Iron in PDB 7qza: Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida

The structure of Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida, PDB code: 7qza 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)	78.60 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.957, 78.813, 98.931, 91.02, 92.93, 94
R / Rfree (%)	18.9 / 18.9

The binding sites of Iron atom in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida (pdb code 7qza). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida, PDB code: 7qza:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant 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 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:50.0 occ:1.00 FE A:HEM301 0.0 50.0 1.0 NA A:HEM301 2.0 57.2 1.0 NB A:HEM301 2.0 53.5 1.0 ND A:HEM301 2.1 54.7 1.0 NC A:HEM301 2.1 50.4 1.0 NE2 A:HIS197 2.2 52.4 1.0 C1A A:HEM301 3.0 59.8 1.0 C4A A:HEM301 3.0 59.1 1.0 C4B A:HEM301 3.0 52.8 1.0 C1B A:HEM301 3.1 55.4 1.0 C1C A:HEM301 3.1 50.2 1.0 C4C A:HEM301 3.1 48.1 1.0 CD2 A:HIS197 3.1 52.9 1.0 C1D A:HEM301 3.1 53.0 1.0 C4D A:HEM301 3.1 55.5 1.0 CE1 A:HIS197 3.3 52.4 1.0 CHA A:HEM301 3.4 58.4 1.0 CHB A:HEM301 3.4 58.6 1.0 CHC A:HEM301 3.4 51.9 1.0 CHD A:HEM301 3.5 50.4 1.0 C2A A:HEM301 4.2 61.6 1.0 C3A A:HEM301 4.2 58.3 1.0 C3B A:HEM301 4.3 53.3 1.0 C2B A:HEM301 4.3 50.9 1.0 C2C A:HEM301 4.3 47.7 1.0 C3C A:HEM301 4.3 47.1 1.0 CG A:HIS197 4.3 53.2 1.0 C2D A:HEM301 4.3 53.7 1.0 C3D A:HEM301 4.3 56.4 1.0 ND1 A:HIS197 4.3 52.9 1.0 NH1 A:ARG214 4.4 57.7 1.0 CD A:ARG214 4.7 54.5 1.0 OG1 A:THR201 4.8 65.1 1.0 CE1 A:PHE229 4.8 44.4 1.0

Iron binding site 2 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant 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 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:56.0 occ:1.00 FE B:HEM301 0.0 56.0 1.0 NB B:HEM301 2.0 57.5 1.0 NA B:HEM301 2.0 56.5 1.0 NC B:HEM301 2.1 57.5 1.0 NE2 B:HIS197 2.1 76.9 1.0 ND B:HEM301 2.1 60.7 1.0 C4B B:HEM301 3.0 57.7 1.0 CD2 B:HIS197 3.0 73.1 1.0 C1B B:HEM301 3.0 60.6 1.0 C4C B:HEM301 3.0 57.4 1.0 C1C B:HEM301 3.0 57.2 1.0 C4A B:HEM301 3.1 57.0 1.0 C1D B:HEM301 3.1 60.7 1.0 C1A B:HEM301 3.1 60.8 1.0 CE1 B:HIS197 3.1 73.6 1.0 C4D B:HEM301 3.1 62.6 1.0 CHC B:HEM301 3.4 55.9 1.0 CHD B:HEM301 3.4 58.4 1.0 CHB B:HEM301 3.4 60.1 1.0 CHA B:HEM301 3.5 63.5 1.0 NH1 B:ARG214 4.1 63.5 1.0 ND1 B:HIS197 4.2 73.4 1.0 CG B:HIS197 4.2 74.0 1.0 C3C B:HEM301 4.2 56.8 1.0 C2C B:HEM301 4.2 57.1 1.0 C3B B:HEM301 4.2 61.9 1.0 C2B B:HEM301 4.2 60.4 1.0 C3A B:HEM301 4.3 55.4 1.0 C2D B:HEM301 4.3 61.4 1.0 C2A B:HEM301 4.3 59.5 1.0 C3D B:HEM301 4.4 64.7 1.0 OG1 B:THR201 4.8 58.0 1.0 CZ B:ARG214 4.8 61.0 1.0 CD B:ARG214 4.8 55.3 1.0 CE1 B:PHE229 4.9 38.9 1.0 CD1 B:LEU257 5.0 54.6 1.0

