Iron in PDB 4aq6: Substrate Bound Homogentisate 1,2-Dioxygenase

All present enzymatic activity of Substrate Bound Homogentisate 1,2-Dioxygenase:
1.13.11.5;

The structure of Substrate Bound Homogentisate 1,2-Dioxygenase, PDB code: 4aq6 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)	34.17 / 1.98
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	93.393, 93.714, 162.984, 87.69, 80.42, 68.39
R / Rfree (%)	16.1 / 21.6

Pages:

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

Binding sites:

The binding sites of Iron atom in the Substrate Bound Homogentisate 1,2-Dioxygenase (pdb code 4aq6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Substrate Bound Homogentisate 1,2-Dioxygenase, PDB code: 4aq6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe837 b:11.8 occ:1.00 O6' A:OMD838 2.0 11.9 1.0 ND1 A:HIS331 2.1 13.4 1.0 NE2 A:HIS367 2.2 11.8 1.0 OE2 A:GLU337 2.2 14.8 1.0 O A:HOH2396 2.3 18.2 1.0 OE1 A:GLU337 2.4 14.3 1.0 CD A:GLU337 2.6 14.2 1.0 CE1 A:HIS331 2.9 14.0 1.0 CD2 A:HIS367 3.1 15.7 1.0 C6' A:OMD838 3.1 12.4 1.0 CE1 A:HIS367 3.2 14.8 1.0 CG A:HIS331 3.3 14.2 1.0 CB A:HIS331 3.7 11.8 1.0 C5' A:OMD838 3.8 10.8 1.0 C1' A:OMD838 4.0 10.1 1.0 CG A:GLU337 4.1 16.3 1.0 NE2 A:HIS331 4.1 11.8 1.0 C2 A:OMD838 4.2 16.9 1.0 O A:HOH2394 4.2 14.0 1.0 CG A:HIS367 4.2 16.0 1.0 ND1 A:HIS367 4.3 12.4 1.0 CD2 A:HIS331 4.3 12.3 1.0 O A:HOH2406 4.3 17.7 1.0 O A:HOH2405 4.5 13.7 1.0 ND2 A:ASN333 4.5 14.1 1.0 O1 A:OMD838 4.8 13.8 1.0 CB A:ASN333 4.8 11.6 1.0 C1 A:OMD838 4.8 15.3 1.0 CB A:GLU337 5.0 12.4 1.0

Iron binding site 2 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe837 b:12.8 occ:1.00 O6' B:OMD838 2.0 13.6 1.0 NE2 B:HIS367 2.2 15.3 1.0 OE2 B:GLU337 2.2 16.6 1.0 O B:HOH2346 2.2 14.7 1.0 ND1 B:HIS331 2.2 15.3 1.0 OE1 B:GLU337 2.4 17.9 1.0 CD B:GLU337 2.6 18.6 1.0 C6' B:OMD838 3.1 18.8 1.0 CD2 B:HIS367 3.1 19.6 1.0 CE1 B:HIS331 3.1 16.0 1.0 CE1 B:HIS367 3.2 14.0 1.0 CG B:HIS331 3.3 13.2 1.0 CB B:HIS331 3.6 15.8 1.0 C5' B:OMD838 3.7 15.2 1.0 C1' B:OMD838 4.0 16.8 1.0 CG B:GLU337 4.2 16.4 1.0 O B:HOH2356 4.2 18.3 1.0 ND1 B:HIS367 4.3 13.1 1.0 C2 B:OMD838 4.3 18.6 1.0 CG B:HIS367 4.3 14.7 1.0 NE2 B:HIS331 4.3 16.1 1.0 O B:HOH2344 4.3 18.7 1.0 CD2 B:HIS331 4.4 12.7 1.0 O B:HOH2355 4.5 13.8 1.0 ND2 B:ASN333 4.6 14.1 1.0 CB B:ASN333 4.8 11.4 1.0 O1 B:OMD838 4.8 15.7 1.0 C1 B:OMD838 4.9 18.6 1.0 C4' B:OMD838 5.0 14.0 1.0

