Iron in PDB 7v25: Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate

The structure of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate, PDB code: 7v25 was solved by J.K.Mahto, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	159.88 / 2.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.03, 122.18, 162.94, 90, 101.13, 90
R / Rfree (%)	20.7 / 28.3

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate (pdb code 7v25). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate, PDB code: 7v25:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:36.8 occ:1.00 O B:HOH645 1.9 60.0 1.0 NE2 B:HIS181 2.0 50.3 1.0 NE2 B:HIS186 2.1 35.2 1.0 OD1 B:ASP343 2.1 38.4 1.0 OD2 B:ASP343 2.2 36.4 1.0 CG B:ASP343 2.4 38.1 1.0 CE1 B:HIS181 2.9 48.0 1.0 CE1 B:HIS186 3.0 34.7 1.0 CD2 B:HIS181 3.1 47.8 1.0 CD2 B:HIS186 3.1 38.1 1.0 CB B:ASP343 3.9 35.9 1.0 O B:HOH713 4.0 28.7 1.0 O B:HOH772 4.1 24.6 1.0 ND1 B:HIS181 4.1 49.2 1.0 ND1 B:HIS186 4.1 35.4 1.0 CG B:HIS181 4.2 47.3 1.0 CG B:HIS186 4.2 40.2 1.0 C5 B:PHT503 4.3 75.4 1.0 O B:GLY175 4.4 41.6 1.0 CD2 B:LEU185 4.5 29.9 1.0 C6 B:PHT503 4.5 77.3 1.0 OG B:SER182 4.7 52.2 1.0 CD1 B:PHE339 4.8 29.8 1.0 C4 B:PHT503 4.8 73.4 1.0 CA B:ASP343 4.9 35.1 1.0 O B:PHE339 4.9 27.4 1.0

Iron binding site 2 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:29.8 occ:1.00 FE1 B:FES502 0.0 29.8 1.0 S1 B:FES502 2.2 33.2 1.0 S2 B:FES502 2.2 29.4 1.0 SG B:CYS70 2.2 30.9 1.0 SG B:CYS89 2.3 27.0 1.0 FE2 B:FES502 2.8 35.1 1.0 CB B:CYS89 3.1 25.0 1.0 CB B:CYS70 3.1 29.6 1.0 CB B:HIS72 4.0 32.7 1.0 CB B:TYR91 4.3 29.4 1.0 CA B:CYS89 4.5 28.4 1.0 CA B:CYS70 4.6 30.8 1.0 ND1 B:HIS72 4.6 38.3 1.0 CB B:ALA75 4.6 32.3 1.0 ND1 B:HIS92 4.7 31.4 1.0 N B:ARG73 4.7 34.8 1.0 N B:HIS92 4.8 28.9 1.0 CG B:HIS72 4.8 36.8 1.0 N B:HIS72 4.9 38.3 1.0 N B:TYR91 4.9 28.1 1.0 CA B:HIS72 4.9 34.8 1.0

Iron binding site 3 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:35.1 occ:1.00 FE2 B:FES502 0.0 35.1 1.0 ND1 B:HIS92 2.2 31.4 1.0 ND1 B:HIS72 2.2 38.3 1.0 S2 B:FES502 2.2 29.4 1.0 S1 B:FES502 2.2 33.2 1.0 FE1 B:FES502 2.8 29.8 1.0 CG B:HIS72 3.1 36.8 1.0 CE1 B:HIS92 3.1 30.7 1.0 CG B:HIS92 3.2 30.4 1.0 CE1 B:HIS72 3.2 35.6 1.0 CB B:HIS72 3.3 32.7 1.0 CB B:HIS92 3.5 28.4 1.0 N B:HIS92 3.9 28.9 1.0 CB B:TYR91 3.9 29.4 1.0 NE2 B:HIS92 4.2 31.3 1.0 N B:ARG73 4.2 34.8 1.0 CD2 B:HIS72 4.2 34.9 1.0 CD2 B:HIS92 4.2 30.7 1.0 NE2 B:HIS72 4.3 37.7 1.0 CA B:HIS92 4.3 28.9 1.0 CD2 B:TYR91 4.4 29.6 1.0 SG B:CYS70 4.4 30.9 1.0 CG B:TYR91 4.4 29.5 1.0 CB B:ARG73 4.5 36.0 1.0 CA B:HIS72 4.6 34.8 1.0 C B:TYR91 4.7 31.1 1.0 SG B:CYS89 4.7 27.0 1.0 C B:HIS72 4.8 37.7 1.0 CA B:TYR91 4.9 30.0 1.0 CD1 B:TRP94 4.9 33.6 1.0 CA B:ARG73 4.9 33.9 1.0 NE1 B:TRP94 5.0 32.1 1.0