Iron binding site 3 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant 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 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:52.6 occ:1.00 FE C:HEM301 0.0 52.6 1.0 NA C:HEM301 2.1 55.5 1.0 NC C:HEM301 2.1 53.0 1.0 ND C:HEM301 2.1 59.7 1.0 NE2 C:HIS197 2.1 73.3 1.0 NB C:HEM301 2.1 56.4 1.0 CD2 C:HIS197 3.0 71.4 1.0 C4C C:HEM301 3.0 54.9 1.0 C1D C:HEM301 3.1 60.1 1.0 C1B C:HEM301 3.1 59.1 1.0 CE1 C:HIS197 3.1 70.5 1.0 C4A C:HEM301 3.1 58.8 1.0 C1A C:HEM301 3.1 59.0 1.0 C4B C:HEM301 3.1 56.6 1.0 C1C C:HEM301 3.1 55.1 1.0 C4D C:HEM301 3.1 64.7 1.0 CHD C:HEM301 3.4 56.9 1.0 CHB C:HEM301 3.4 60.4 1.0 CHA C:HEM301 3.4 63.9 1.0 CHC C:HEM301 3.5 55.5 1.0 ND1 C:HIS197 4.2 71.0 1.0 CG C:HIS197 4.2 71.1 1.0 C2B C:HEM301 4.3 56.0 1.0 C3B C:HEM301 4.3 57.5 1.0 C3C C:HEM301 4.3 55.0 1.0 C3A C:HEM301 4.3 54.9 1.0 C2A C:HEM301 4.3 56.2 1.0 C2C C:HEM301 4.3 51.8 1.0 C2D C:HEM301 4.3 62.9 1.0 C3D C:HEM301 4.3 66.9 1.0 NH1 C:ARG214 4.5 65.6 1.0 CD1 C:LEU257 4.8 62.9 1.0 CD C:ARG214 4.9 61.6 1.0 OG1 C:THR201 4.9 59.6 1.0 CE1 C:PHE229 4.9 52.0 1.0

Iron binding site 4 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant 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 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:66.7 occ:1.00 FE D:HEM301 0.0 66.7 1.0 NA D:HEM301 2.0 71.8 1.0 NB D:HEM301 2.0 67.5 1.0 NC D:HEM301 2.1 62.1 1.0 ND D:HEM301 2.1 68.8 1.0 NE2 D:HIS197 2.2 121.8 1.0 C1A D:HEM301 3.0 75.0 1.0 C4B D:HEM301 3.0 68.6 1.0 C1C D:HEM301 3.0 61.4 1.0 C4A D:HEM301 3.0 71.5 1.0 C1B D:HEM301 3.1 67.1 1.0 C4D D:HEM301 3.1 71.1 1.0 C4C D:HEM301 3.1 60.2 1.0 CE1 D:HIS197 3.1 120.5 1.0 C1D D:HEM301 3.1 66.5 1.0 CD2 D:HIS197 3.2 120.3 1.0 CHA D:HEM301 3.4 74.2 1.0 CHC D:HEM301 3.4 66.2 1.0 CHB D:HEM301 3.4 68.6 1.0 CHD D:HEM301 3.5 62.6 1.0 NH1 D:ARG214 4.1 58.7 1.0 C2A D:HEM301 4.2 76.1 1.0 C2C D:HEM301 4.2 58.6 1.0 C3A D:HEM301 4.2 72.8 1.0 ND1 D:HIS197 4.2 119.0 1.0 C3C D:HEM301 4.3 59.5 1.0 C3B D:HEM301 4.3 68.8 1.0 C2B D:HEM301 4.3 66.0 1.0 C3D D:HEM301 4.3 70.4 1.0 C2D D:HEM301 4.3 66.5 1.0 CG D:HIS197 4.3 115.1 1.0 CE1 D:PHE229 4.8 58.8 1.0 CD D:ARG214 4.8 48.3 1.0 OG1 D:THR201 4.9 109.8 1.0 OD1 D:ASP132 4.9 115.0 1.0 CZ D:ARG214 5.0 60.8 1.0 CG2 D:THR201 5.0 107.2 1.0

