Iron in PDB 7qr6: Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant

The structure of Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant, PDB code: 7qr6 was solved by L.Alvigini, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 2.90
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	178.471, 187.984, 105.867, 90, 90, 90
R / Rfree (%)	21.4 / 29.1

The binding sites of Iron atom in the Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant (pdb code 7qr6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant, PDB code: 7qr6:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:41.8 occ:0.75 O1 A:OXY502 1.6 35.8 0.8 NE2 A:HIS284 1.8 58.8 1.0 NE2 A:HIS476 1.8 56.7 1.0 NE2 A:HIS218 1.9 57.3 1.0 NE2 A:HIS167 2.0 51.9 1.0 O2 A:OXY502 2.1 43.1 0.8 CE1 A:HIS218 2.6 53.0 1.0 CE1 A:HIS284 2.6 61.4 1.0 CE1 A:HIS476 2.8 53.4 1.0 CE1 A:HIS167 2.8 51.7 1.0 CD2 A:HIS476 2.9 61.2 1.0 CD2 A:HIS284 3.0 61.2 1.0 CD2 A:HIS167 3.1 50.2 1.0 CD2 A:HIS218 3.1 56.0 1.0 ND1 A:HIS284 3.8 61.0 1.0 ND1 A:HIS218 3.8 49.7 1.0 ND1 A:HIS476 3.9 53.1 1.0 ND1 A:HIS167 4.0 47.4 1.0 CG A:HIS476 4.0 58.4 1.0 CG A:HIS284 4.0 59.2 1.0 CG A:HIS218 4.1 55.8 1.0 CG A:HIS167 4.1 48.8 1.0 CE2 A:PHE283 4.5 54.1 1.0 CZ A:PHE283 4.5 55.8 1.0 CG2 A:THR121 4.8 49.7 1.0

Iron binding site 2 out of 3 in the Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:51.1 occ:0.75 O1 B:OXY502 1.7 68.2 0.8 NE2 B:HIS218 1.7 52.4 1.0 NE2 B:HIS167 1.8 64.7 1.0 NE2 B:HIS476 2.1 47.9 1.0 O2 B:OXY502 2.1 70.8 0.8 NE2 B:HIS284 2.1 53.2 1.0 CE1 B:HIS218 2.5 50.1 1.0 CE1 B:HIS167 2.6 63.5 1.0 CD2 B:HIS218 2.8 47.4 1.0 CD2 B:HIS476 2.8 50.3 1.0 CD2 B:HIS167 2.9 63.5 1.0 CE1 B:HIS284 3.0 55.3 1.0 CE1 B:HIS476 3.2 49.7 1.0 CD2 B:HIS284 3.2 49.5 1.0 ND1 B:HIS218 3.7 52.2 1.0 ND1 B:HIS167 3.8 58.2 1.0 CG B:HIS218 3.8 48.3 1.0 CG B:HIS167 3.9 59.6 1.0 CG B:HIS476 4.1 48.0 1.0 ND1 B:HIS284 4.2 52.2 1.0 ND1 B:HIS476 4.2 46.1 1.0 CG B:HIS284 4.3 50.0 1.0 CG2 B:THR121 4.6 48.0 1.0 CZ B:PHE283 4.6 65.8 1.0 CE2 B:PHE283 4.6 66.3 1.0

Iron binding site 3 out of 3 in the Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Stilbene Dioxygenase (NOV1) From Novosphingobium Aromaticivorans: SER283PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:60.6 occ:0.75 O1 C:OXY502 1.8 59.7 0.8 NE2 C:HIS476 1.8 62.4 1.0 NE2 C:HIS167 2.0 60.8 1.0 NE2 C:HIS218 2.1 74.2 1.0 NE2 C:HIS284 2.1 92.1 1.0 O2 C:OXY502 2.2 67.1 0.8 CE1 C:HIS218 2.5 75.5 1.0 CE1 C:HIS476 2.8 59.5 1.0 CD2 C:HIS476 2.8 65.2 1.0 CE1 C:HIS284 2.9 95.3 1.0 CE1 C:HIS167 3.0 53.6 1.0 CD2 C:HIS167 3.0 58.2 1.0 CD2 C:HIS284 3.2 86.7 1.0 CD2 C:HIS218 3.4 79.2 1.0 ND1 C:HIS218 3.8 77.9 1.0 ND1 C:HIS476 3.9 59.1 1.0 CG C:HIS476 3.9 65.1 1.0 ND1 C:HIS167 4.1 55.3 1.0 CG C:HIS167 4.1 56.0 1.0 ND1 C:HIS284 4.1 85.1 1.0 CG C:HIS218 4.2 75.4 1.0 CG C:HIS284 4.3 83.3 1.0 CG2 C:THR121 4.7 76.5 1.0 CE2 C:PHE283 4.7 99.2 1.0 CZ C:PHE283 4.8 93.4 1.0

M.De Simone, L.Alvigini, L.Alonso-Cotchico, V.Brissos, J.Caroli, M.F.Lucas, E.Monza, E.P.Melo, A.Mattevi, L.O.Martins. Rationally Guided Improvement of NOV1 Dioxygenase For the Conversion of Lignin-Derived Isoeugenol to Vanillin. Biochemistry 2022.
ISSN: ISSN 0006-2960
PubMed: 35687874
DOI: 10.1021/ACS.BIOCHEM.2C00168