Iron binding site 3 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe837 b:11.3 occ:1.00 O6' C:OMD838 2.1 9.8 0.9 NE2 C:HIS367 2.1 8.4 1.0 ND1 C:HIS331 2.2 12.1 1.0 OE2 C:GLU337 2.3 11.9 1.0 O C:HOH2319 2.4 11.2 1.0 OE1 C:GLU337 2.4 7.6 1.0 CD C:GLU337 2.7 10.6 1.0 CE1 C:HIS331 3.0 12.4 1.0 CD2 C:HIS367 3.1 11.1 1.0 CE1 C:HIS367 3.1 9.8 1.0 C6' C:OMD838 3.1 14.3 0.9 CG C:HIS331 3.3 10.5 1.0 CB C:HIS331 3.7 10.2 1.0 C5' C:OMD838 3.9 11.1 0.9 C1' C:OMD838 4.0 14.1 0.9 C2 C:OMD838 4.0 13.2 0.9 CG C:GLU337 4.2 9.2 1.0 O C:HOH2318 4.2 11.5 1.0 NE2 C:HIS331 4.2 12.1 1.0 ND1 C:HIS367 4.2 10.2 1.0 CG C:HIS367 4.2 12.9 1.0 O C:HOH2326 4.3 16.3 1.0 CD2 C:HIS331 4.3 15.4 1.0 ND2 C:ASN333 4.4 11.1 1.0 O C:HOH2325 4.5 11.8 1.0 C1 C:OMD838 4.8 16.6 0.9 CB C:ASN333 4.8 10.2 1.0 O1 C:OMD838 4.9 14.5 0.9

Iron binding site 4 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe837 b:11.9 occ:1.00 ND1 D:HIS331 2.1 13.3 1.0 O6' D:OMD838 2.1 12.8 1.0 NE2 D:HIS367 2.1 14.6 1.0 OE2 D:GLU337 2.2 11.7 1.0 O D:HOH2360 2.3 14.9 1.0 OE1 D:GLU337 2.4 16.0 1.0 CD D:GLU337 2.6 10.0 1.0 CE1 D:HIS331 2.9 12.3 1.0 CE1 D:HIS367 3.0 15.6 1.0 C6' D:OMD838 3.1 16.3 1.0 CD2 D:HIS367 3.2 13.1 1.0 CG D:HIS331 3.2 16.7 1.0 CB D:HIS331 3.7 12.4 1.0 C5' D:OMD838 3.8 14.5 1.0 C1' D:OMD838 4.0 17.9 1.0 NE2 D:HIS331 4.1 12.5 1.0 CG D:GLU337 4.1 15.7 1.0 ND1 D:HIS367 4.2 9.7 1.0 O D:HOH2358 4.2 15.2 1.0 C2 D:OMD838 4.2 14.2 1.0 O D:HOH2370 4.2 15.0 1.0 CD2 D:HIS331 4.3 12.2 1.0 CG D:HIS367 4.3 15.2 1.0 ND2 D:ASN333 4.5 11.7 1.0 O1 D:OMD838 4.7 18.7 1.0 O D:HOH2369 4.8 11.7 1.0 C1 D:OMD838 4.8 22.4 1.0 CB D:ASN333 4.8 10.6 1.0 CB D:GLU337 5.0 11.9 1.0

Iron binding site 5 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe837 b:13.5 occ:1.00 O6' E:OMD838 2.0 11.4 0.9 OE2 E:GLU337 2.1 10.9 1.0 ND1 E:HIS331 2.1 16.6 1.0 NE2 E:HIS367 2.2 14.7 1.0 O E:HOH2334 2.2 16.9 1.0 OE1 E:GLU337 2.4 11.4 1.0 CD E:GLU337 2.6 11.0 1.0 CE1 E:HIS331 3.0 15.2 1.0 C6' E:OMD838 3.1 12.9 0.9 CE1 E:HIS367 3.2 13.7 1.0 CD2 E:HIS367 3.2 14.3 1.0 CG E:HIS331 3.2 14.7 1.0 CB E:HIS331 3.6 11.8 1.0 C5' E:OMD838 3.8 13.4 0.9 C1' E:OMD838 4.0 13.6 0.9 C2 E:OMD838 4.1 11.6 0.9 CG E:GLU337 4.1 11.5 1.0 NE2 E:HIS331 4.2 16.1 1.0 O E:HOH2341 4.3 16.3 1.0 O E:HOH2333 4.3 12.4 1.0 CD2 E:HIS331 4.3 12.9 1.0 O E:HOH2340 4.3 10.6 1.0 ND1 E:HIS367 4.3 13.1 1.0 CG E:HIS367 4.4 12.7 1.0 ND2 E:ASN333 4.4 10.7 1.0 CB E:ASN333 4.8 12.9 1.0 C1 E:OMD838 4.9 18.3 0.9 O1 E:OMD838 5.0 16.0 0.9 CB E:GLU337 5.0 10.2 1.0