Iron binding site 5 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida


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 A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:67.5 occ:1.00 FE E:HEM301 0.0 67.5 1.0 NA E:HEM301 2.0 68.6 1.0 NB E:HEM301 2.0 68.6 1.0 ND E:HEM301 2.1 75.9 1.0 NC E:HEM301 2.1 70.8 1.0 NE2 E:HIS197 2.1 127.3 1.0 C4A E:HEM301 3.0 67.8 1.0 C1A E:HEM301 3.0 72.6 1.0 C1B E:HEM301 3.0 67.9 1.0 CD2 E:HIS197 3.0 123.7 1.0 C4B E:HEM301 3.0 68.9 1.0 C1C E:HEM301 3.1 68.8 1.0 C4C E:HEM301 3.1 70.7 1.0 CE1 E:HIS197 3.1 122.6 1.0 C1D E:HEM301 3.1 76.2 1.0 C4D E:HEM301 3.1 78.4 1.0 CHB E:HEM301 3.4 67.7 1.0 CHA E:HEM301 3.4 77.4 1.0 CHC E:HEM301 3.4 68.0 1.0 CHD E:HEM301 3.5 74.8 1.0 NH1 E:ARG214 4.0 128.5 1.0 ND1 E:HIS197 4.2 123.5 1.0 CG E:HIS197 4.2 123.8 1.0 C3A E:HEM301 4.2 70.1 1.0 C2A E:HEM301 4.2 73.4 1.0 C2B E:HEM301 4.3 66.3 1.0 C3B E:HEM301 4.3 70.0 1.0 C2C E:HEM301 4.3 66.5 1.0 C3C E:HEM301 4.3 66.8 1.0 C2D E:HEM301 4.3 76.5 1.0 C3D E:HEM301 4.3 79.8 1.0 OD1 E:ASP132 4.7 126.7 1.0 CD E:ARG214 4.7 103.1 1.0 CZ E:ARG214 4.8 129.1 1.0 CE1 E:PHE229 4.8 56.7 1.0 OG1 E:THR201 4.9 91.6 1.0 CD1 E:LEU257 4.9 72.4 1.0

Iron binding site 6 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida


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 A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe301 b:67.1 occ:1.00 FE F:HEM301 0.0 67.1 1.0 ND F:HEM301 2.0 75.8 1.0 NC F:HEM301 2.1 73.9 1.0 NE2 F:HIS197 2.1 90.1 1.0 NA F:HEM301 2.1 70.7 1.0 NB F:HEM301 2.1 80.3 1.0 CE1 F:HIS197 3.0 86.0 1.0 C4C F:HEM301 3.0 75.2 1.0 C1D F:HEM301 3.0 77.1 1.0 C4B F:HEM301 3.1 74.0 1.0 C1C F:HEM301 3.1 73.2 1.0 C1A F:HEM301 3.1 72.1 1.0 C1B F:HEM301 3.1 75.1 1.0 C4A F:HEM301 3.1 70.6 1.0 C4D F:HEM301 3.1 74.6 1.0 CD2 F:HIS197 3.2 85.8 1.0 CHD F:HEM301 3.4 77.5 1.0 CHA F:HEM301 3.4 70.9 1.0 CHC F:HEM301 3.5 73.6 1.0 CHB F:HEM301 3.5 73.3 1.0 ND1 F:HIS197 4.1 86.0 1.0 C3C F:HEM301 4.2 74.1 1.0 CG F:HIS197 4.2 85.3 1.0 C2C F:HEM301 4.3 73.3 1.0 C3B F:HEM301 4.3 71.2 1.0 C2D F:HEM301 4.3 78.1 1.0 C2B F:HEM301 4.3 70.2 1.0 C2A F:HEM301 4.3 74.6 1.0 C3A F:HEM301 4.3 70.0 1.0 C3D F:HEM301 4.3 78.4 1.0 NH1 F:ARG214 4.4 94.2 1.0 CD F:ARG214 4.8 91.6 1.0 CE1 F:PHE229 4.8 72.4 1.0 CD1 F:LEU257 4.9 74.8 1.0

