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Iron in PDB 4aq2: Resting State of Homogentisate 1,2-Dioxygenase

Enzymatic activity of Resting State of Homogentisate 1,2-Dioxygenase

All present enzymatic activity of Resting State of Homogentisate 1,2-Dioxygenase:
1.13.11.5;

Protein crystallography data

The structure of Resting State of Homogentisate 1,2-Dioxygenase, PDB code: 4aq2 was solved by J.-H.Jeoung, T.-Y.Lin, M.Bommer, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.94 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 93.737, 93.901, 162.810, 87.46, 80.45, 68.33
R / Rfree (%) 19.3 / 25.7

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Resting State of Homogentisate 1,2-Dioxygenase (pdb code 4aq2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Resting State of Homogentisate 1,2-Dioxygenase, PDB code: 4aq2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4aq2

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Iron binding site 1 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:14.4
occ:1.00
 OE2 A:GLU337 2.0 11.5 1.0
O A:HOH2433 2.1 15.8 1.0
O A:HOH2432 2.2 12.0 1.0
NE2 A:HIS367 2.2 13.5 1.0
ND1 A:HIS331 2.2 14.1 1.0
OE1 A:GLU337 2.3 9.7 1.0
CD A:GLU337 2.5 11.5 1.0
CE1 A:HIS331 3.1 13.9 1.0
CD2 A:HIS367 3.2 14.3 1.0
CE1 A:HIS367 3.2 16.7 1.0
CG A:HIS331 3.4 16.2 1.0
CB A:HIS331 3.8 14.6 1.0
CG A:GLU337 4.0 13.9 1.0
O A:HOH2448 4.0 7.1 0.4
O A:HOH2443 4.0 19.2 1.0
NE2 A:HIS331 4.3 12.2 1.0
O A:HOH2442 4.3 15.3 1.0
ND1 A:HIS367 4.3 14.4 1.0
CG A:HIS367 4.3 12.0 1.0
O A:HOH2430 4.4 20.6 1.0
CD2 A:HIS331 4.4 14.3 1.0
ND2 A:ASN333 4.6 16.4 1.0
CB A:ASN333 4.7 13.5 1.0
CB A:GLU337 4.9 11.7 1.0
O A:HOH2448 5.0 6.0 0.6

Iron binding site 2 out of 12 in 4aq2

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Iron binding site 2 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe800

b:12.2
occ:1.00
 O B:HOH2426 2.1 18.6 1.0
O B:HOH2425 2.1 10.3 1.0
NE2 B:HIS367 2.2 18.1 1.0
OE2 B:GLU337 2.2 9.1 1.0
OE1 B:GLU337 2.3 9.0 1.0
ND1 B:HIS331 2.4 13.9 1.0
CD B:GLU337 2.5 11.3 1.0
CD2 B:HIS367 3.1 20.8 1.0
CE1 B:HIS367 3.2 13.4 1.0
CE1 B:HIS331 3.2 7.3 1.0
CG B:HIS331 3.4 10.0 1.0
CB B:HIS331 3.8 7.6 1.0
O B:HOH2236 3.9 19.9 1.0
O B:HOH2435 4.0 9.4 1.0
CG B:GLU337 4.1 10.6 1.0
ND1 B:HIS367 4.3 12.1 1.0
CG B:HIS367 4.3 12.4 1.0
O B:HOH2475 4.3 8.5 1.0
NE2 B:HIS331 4.4 12.7 1.0
O B:HOH2423 4.5 24.1 1.0
CD2 B:HIS331 4.5 10.2 1.0
ND2 B:ASN333 4.6 9.3 1.0
O B:HOH2238 4.8 21.5 1.0
CB B:ASN333 4.9 9.7 1.0
CB B:GLU337 4.9 9.8 1.0

Iron binding site 3 out of 12 in 4aq2

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Iron binding site 3 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe800

b:8.5
occ:1.00
 NE2 C:HIS367 2.2 2.0 1.0
OE1 C:GLU337 2.2 5.8 1.0
OE2 C:GLU337 2.2 2.8 1.0
O C:HOH2392 2.2 5.7 1.0
O C:HOH2391 2.3 10.1 1.0
ND1 C:HIS331 2.3 9.7 1.0
CD C:GLU337 2.5 4.9 1.0
CE1 C:HIS331 3.1 12.0 1.0
CD2 C:HIS367 3.2 8.8 1.0
CE1 C:HIS367 3.2 8.8 1.0
CG C:HIS331 3.4 12.0 1.0
O C:HOH2213 3.7 13.8 1.0
CB C:HIS331 3.7 11.0 1.0
CG C:GLU337 4.0 6.4 1.0
O C:HOH2399 4.2 12.7 1.0
ND1 C:HIS367 4.3 5.2 1.0
NE2 C:HIS331 4.3 12.5 1.0
CG C:HIS367 4.3 8.6 1.0
CD2 C:HIS331 4.4 7.8 1.0
O C:HOH2390 4.4 14.3 1.0
ND2 C:ASN333 4.5 7.9 1.0
O C:HOH2398 4.5 13.3 1.0
CB C:ASN333 4.8 6.1 1.0
CB C:GLU337 4.9 7.5 1.0