Iron binding site 6 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe837 b:13.8 occ:1.00 O6' F:OMD838 2.0 14.1 0.9 NE2 F:HIS367 2.1 13.7 1.0 OE2 F:GLU337 2.2 10.7 1.0 O F:HOH2273 2.2 12.3 1.0 ND1 F:HIS331 2.3 13.8 1.0 OE1 F:GLU337 2.4 15.1 1.0 CD F:GLU337 2.6 17.1 1.0 C6' F:OMD838 3.0 13.2 0.9 CD2 F:HIS367 3.1 14.5 1.0 CE1 F:HIS367 3.1 12.2 1.0 CE1 F:HIS331 3.2 13.8 1.0 CG F:HIS331 3.4 13.5 1.0 C5' F:OMD838 3.7 17.5 0.9 CB F:HIS331 3.7 9.6 1.0 C1' F:OMD838 3.9 16.0 0.9 CG F:GLU337 4.1 12.1 1.0 C2 F:OMD838 4.1 17.5 0.9 ND1 F:HIS367 4.2 13.2 1.0 O F:HOH2280 4.2 14.9 1.0 CG F:HIS367 4.2 18.3 1.0 O F:HOH2272 4.3 15.6 1.0 O F:HOH2279 4.3 14.4 1.0 NE2 F:HIS331 4.3 13.4 1.0 CD2 F:HIS331 4.5 13.0 1.0 ND2 F:ASN333 4.6 14.3 1.0 CB F:ASN333 4.9 11.4 1.0 C1 F:OMD838 4.9 20.5 0.9 C4' F:OMD838 5.0 18.9 0.9 O1 F:OMD838 5.0 18.6 0.9

Iron binding site 7 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe837 b:16.9 occ:1.00 O6' G:OMD838 2.1 21.6 0.9 O G:HOH2320 2.1 22.7 1.0 NE2 G:HIS367 2.1 19.2 1.0 ND1 G:HIS331 2.2 15.1 1.0 OE2 G:GLU337 2.2 15.6 1.0 OE1 G:GLU337 2.4 19.6 1.0 CD G:GLU337 2.6 18.9 1.0 CE1 G:HIS331 3.0 20.1 1.0 CD2 G:HIS367 3.1 18.6 1.0 C6' G:OMD838 3.1 18.6 0.9 CE1 G:HIS367 3.2 20.6 1.0 CG G:HIS331 3.3 20.5 1.0 CB G:HIS331 3.7 16.5 1.0 C5' G:OMD838 3.8 18.1 0.9 C1' G:OMD838 4.0 18.6 0.9 O G:HOH2325 4.1 20.3 1.0 CG G:GLU337 4.2 16.6 1.0 NE2 G:HIS331 4.2 17.3 1.0 O G:HOH2318 4.2 23.9 1.0 C2 G:OMD838 4.2 19.0 0.9 CG G:HIS367 4.3 21.9 1.0 ND1 G:HIS367 4.3 18.0 1.0 CD2 G:HIS331 4.3 16.5 1.0 ND2 G:ASN333 4.5 14.0 1.0 O G:HOH2330 4.6 17.7 1.0 CB G:ASN333 4.8 15.3 1.0