Iron binding site 7 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida


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 A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe301 b:82.9 occ:1.00 FE G:HEM301 0.0 82.9 1.0 NA G:HEM301 2.0 83.2 1.0 ND G:HEM301 2.0 87.7 1.0 NC G:HEM301 2.1 87.6 1.0 NB G:HEM301 2.1 84.2 1.0 NE2 G:HIS197 2.3 71.5 1.0 C1A G:HEM301 3.0 85.5 1.0 C4C G:HEM301 3.0 87.7 1.0 C1C G:HEM301 3.0 89.5 1.0 C4A G:HEM301 3.1 82.5 1.0 C1D G:HEM301 3.1 87.7 1.0 C4D G:HEM301 3.1 89.7 1.0 C4B G:HEM301 3.1 84.2 1.0 C1B G:HEM301 3.1 83.8 1.0 CE1 G:HIS197 3.3 71.6 1.0 CD2 G:HIS197 3.3 71.7 1.0 CHA G:HEM301 3.4 88.4 1.0 CHD G:HEM301 3.4 87.5 1.0 CHC G:HEM301 3.4 86.6 1.0 CHB G:HEM301 3.4 83.5 1.0 C3C G:HEM301 4.2 88.2 1.0 C2C G:HEM301 4.2 89.9 1.0 C2A G:HEM301 4.2 84.4 1.0 C3A G:HEM301 4.3 81.2 1.0 C2D G:HEM301 4.3 87.8 1.0 C2B G:HEM301 4.3 83.2 1.0 C3D G:HEM301 4.3 91.2 1.0 C3B G:HEM301 4.3 83.1 1.0 ND1 G:HIS197 4.4 71.9 1.0 CG G:HIS197 4.5 72.0 1.0 CD G:ARG214 4.6 89.4 1.0 NH1 G:ARG214 4.6 100.6 1.0 CE2 G:PHE229 4.8 70.2 1.0 CD1 G:LEU257 5.0 73.5 1.0

Iron binding site 8 out of 8 in the Crystal Structure of A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida


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 A Dyp-Type Peroxidase 29E4 Variant From Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:103.8 occ:1.00 FE H:HEM301 0.0 103.8 1.0 NE2 H:HIS197 2.0 124.0 1.0 NA H:HEM301 2.0 99.2 1.0 NB H:HEM301 2.0 97.4 1.0 ND H:HEM301 2.1 102.8 1.0 NC H:HEM301 2.1 102.0 1.0 CD2 H:HIS197 3.0 117.0 1.0 CE1 H:HIS197 3.0 119.2 1.0 C4B H:HEM301 3.0 94.1 1.0 C1C H:HEM301 3.0 97.0 1.0 C4C H:HEM301 3.0 101.0 1.0 C1A H:HEM301 3.0 100.0 1.0 C1B H:HEM301 3.1 92.6 1.0 C4A H:HEM301 3.1 94.9 1.0 C1D H:HEM301 3.1 99.4 1.0 C4D H:HEM301 3.1 103.1 1.0 CHA H:HEM301 3.4 103.1 1.0 CHC H:HEM301 3.4 96.2 1.0 CHD H:HEM301 3.4 100.6 1.0 CHB H:HEM301 3.4 94.0 1.0 ND1 H:HIS197 4.1 117.5 1.0 CG H:HIS197 4.1 113.8 1.0 C2C H:HEM301 4.2 97.6 1.0 C3C H:HEM301 4.2 99.4 1.0 C3B H:HEM301 4.2 90.9 1.0 C2B H:HEM301 4.3 88.8 1.0 C2A H:HEM301 4.3 97.8 1.0 C3A H:HEM301 4.3 93.7 1.0 C2D H:HEM301 4.3 97.5 1.0 NH2 H:ARG214 4.3 93.6 1.0 C3D H:HEM301 4.3 100.1 1.0 NE H:ARG214 4.6 85.1 1.0 OG1 H:THR201 4.9 119.2 1.0 CD1 H:LEU257 5.0 67.8 1.0 CZ H:ARG214 5.0 91.6 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