Iron binding site 4 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.7 occ:1.00 NE2 A:HIS186 2.0 30.5 1.0 NE2 A:HIS181 2.1 39.9 1.0 OD2 A:ASP343 2.2 27.4 1.0 O A:HOH657 2.2 30.1 1.0 OD1 A:ASP343 2.3 30.6 1.0 CG A:ASP343 2.5 30.7 1.0 CD2 A:HIS186 2.9 32.4 1.0 CE1 A:HIS181 3.0 39.6 1.0 CE1 A:HIS186 3.1 31.7 1.0 CD2 A:HIS181 3.2 41.4 1.0 O A:HOH643 3.9 30.6 1.0 CB A:ASP343 4.1 30.2 1.0 CG A:HIS186 4.1 34.6 1.0 O E:HOH601 4.1 36.2 1.0 ND1 A:HIS181 4.1 40.5 1.0 ND1 A:HIS186 4.1 32.4 1.0 CG A:HIS181 4.3 41.0 1.0 O A:GLY175 4.5 33.8 1.0 CD2 A:LEU185 4.8 32.3 1.0 CD2 A:PHE339 4.9 49.8 1.0 CA A:ASP343 5.0 29.6 1.0

Iron binding site 5 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:41.0 occ:1.00 FE1 A:FES502 0.0 41.0 1.0 ND1 A:HIS72 2.1 44.4 1.0 S2 A:FES502 2.2 36.5 1.0 S1 A:FES502 2.2 31.0 1.0 ND1 A:HIS92 2.3 38.7 1.0 FE2 A:FES502 2.8 33.8 1.0 CE1 A:HIS72 3.0 43.6 1.0 CG A:HIS72 3.1 39.3 1.0 CG A:HIS92 3.2 38.1 1.0 CE1 A:HIS92 3.2 38.3 1.0 CB A:HIS92 3.4 36.7 1.0 CB A:HIS72 3.4 33.9 1.0 N A:HIS92 3.8 36.5 1.0 CB A:TYR91 3.9 35.4 1.0 NE2 A:HIS72 4.1 42.1 1.0 CD2 A:HIS72 4.2 41.9 1.0 CA A:HIS92 4.2 37.1 1.0 CB A:ARG73 4.3 33.7 1.0 CD2 A:HIS92 4.3 36.8 1.0 CD2 A:TYR91 4.3 33.9 1.0 NE2 A:HIS92 4.3 38.5 1.0 N A:ARG73 4.3 33.7 1.0 CG A:TYR91 4.3 34.4 1.0 C A:TYR91 4.5 38.3 1.0 SG A:CYS89 4.6 40.5 1.0 SG A:CYS70 4.6 35.8 1.0 CA A:HIS72 4.7 34.3 1.0 CA A:TYR91 4.8 36.3 1.0 CA A:ARG73 4.9 36.3 1.0 C A:HIS72 4.9 33.4 1.0 NE1 A:TRP94 5.0 33.1 1.0

Iron binding site 6 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:33.8 occ:1.00 FE2 A:FES502 0.0 33.8 1.0 S1 A:FES502 2.2 31.0 1.0 S2 A:FES502 2.2 36.5 1.0 SG A:CYS89 2.3 40.5 1.0 SG A:CYS70 2.4 35.8 1.0 FE1 A:FES502 2.8 41.0 1.0 CB A:CYS89 3.1 36.6 1.0 CB A:CYS70 3.3 37.3 1.0 CB A:HIS72 3.9 33.9 1.0 CB A:TYR91 4.2 35.4 1.0 ND1 A:HIS72 4.3 44.4 1.0 N A:HIS92 4.5 36.5 1.0 CA A:CYS89 4.6 34.6 1.0 CG A:HIS72 4.6 39.3 1.0 CA A:CYS70 4.7 36.3 1.0 ND1 A:HIS92 4.7 38.7 1.0 N A:ARG73 4.8 33.7 1.0 N A:TYR91 4.8 34.3 1.0 CB A:ALA75 4.8 29.0 1.0 CA A:HIS72 5.0 34.3 1.0 CA A:TYR91 5.0 36.3 1.0

Iron binding site 7 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:30.6 occ:1.00 NE2 C:HIS181 1.9 40.9 1.0 OD1 C:ASP343 2.0 33.1 1.0 NE2 C:HIS186 2.1 34.9 1.0 OD2 C:ASP343 2.4 32.5 1.0 CG C:ASP343 2.5 33.2 1.0 CE1 C:HIS181 2.7 35.0 1.0 CE1 C:HIS186 3.0 39.1 1.0 CD2 C:HIS181 3.1 41.4 1.0 CD2 C:HIS186 3.2 36.2 1.0 O C:HOH668 3.2 24.2 1.0 ND1 C:HIS181 3.9 36.0 1.0 CB C:ASP343 4.0 31.9 1.0 O C:HOH665 4.1 29.6 1.0 CG C:HIS181 4.1 39.7 1.0 ND1 C:HIS186 4.1 37.4 1.0 CG C:HIS186 4.2 36.0 1.0 O C:GLY175 4.4 38.7 1.0 CD2 C:LEU185 4.9 28.1 1.0 CD1 C:PHE339 5.0 41.0 1.0

