3.2 11.8 1.0
CG E:HIS331 3.3 6.8 1.0
CB E:HIS331 3.8 5.7 1.0
C5' E:OMD2001 3.9 18.1 0.8
C1' E:OMD2001 4.0 19.1 0.8
CG E:GLU337 4.1 14.7 1.0
C2 E:OMD2001 4.1 17.7 0.8
O E:HOH3400 4.2 10.2 0.7
ND1 E:HIS367 4.2 11.2 1.0
NE2 E:HIS331 4.3 8.0 1.0
O E:HOH3387 4.3 10.2 1.0
CG E:HIS367 4.3 11.1 1.0
CD2 E:HIS331 4.4 7.6 1.0
O E:HOH3399 4.5 8.0 0.8
ND2 E:ASN333 4.6 16.2 1.0
O1 E:OMD2001 4.8 14.0 0.8
C1 E:OMD2001 4.9 14.9 0.8
CB E:ASN333 5.0 11.0 1.0

Iron binding site 6 out of 12 in 3zds

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Iron binding site 6 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe2000

b:13.0
occ:1.00
 NE2 F:HIS367 2.1 14.2 1.0
ND1 F:HIS331 2.2 11.3 1.0
OE2 F:GLU337 2.3 11.5 1.0
O2 F:HMQ2001 2.3 13.1 0.8
O7 F:HMQ2001 2.4 11.6 0.8
OE1 F:GLU337 2.5 17.5 1.0
O6 F:HMQ2001 2.6 18.2 0.8
CD F:GLU337 2.7 15.7 1.0
C2 F:HMQ2001 2.9 16.6 0.8
CD2 F:HIS367 3.0 15.5 1.0
CE1 F:HIS367 3.1 14.1 1.0
CE1 F:HIS331 3.1 9.1 1.0
CG F:HIS331 3.3 10.0 1.0
CB F:HIS331 3.7 7.4 1.0
C3 F:HMQ2001 3.7 17.9 0.8
O F:HOH3397 4.1 9.5 1.0
C1 F:HMQ2001 4.1 16.1 0.8
CG F:HIS367 4.2 14.4 1.0
CG F:GLU337 4.2 13.3 1.0
ND1 F:HIS367 4.2 15.7 1.0
NE2 F:HIS331 4.3 9.7 1.0
C7 F:HMQ2001 4.3 13.4 0.8
CD2 F:HIS331 4.4 10.8 1.0
O F:HOH3406 4.5 10.5 0.7
O F:HOH3405 4.5 4.4 0.6
ND2 F:ASN333 4.7 11.3 1.0
OD1 F:HMQ2001 4.9 14.6 0.8
CB F:ASN333 4.9 6.8 1.0
C4 F:HMQ2001 5.0 23.1 0.8

Iron binding site 7 out of 12 in 3zds

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Iron binding site 7 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe2000

b:10.5
occ:1.00
 NE2 G:HIS367 2.1 9.5 1.0
O G:HOH3362 2.1 6.3 0.7
ND1 G:HIS331 2.2 10.3 1.0
OE2 G:GLU337 2.2 5.2 1.0
O6' G:OMD2001 2.3 18.1 1.0
OE1 G:GLU337 2.5 12.5 1.0
CD G:GLU337 2.7 11.4 1.0
CE1 G:HIS331 3.1 9.9 1.0
CE1 G:HIS367 3.1 9.8 1.0
CD2 G:HIS367 3.1 11.6 1.0
C6' G:OMD2001 3.2 17.5 1.0
CG G:HIS331 3.3 8.8 1.0
CB G:HIS331 3.8 6.3 1.0
C5' G:OMD2001 4.1 18.5 1.0
C1' G:OMD2001 4.1 19.2 1.0
C2 G:OMD2001 4.2 16.2 1.0
CG G:GLU337 4.2 17.3 1.0
O G:HOH3361 4.2 3.2 0.6
ND1 G:HIS367 4.3 10.6 1.0
CG G:HIS367 4.3 9.9 1.0
NE2 G:HIS331 4.3 10.1 1.0
CD2 G:HIS331 4.4 9.9 1.0
O G:HOH3369 4.4 13.2 0.7
ND2 G:ASN333 4.5 8.7 1.0
O G:HOH3368 4.5 6.7 0.6
O1 G:OMD2001 4.6 23.1 1.0
C1 G:OMD2001 4.7 19.2 1.0
CB G:ASN333 4.8 9.0 1.0

