Iron in PDB 7qyq: Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida

The structure of Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida, PDB code: 7qyq was solved by P.T.Borges, D.Silva, C.Frazao, L.O.Martins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.05 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.951, 141.951, 177.44, 90, 90, 120
R / Rfree (%)	21.9 / 23.5

The binding sites of Iron atom in the Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida (pdb code 7qyq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida, PDB code: 7qyq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida


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 A Dyp-Type Peroxidase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:31.4 occ:1.00 FE A:HEM301 0.0 31.4 1.0 NB A:HEM301 2.0 26.9 1.0 ND A:HEM301 2.0 27.4 1.0 NA A:HEM301 2.1 27.0 1.0 NC A:HEM301 2.1 25.3 1.0 NE2 A:HIS197 2.1 53.8 1.0 C1D A:HEM301 3.1 28.7 1.0 C1B A:HEM301 3.1 28.0 1.0 C4B A:HEM301 3.1 29.6 1.0 C4D A:HEM301 3.1 30.0 1.0 C1A A:HEM301 3.1 31.2 1.0 C4C A:HEM301 3.1 27.0 1.0 CE1 A:HIS197 3.1 53.8 1.0 C4A A:HEM301 3.1 28.5 1.0 C1C A:HEM301 3.1 28.6 1.0 CD2 A:HIS197 3.1 53.5 1.0 CHD A:HEM301 3.4 27.4 1.0 CHB A:HEM301 3.4 29.9 1.0 CHA A:HEM301 3.4 31.6 1.0 CHC A:HEM301 3.4 29.5 1.0 O A:HOH440 3.6 35.2 1.0 ND1 A:HIS197 4.2 54.4 1.0 CG A:HIS197 4.3 54.0 1.0 C2D A:HEM301 4.3 32.4 1.0 C3D A:HEM301 4.3 31.8 1.0 C2B A:HEM301 4.3 27.4 1.0 C3B A:HEM301 4.3 30.7 1.0 C2A A:HEM301 4.3 30.1 1.0 C3A A:HEM301 4.3 27.7 1.0 C3C A:HEM301 4.3 28.1 1.0 C2C A:HEM301 4.3 28.7 1.0 NH1 A:ARG214 4.5 39.5 1.0 CD A:ARG214 4.6 35.9 1.0 CE1 A:PHE229 4.7 26.3 1.0 CZ A:ARG214 4.9 38.7 1.0 OG1 A:THR201 4.9 48.7 1.0 NE A:ARG214 4.9 37.1 1.0 CD1 A:LEU257 5.0 31.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida


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 A Dyp-Type Peroxidase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:47.4 occ:1.00 FE B:HEM301 0.0 47.4 1.0 ND B:HEM301 2.0 48.1 1.0 NB B:HEM301 2.0 46.8 1.0 NA B:HEM301 2.0 51.4 1.0 NC B:HEM301 2.1 48.3 1.0 NE2 B:HIS197 2.2 52.7 1.0 O B:HOH431 2.9 26.7 1.0 C4B B:HEM301 3.1 48.1 1.0 C1A B:HEM301 3.1 51.1 1.0 C1D B:HEM301 3.1 47.8 1.0 C4D B:HEM301 3.1 48.8 1.0 C4A B:HEM301 3.1 49.5 1.0 C1C B:HEM301 3.1 47.3 1.0 C1B B:HEM301 3.1 44.9 1.0 C4C B:HEM301 3.1 48.1 1.0 CE1 B:HIS197 3.2 51.5 1.0 CD2 B:HIS197 3.2 51.9 1.0 CHC B:HEM301 3.4 48.1 1.0 CHA B:HEM301 3.4 50.1 1.0 CHD B:HEM301 3.4 47.8 1.0 CHB B:HEM301 3.4 46.4 1.0 C2A B:HEM301 4.3 49.9 1.0 C2C B:HEM301 4.3 47.1 1.0 C3A B:HEM301 4.3 50.2 1.0 C3B B:HEM301 4.3 46.6 1.0 C2D B:HEM301 4.3 46.1 1.0 C3C B:HEM301 4.3 47.9 1.0 C2B B:HEM301 4.3 44.2 1.0 C3D B:HEM301 4.3 47.6 1.0 ND1 B:HIS197 4.3 51.5 1.0 CG B:HIS197 4.3 50.7 1.0 NH1 B:ARG214 4.5 44.3 1.0 CD B:ARG214 4.6 38.9 1.0 CE1 B:PHE229 4.7 43.8 1.0 CZ B:ARG214 4.9 43.7 1.0 NE B:ARG214 4.9 41.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida


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 A Dyp-Type Peroxidase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:33.5 occ:1.00 FE C:HEM301 0.0 33.5 1.0 NB C:HEM301 2.0 34.0 1.0 ND C:HEM301 2.0 33.8 1.0 NC C:HEM301 2.1 31.6 1.0 NA C:HEM301 2.1 34.7 1.0 NE2 C:HIS197 2.2 55.3 1.0 C1D C:HEM301 3.1 36.1 1.0 C4B C:HEM301 3.1 33.1 1.0 C4C C:HEM301 3.1 33.8 1.0 C1B C:HEM301 3.1 35.7 1.0 C4A C:HEM301 3.1 37.7 1.0 C4D C:HEM301 3.1 36.0 1.0 C1C C:HEM301 3.1 30.7 1.0 C1A C:HEM301 3.1 37.6 1.0 CE1 C:HIS197 3.1 52.8 1.0 CD2 C:HIS197 3.2 54.2 1.0 CHD C:HEM301 3.4 35.4 1.0 CHB C:HEM301 3.4 37.8 1.0 O C:HOH426 3.4 35.3 1.0 CHC C:HEM301 3.4 31.0 1.0 CHA C:HEM301 3.4 37.1 1.0 ND1 C:HIS197 4.3 53.1 1.0 C2D C:HEM301 4.3 37.2 1.0 C3D C:HEM301 4.3 38.8 1.0 C3B C:HEM301 4.3 33.5 1.0 C2B C:HEM301 4.3 33.7 1.0 C3C C:HEM301 4.3 35.1 1.0 C2C C:HEM301 4.3 31.9 1.0 C3A C:HEM301 4.3 40.2 1.0 C2A C:HEM301 4.3 40.7 1.0 CG C:HIS197 4.3 53.3 1.0 CD C:ARG214 4.6 38.0 1.0 NH1 C:ARG214 4.6 39.9 1.0 CE1 C:PHE229 4.8 38.9 1.0 NE C:ARG214 5.0 39.9 1.0 CZ C:ARG214 5.0 40.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase From Pseudomonas Putida


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 A Dyp-Type Peroxidase From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:47.4 occ:1.00 FE D:HEM301 0.0 47.4 1.0 NB D:HEM301 2.0 47.9 1.0 ND D:HEM301 2.0 47.6 1.0 NC D:HEM301 2.1 49.2 1.0 NA D:HEM301 2.1 50.2 1.0 NE2 D:HIS197 2.2 33.9 1.0 C4B D:HEM301 3.1 47.5 1.0 C1D D:HEM301 3.1 46.3 1.0 C1B D:HEM301 3.1 48.0 1.0 C4C D:HEM301 3.1 49.9 1.0 C1C D:HEM301 3.1 49.0 1.0 C4A D:HEM301 3.1 50.0 1.0 C4D D:HEM301 3.1 48.0 1.0 C1A D:HEM301 3.1 48.8 1.0 CD2 D:HIS197 3.2 34.5 1.0 CE1 D:HIS197 3.2 34.0 1.0 CHC D:HEM301 3.4 47.2 1.0 CHD D:HEM301 3.4 48.1 1.0 CHB D:HEM301 3.4 50.3 1.0 CHA D:HEM301 3.4 48.4 1.0 O D:HOH425 3.5 27.9 1.0 C3B D:HEM301 4.3 46.3 1.0 C2D D:HEM301 4.3 44.1 1.0 C2B D:HEM301 4.3 45.7 1.0 C3A D:HEM301 4.3 48.2 1.0 C3D D:HEM301 4.3 47.3 1.0 C2A D:HEM301 4.3 47.6 1.0 C2C D:HEM301 4.3 52.5 1.0 C3C D:HEM301 4.3 52.2 1.0 ND1 D:HIS197 4.3 35.1 1.0 NH1 D:ARG214 4.3 37.9 1.0 CG D:HIS197 4.4 35.4 1.0 CD D:ARG214 4.5 36.2 1.0 CE1 D:PHE229 4.6 40.1 1.0 CZ D:ARG214 4.7 39.5 1.0 NE D:ARG214 4.8 40.5 1.0 OG1 D:THR201 5.0 39.1 1.0

P.T.Borges, D.Silva, T.F.D.Silva, V.Brissos, M.Canellas, M.F.Lucas, L.Masgrau, E.P.Melo, M.Machuqueiro, C.Frazao, L.O.Martins. Unveiling Molecular Details Behind Improved Activity at Neutral to Alkaline pH of An Engineered Dyp-Type Peroxidase. Comput Struct Biotechnol J V. 20 3899 2022.
ISSN: ESSN 2001-0370
PubMed: 35950185
DOI: 10.1016/J.CSBJ.2022.07.032