Iron binding site 4 out of 12 in 4aq2

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Iron binding site 4 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe800

b:9.7
occ:1.00
 ND1 D:HIS331 2.1 7.9 1.0
OE2 D:GLU337 2.2 9.1 1.0
O D:HOH2399 2.2 8.5 1.0
NE2 D:HIS367 2.2 11.5 1.0
OE1 D:GLU337 2.2 8.6 1.0
O D:HOH2400 2.3 11.6 1.0
CD D:GLU337 2.5 10.2 1.0
CE1 D:HIS331 2.9 13.2 1.0
CD2 D:HIS367 3.1 10.9 1.0
CG D:HIS331 3.2 6.2 1.0
CE1 D:HIS367 3.3 10.8 1.0
CB D:HIS331 3.7 7.5 1.0
O D:HOH2397 4.0 12.0 1.0
O D:HOH2234 4.0 17.1 1.0
CG D:GLU337 4.0 10.0 1.0
NE2 D:HIS331 4.1 7.7 1.0
CG D:HIS367 4.3 10.3 1.0
CD2 D:HIS331 4.3 14.9 1.0
ND1 D:HIS367 4.3 11.4 1.0
O D:HOH2438 4.4 12.1 1.0
O D:HOH2409 4.4 12.7 1.0
ND2 D:ASN333 4.5 10.0 1.0
CB D:ASN333 4.8 11.0 1.0
CB D:GLU337 4.9 10.2 1.0

Iron binding site 5 out of 12 in 4aq2

Go back to Iron Binding Sites List in 4aq2
Iron binding site 5 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe800

b:11.2
occ:1.00
 ND1 E:HIS331 2.0 10.2 1.0
O E:HOH2404 2.1 11.2 1.0
O E:HOH2403 2.2 7.5 1.0
NE2 E:HIS367 2.2 13.3 1.0
OE2 E:GLU337 2.3 14.0 1.0
OE1 E:GLU337 2.3 10.7 1.0
CD E:GLU337 2.6 10.1 1.0
CE1 E:HIS331 2.8 20.4 1.0
CD2 E:HIS367 3.1 12.4 1.0
CG E:HIS331 3.2 18.2 1.0
CE1 E:HIS367 3.3 10.4 1.0
CB E:HIS331 3.7 7.0 1.0
NE2 E:HIS331 4.0 12.1 1.0
CG E:GLU337 4.1 10.4 1.0
O E:HOH2406 4.2 10.1 1.0
CD2 E:HIS331 4.2 10.3 1.0
CG E:HIS367 4.3 9.1 1.0
ND1 E:HIS367 4.4 7.7 1.0
O E:HOH2402 4.4 8.6 1.0
O E:HOH2411 4.5 14.8 1.0
ND2 E:ASN333 4.5 6.0 1.0
CB E:ASN333 4.8 4.4 1.0

Iron binding site 6 out of 12 in 4aq2

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Iron binding site 6 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe800

b:10.7
occ:1.00
 O F:HOH2363 2.2 9.1 1.0
OE2 F:GLU337 2.2 10.3 1.0
NE2 F:HIS367 2.3 11.0 1.0
ND1 F:HIS331 2.3 9.7 1.0
O F:HOH2364 2.3 7.5 1.0
OE1 F:GLU337 2.4 11.2 1.0
CD F:GLU337 2.6 13.2 1.0
CD2 F:HIS367 3.1 10.7 1.0
CE1 F:HIS331 3.1 10.3 1.0
CG F:HIS331 3.3 8.0 1.0
CE1 F:HIS367 3.3 12.4 1.0
CB F:HIS331 3.7 3.9 1.0
O F:HOH2205 3.8 17.7 0.9
O F:HOH2362 4.1 14.9 1.0
CG F:GLU337 4.1 11.6 1.0
O F:HOH2370 4.2 7.8 1.0
NE2 F:HIS331 4.3 8.5 1.0
CG F:HIS367 4.3 12.3 1.0
ND1 F:HIS367 4.4 8.5 1.0
CD2 F:HIS331 4.4 5.3 1.0
O F:HOH2371 4.4 8.0 1.0
ND2 F:ASN333 4.8 9.9 1.0
CB F:ASN333 4.8 8.5 1.0

Iron binding site 7 out of 12 in 4aq2

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Iron binding site 7 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe800

b:12.1
occ:1.00
 O G:HOH2393 2.2 15.4 1.0
ND1 G:HIS331 2.2 14.9 1.0
O G:HOH2392 2.2 14.5 1.0
OE2 G:GLU337 2.2 10.8 1.0
NE2 G:HIS367 2.3 22.1 1.0
OE1 G:GLU337 2.3 13.2 1.0
CD G:GLU337 2.6 12.2 1.0
CE1 G:HIS331 3.0 13.0 1.0
CD2 G:HIS367 3.2 14.8 1.0
CG G:HIS331 3.3 14.6 1.0
CE1 G:HIS367 3.4 19.1 1.0
CB G:HIS331 3.8 10.2 1.0
O G:HOH2402 4.1 13.0 1.0
CG G:GLU337 4.1 9.9 1.0
NE2 G:HIS331 4.2 11.4 1.0
CD2 G:HIS331 4.4 9.3 1.0
CG G:HIS367 4.4 12.0 1.0
O G:HOH2403 4.4 11.8 1.0
O G:HOH2390 4.4 17.3 1.0
ND1 G:HIS367 4.4 15.6 1.0
ND2 G:ASN333 4.6 10.6 1.0
CB G:ASN333 4.8 9.7 1.0