Iron binding site 8 out of 12 in 3zds

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Iron binding site 8 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe2000

b:14.8
occ:1.00
 O6' H:OMD2001 2.0 20.1 0.8
ND1 H:HIS331 2.1 14.2 1.0
OE2 H:GLU337 2.2 15.1 1.0
NE2 H:HIS367 2.2 17.0 1.0
OE1 H:GLU337 2.3 13.5 1.0
O H:HOH3386 2.4 17.0 1.0
CD H:GLU337 2.6 13.0 1.0
C6' H:OMD2001 3.0 21.8 0.8
CE1 H:HIS331 3.0 13.0 1.0
CD2 H:HIS367 3.1 17.6 1.0
CG H:HIS331 3.2 12.5 1.0
CE1 H:HIS367 3.3 16.7 1.0
CB H:HIS331 3.6 10.7 1.0
C5' H:OMD2001 3.8 20.3 0.8
C1' H:OMD2001 4.0 22.4 0.8
O H:HOH3384 4.1 6.8 0.6
CG H:GLU337 4.1 22.6 1.0
NE2 H:HIS331 4.2 13.2 1.0
C2 H:OMD2001 4.3 22.7 0.8
CG H:HIS367 4.3 16.4 1.0
CD2 H:HIS331 4.3 14.4 1.0
O H:HOH3430 4.4 15.9 0.7
ND1 H:HIS367 4.4 17.5 1.0
O H:HOH3395 4.5 9.3 0.7
ND2 H:ASN333 4.6 16.0 1.0
CB H:ASN333 4.9 10.7 1.0

Iron binding site 9 out of 12 in 3zds

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Iron binding site 9 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe2000

b:15.9
occ:1.00
 NE2 I:HIS367 2.1 13.2 1.0
OE2 I:GLU337 2.2 13.2 1.0
O6' I:OMD2001 2.2 12.8 0.8
ND1 I:HIS331 2.2 16.8 1.0
O I:HOH3318 2.2 13.7 1.0
OE1 I:GLU337 2.4 19.9 1.0
CD I:GLU337 2.6 18.5 1.0
CE1 I:HIS367 3.1 12.8 1.0
CD2 I:HIS367 3.1 14.8 1.0
CE1 I:HIS331 3.1 15.6 1.0
C6' I:OMD2001 3.2 20.0 0.8
CG I:HIS331 3.3 16.1 1.0
CB I:HIS331 3.6 13.6 1.0
C5' I:OMD2001 4.1 22.6 0.8
C1' I:OMD2001 4.1 22.4 0.8
CG I:GLU337 4.1 19.9 1.0
C2 I:OMD2001 4.1 22.3 0.8
O I:HOH3323 4.2 15.1 0.8
ND1 I:HIS367 4.2 14.1 1.0
CG I:HIS367 4.3 13.8 1.0
NE2 I:HIS331 4.3 15.8 1.0
O I:HOH3316 4.4 4.7 0.7
CD2 I:HIS331 4.4 17.0 1.0
ND2 I:ASN333 4.6 13.0 1.0
O I:HOH3328 4.6 10.2 0.8
CB I:ASN333 4.8 15.1 1.0
C1 I:OMD2001 5.0 25.3 0.8

Iron binding site 10 out of 12 in 3zds

Go back to Iron Binding Sites List in 3zds
Iron binding site 10 out of 12 in the Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Homogentisate 1,2-Dioxygenase in Complex with Reaction Intermediates of Homogentisate with Oxygen. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe2000

b:13.7
occ:1.00
 NE2 J:HIS367 2.1 12.9 1.0
O6' J:OMD2001 2.1 15.3 0.8
OE2 J:GLU337 2.1 11.8 1.0
ND1 J:HIS331 2.2 14.9 1.0
OE1 J:GLU337 2.4 14.2 1.0
O J:HOH3402 2.4 11.4 0.8
CD J:GLU337 2.6 16.5 1.0
CD2 J:HIS367 3.0 14.8 1.0
C6' J:OMD2001 3.0 16.0 0.8
CE1 J:HIS331 3.1 15.0 1.0
CE1 J:HIS367 3.1 12.2 1.0
CG J:HIS331 3.3 13.8 1.0
CB J:HIS331 3.7 10.9 1.0
C5' J:OMD2001 3.8 16.3 0.8
C1' J:OMD2001 3.9 16.0 0.8
C2 J:OMD2001 4.1 15.5 0.8
CG J:GLU337 4.1 10.9 1.0
CG J:HIS367 4.2 12.8 1.0
ND1 J:HIS367 4.2 13.5 1.0
NE2 J:HIS331 4.3 15.7 1.0
O J:HOH3401 4.3 9.3 0.7
CD2 J:HIS331 4.4 16.3 1.0
O J:HOH3410 4.4 3.8 0.6
O J:HOH3455 4.5 23.3 1.0
ND2 J:ASN333 4.6 7.3 1.0
C1 J:OMD2001 4.8 18.4 0.8
O1 J:OMD2001 4.9 17.9 0.8
CB J:ASN333 4.9 8.2 1.0

Reference:

J.-H.Jeoung, M.Bommer, T.-Y.Lin, H.Dobbek. Visualizing the Substrate-, Superoxo-, Alkylperoxo- and Product-Bound States at the Non-Heme Fe(II) Site of Homogentisate Dioxygenase Proc.Natl.Acad.Sci.Usa V. 110 12625 2013.
ISSN: ISSN 0027-8424
PubMed: 23858455
DOI: 10.1073/PNAS.1302144110
Page generated: Sun Aug 4 23:00:09 2024

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