Iron binding site 8 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe837 b:17.9 occ:1.00 O6' H:OMD838 1.9 18.4 1.0 OE2 H:GLU337 2.1 18.7 1.0 NE2 H:HIS367 2.2 16.4 1.0 ND1 H:HIS331 2.2 20.9 1.0 O H:HOH2305 2.3 19.0 1.0 OE1 H:GLU337 2.4 17.3 1.0 CD H:GLU337 2.5 15.0 1.0 C6' H:OMD838 2.9 22.6 1.0 CE1 H:HIS331 3.1 18.6 1.0 CD2 H:HIS367 3.1 19.1 1.0 CE1 H:HIS367 3.2 16.9 1.0 CG H:HIS331 3.3 18.8 1.0 C5' H:OMD838 3.7 21.2 1.0 CB H:HIS331 3.7 18.6 1.0 C1' H:OMD838 3.8 21.7 1.0 C2 H:OMD838 4.0 21.9 1.0 O H:HOH2303 4.1 19.2 1.0 CG H:GLU337 4.1 17.9 1.0 NE2 H:HIS331 4.2 17.9 1.0 CG H:HIS367 4.3 20.6 1.0 ND1 H:HIS367 4.3 14.8 1.0 CD2 H:HIS331 4.4 15.8 1.0 O H:HOH2314 4.4 21.9 1.0 ND2 H:ASN333 4.5 16.8 1.0 O H:HOH2313 4.6 19.4 1.0 CB H:ASN333 4.8 18.4 1.0 C1 H:OMD838 4.9 26.0 1.0 C4' H:OMD838 4.9 19.0 1.0 CB H:GLU337 5.0 18.1 1.0

Iron binding site 9 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe837 b:18.9 occ:1.00 O6' I:OMD838 1.9 20.1 0.9 OE2 I:GLU337 2.0 20.0 1.0 O I:HOH2286 2.2 19.1 1.0 ND1 I:HIS331 2.3 27.0 1.0 NE2 I:HIS367 2.3 19.7 1.0 OE1 I:GLU337 2.4 21.3 1.0 CD I:GLU337 2.5 19.9 1.0 C6' I:OMD838 3.0 24.6 0.9 CE1 I:HIS331 3.1 22.8 1.0 CE1 I:HIS367 3.2 18.5 1.0 CD2 I:HIS367 3.3 21.1 1.0 CG I:HIS331 3.4 22.6 1.0 C5' I:OMD838 3.6 20.6 0.9 CB I:HIS331 3.8 17.8 1.0 C1' I:OMD838 3.9 21.9 0.9 CG I:GLU337 4.0 18.6 1.0 C2 I:OMD838 4.1 24.3 0.9 O I:HOH2293 4.2 24.9 1.0 NE2 I:HIS331 4.3 22.3 1.0 O I:HOH2292 4.3 18.2 1.0 ND1 I:HIS367 4.4 19.6 1.0 CG I:HIS367 4.4 19.3 1.0 CD2 I:HIS331 4.4 20.4 1.0 O I:HOH2285 4.5 19.3 1.0 ND2 I:ASN333 4.5 22.1 1.0 CB I:ASN333 4.8 17.6 1.0 C1 I:OMD838 4.9 28.1 0.9 C4' I:OMD838 4.9 21.5 0.9 CB I:GLU337 5.0 18.3 1.0

Iron binding site 10 out of 12 in the Substrate Bound 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 Substrate Bound Homogentisate 1,2-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe837 b:16.1 occ:1.00 O6' J:OMD838 2.0 18.8 0.9 OE2 J:GLU337 2.0 17.4 1.0 ND1 J:HIS331 2.2 18.1 1.0 NE2 J:HIS367 2.2 16.2 1.0 O J:HOH2287 2.2 21.9 1.0 OE1 J:GLU337 2.3 15.9 1.0 CD J:GLU337 2.5 18.8 1.0 C6' J:OMD838 3.0 20.6 0.9 CE1 J:HIS331 3.0 19.3 1.0 CD2 J:HIS367 3.2 17.7 1.0 CE1 J:HIS367 3.2 16.4 1.0 CG J:HIS331 3.3 19.8 1.0 C5' J:OMD838 3.6 23.3 0.9 CB J:HIS331 3.6 16.8 1.0 C1' J:OMD838 4.0 24.4 0.9 CG J:GLU337 4.0 20.3 1.0 NE2 J:HIS331 4.2 16.5 1.0 C2 J:OMD838 4.3 24.3 0.9 O J:HOH2297 4.3 22.6 1.0 ND1 J:HIS367 4.3 19.1 1.0 CG J:HIS367 4.3 19.4 1.0 CD2 J:HIS331 4.3 18.4 1.0 O J:HOH2285 4.4 21.4 1.0 O J:HOH2296 4.4 14.8 1.0 ND2 J:ASN333 4.6 16.7 1.0 CB J:ASN333 4.8 13.7 1.0 O1 J:OMD838 4.8 19.1 0.9 C4' J:OMD838 4.9 22.6 0.9 C1 J:OMD838 4.9 25.7 0.9 CB J:GLU337 4.9 21.1 1.0

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