Iron binding site 8 out of 12 in 4aq2

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Iron binding site 8 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe800

b:13.9
occ:1.00
 O H:HOH2430 2.1 10.3 1.0
O H:HOH2429 2.2 10.4 1.0
ND1 H:HIS331 2.2 10.7 1.0
OE2 H:GLU337 2.2 12.2 1.0
OE1 H:GLU337 2.3 10.4 1.0
NE2 H:HIS367 2.3 14.4 1.0
CD H:GLU337 2.6 11.0 1.0
CD2 H:HIS367 3.1 10.0 1.0
CE1 H:HIS331 3.1 9.8 1.0
CG H:HIS331 3.3 11.9 1.0
CE1 H:HIS367 3.4 11.2 1.0
CB H:HIS331 3.6 9.1 1.0
CG H:GLU337 4.1 14.1 1.0
O H:HOH2219 4.2 16.9 1.0
NE2 H:HIS331 4.3 9.1 1.0
O H:HOH2427 4.3 18.4 1.0
CG H:HIS367 4.3 13.3 1.0
CD2 H:HIS331 4.4 11.6 1.0
O H:HOH2438 4.4 12.1 1.0
ND1 H:HIS367 4.5 11.6 1.0
O H:HOH2480 4.5 8.4 1.0
ND2 H:ASN333 4.5 12.3 1.0
CB H:ASN333 4.9 9.1 1.0

Iron binding site 9 out of 12 in 4aq2

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Iron binding site 9 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe800

b:15.1
occ:1.00
 OE2 I:GLU337 2.1 8.1 1.0
O I:HOH2377 2.1 13.2 1.0
O I:HOH2376 2.2 14.3 1.0
NE2 I:HIS367 2.3 16.6 1.0
ND1 I:HIS331 2.3 17.5 1.0
OE1 I:GLU337 2.3 10.4 1.0
CD I:GLU337 2.5 9.2 1.0
CE1 I:HIS331 3.1 13.6 1.0
CD2 I:HIS367 3.1 16.7 1.0
CE1 I:HIS367 3.3 14.6 1.0
CG I:HIS331 3.4 17.3 1.0
CB I:HIS331 3.8 17.9 1.0
CG I:GLU337 4.0 11.9 1.0
O I:HOH2180 4.0 29.4 1.0
O I:HOH2404 4.1 13.4 1.0
NE2 I:HIS331 4.3 13.0 1.0
CG I:HIS367 4.3 15.2 1.0
O I:HOH2375 4.4 14.9 1.0
ND1 I:HIS367 4.4 9.8 1.0
O I:HOH2383 4.4 11.4 1.0
ND2 I:ASN333 4.4 15.2 1.0
CD2 I:HIS331 4.4 11.9 1.0
CB I:ASN333 4.8 8.6 1.0
CB I:GLU337 5.0 8.9 1.0

Iron binding site 10 out of 12 in 4aq2

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Iron binding site 10 out of 12 in the Resting State of Homogentisate 1,2-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Resting State of Homogentisate 1,2-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe800

b:13.7
occ:1.00
 OE2 J:GLU337 2.1 16.5 1.0
O J:HOH2380 2.1 15.0 1.0
O J:HOH2381 2.1 11.4 1.0
ND1 J:HIS331 2.2 13.6 1.0
NE2 J:HIS367 2.2 13.2 1.0
OE1 J:GLU337 2.3 18.3 1.0
CD J:GLU337 2.5 18.2 1.0
CE1 J:HIS331 2.9 18.1 1.0
CD2 J:HIS367 3.0 10.4 1.0
CE1 J:HIS367 3.2 11.2 1.0
CG J:HIS331 3.3 16.4 1.0
O J:HOH2458 3.6 22.7 1.0
CB J:HIS331 3.7 13.7 1.0
O J:HOH2389 3.9 15.7 1.0
CG J:GLU337 4.1 16.6 1.0
NE2 J:HIS331 4.1 14.6 1.0
CG J:HIS367 4.2 13.8 1.0
ND1 J:HIS367 4.3 12.8 1.0
CD2 J:HIS331 4.3 14.4 1.0
O J:HOH2388 4.4 11.3 1.0
O J:HOH2378 4.5 18.3 1.0
ND2 J:ASN333 4.6 16.6 1.0
CB J:ASN333 4.8 18.1 1.0
CB J:GLU337 5.0 14.0 1.0

Reference:

J.-H.Jeoung, M.Bommer, T.-Y.Lin, H.Dobbek. Visualizing the Substrate-, Superoxo-, Alkylperoxo-, and Product-Bound States at the Nonheme 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 Dec 13 15:28:11 2020

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