Iron binding site 8 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:41.6 occ:1.00 FE1 C:FES502 0.0 41.6 1.0 SG C:CYS70 2.2 46.4 1.0 S2 C:FES502 2.2 41.1 1.0 S1 C:FES502 2.2 39.7 1.0 SG C:CYS89 2.3 28.1 1.0 CB C:CYS70 2.9 44.5 1.0 FE2 C:FES502 3.0 50.3 1.0 CB C:CYS89 3.1 27.6 1.0 CB C:HIS72 4.1 51.6 1.0 CB C:TYR91 4.3 39.2 1.0 CA C:CYS70 4.4 41.9 1.0 CA C:CYS89 4.6 32.0 1.0 ND1 C:HIS72 4.6 59.8 1.0 N C:ARG73 4.6 43.0 1.0 CB C:ALA75 4.7 36.4 1.0 N C:HIS92 4.8 50.3 1.0 CG C:HIS72 4.8 56.1 1.0 N C:HIS72 4.9 44.2 1.0 C C:CYS70 4.9 42.5 1.0 CD2 C:LEU77 4.9 39.8 1.0 N C:ALA75 5.0 45.0 1.0 CA C:HIS72 5.0 46.0 1.0

Iron binding site 9 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:50.3 occ:1.00 FE2 C:FES502 0.0 50.3 1.0 S1 C:FES502 2.2 39.7 1.0 S2 C:FES502 2.3 41.1 1.0 ND1 C:HIS72 2.3 59.8 1.0 ND1 C:HIS92 2.4 49.4 1.0 FE1 C:FES502 3.0 41.6 1.0 CB C:HIS92 3.1 42.3 1.0 CG C:HIS92 3.1 45.0 1.0 CE1 C:HIS72 3.2 61.4 1.0 CG C:HIS72 3.4 56.1 1.0 CE1 C:HIS92 3.5 47.9 1.0 N C:HIS92 3.6 50.3 1.0 CB C:HIS72 3.7 51.6 1.0 CB C:TYR91 3.7 39.2 1.0 CA C:HIS92 3.9 48.7 1.0 CG C:TYR91 4.2 39.4 1.0 CD2 C:HIS92 4.3 46.8 1.0 CD2 C:TYR91 4.3 45.6 1.0 NE2 C:HIS72 4.3 62.0 1.0 N C:ARG73 4.4 43.0 1.0 C C:TYR91 4.4 47.4 1.0 CD2 C:HIS72 4.4 57.5 1.0 NE2 C:HIS92 4.5 52.0 1.0 SG C:CYS89 4.6 28.1 1.0 CA C:TYR91 4.6 40.7 1.0 CB C:ARG73 4.7 45.5 1.0 SG C:CYS70 4.8 46.4 1.0 C C:HIS92 4.9 46.6 1.0 CA C:HIS72 5.0 46.0 1.0 CD1 C:TRP94 5.0 51.4 1.0

Iron binding site 10 out of 18 in the Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Phthalate Dioxygenase in Complex with Phthalate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:34.1 occ:1.00 OD1 D:ASP343 2.0 47.8 1.0 NE2 D:HIS181 2.0 59.8 1.0 NE2 D:HIS186 2.0 29.1 1.0 OD2 D:ASP343 2.3 38.5 1.0 CG D:ASP343 2.4 41.0 1.0 O D:HOH642 2.7 28.8 1.0 CD2 D:HIS181 3.0 54.5 1.0 CD2 D:HIS186 3.0 31.8 1.0 CE1 D:HIS186 3.1 30.6 1.0 CE1 D:HIS181 3.1 52.4 1.0 O D:HOH625 3.8 31.6 1.0 CB D:ASP343 3.9 36.0 1.0 CG D:HIS181 4.1 50.4 1.0 ND1 D:HIS181 4.1 48.7 1.0 CG D:HIS186 4.1 33.9 1.0 ND1 D:HIS186 4.1 32.3 1.0 O D:GLY175 4.5 39.8 1.0 CD2 D:PHE339 4.6 53.2 1.0 CD2 D:LEU185 4.6 41.2 1.0 CE2 D:PHE339 4.8 56.6 1.0 CA D:ASP343 4.9 33.6 1.0

J.K.Mahto, N.Neetu, B.Waghmode, E.Kuatsjah, M.Sharma, D.Sircar, A.K.Sharma, S.Tomar, L.D.Eltis, P.Kumar. Molecular Insights Into Substrate Recognition and Catalysis By Phthalate Dioxygenase From Comamonas Testosteroni. J.Biol.Chem. 01416 2021.
ISSN: ESSN 1083-351X
PubMed: 34800435
DOI: 10.1016/J.JBC.2021.101416