Iron in PDB 7pl0: Crystal Structure of A Dyp-Type Peroxidase 5G5 Variant From Bacillus Subtilis

The structure of Crystal Structure of A Dyp-Type Peroxidase 5G5 Variant From Bacillus Subtilis, PDB code: 7pl0 was solved by P.T.Borges, C.Rodrigues, D.Silva, A.Taborda, V.Brissos, C.Frazao, L.O.Martins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.96 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.852, 114.76, 116.819, 90, 104, 90
R / Rfree (%)	19.1 / 21.5

The binding sites of Iron atom in the Crystal Structure of A Dyp-Type Peroxidase 5G5 Variant From Bacillus Subtilis (pdb code 7pl0). 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 5G5 Variant From Bacillus Subtilis, PDB code: 7pl0:
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 5G5 Variant From Bacillus Subtilis


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 5G5 Variant From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:24.6 occ:1.00 FE A:HEM501 0.0 24.6 1.0 NC A:HEM501 2.0 23.6 1.0 NB A:HEM501 2.0 24.9 1.0 ND A:HEM501 2.0 24.7 1.0 NA A:HEM501 2.1 26.7 1.0 NE2 A:HIS326 2.2 38.6 1.0 C4C A:HEM501 3.0 23.7 1.0 C1C A:HEM501 3.0 22.7 1.0 C1D A:HEM501 3.1 24.6 1.0 C4B A:HEM501 3.1 25.0 1.0 CE1 A:HIS326 3.1 38.1 1.0 C4D A:HEM501 3.1 25.8 1.0 C1B A:HEM501 3.1 25.1 1.0 C1A A:HEM501 3.1 27.3 1.0 O A:HOH773 3.1 43.6 1.0 C4A A:HEM501 3.1 27.5 1.0 CD2 A:HIS326 3.2 37.2 1.0 CHC A:HEM501 3.4 23.2 1.0 CHD A:HEM501 3.4 24.8 1.0 CHA A:HEM501 3.4 26.4 1.0 CHB A:HEM501 3.5 25.9 1.0 NH2 A:ARG339 4.1 26.5 1.0 ND1 A:HIS326 4.2 37.2 1.0 C2C A:HEM501 4.3 24.1 1.0 C3C A:HEM501 4.3 24.6 1.0 C2D A:HEM501 4.3 23.5 1.0 C3D A:HEM501 4.3 24.7 1.0 NE A:ARG339 4.3 31.2 1.0 C3B A:HEM501 4.3 24.3 1.0 C2B A:HEM501 4.3 23.9 1.0 CG A:HIS326 4.3 34.7 1.0 C2A A:HEM501 4.3 28.1 1.0 C3A A:HEM501 4.3 28.5 1.0 CZ A:ARG339 4.5 29.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase 5G5 Variant From Bacillus Subtilis


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 5G5 Variant From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:25.2 occ:1.00 FE B:HEM501 0.0 25.2 1.0 NC B:HEM501 2.0 24.5 1.0 NB B:HEM501 2.1 23.4 1.0 NA B:HEM501 2.1 24.6 1.0 ND B:HEM501 2.1 24.8 1.0 NE2 B:HIS326 2.2 26.7 1.0 C1C B:HEM501 3.1 24.8 1.0 C4C B:HEM501 3.1 25.6 1.0 C4D B:HEM501 3.1 25.2 1.0 C1D B:HEM501 3.1 24.5 1.0 C4B B:HEM501 3.1 22.3 1.0 C1A B:HEM501 3.1 26.5 1.0 C4A B:HEM501 3.1 25.9 1.0 C1B B:HEM501 3.1 25.1 1.0 CE1 B:HIS326 3.1 27.4 1.0 O B:HOH676 3.1 46.3 1.0 CD2 B:HIS326 3.2 28.0 1.0 CHA B:HEM501 3.4 26.8 1.0 CHC B:HEM501 3.4 23.2 1.0 CHD B:HEM501 3.4 25.4 1.0 CHB B:HEM501 3.5 25.9 1.0 NH2 B:ARG339 4.1 30.0 1.0 ND1 B:HIS326 4.3 27.3 1.0 C2C B:HEM501 4.3 24.9 1.0 C3C B:HEM501 4.3 25.5 1.0 C3D B:HEM501 4.3 25.0 1.0 C2D B:HEM501 4.3 24.8 1.0 C2A B:HEM501 4.3 26.5 1.0 C3A B:HEM501 4.3 25.4 1.0 C3B B:HEM501 4.3 23.7 1.0 C2B B:HEM501 4.3 24.2 1.0 NE B:ARG339 4.3 30.9 1.0 CG B:HIS326 4.3 27.4 1.0 CZ B:ARG339 4.6 29.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase 5G5 Variant From Bacillus Subtilis


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 5G5 Variant From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:32.7 occ:1.00 FE C:HEM501 0.0 32.7 1.0 NC C:HEM501 2.1 32.5 1.0 NB C:HEM501 2.1 33.0 1.0 NA C:HEM501 2.1 31.8 1.0 ND C:HEM501 2.1 31.3 1.0 NE2 C:HIS326 2.2 33.5 1.0 C1C C:HEM501 3.0 32.2 1.0 O C:HOH741 3.1 49.1 1.0 C4C C:HEM501 3.1 31.9 1.0 C4D C:HEM501 3.1 32.1 1.0 C4B C:HEM501 3.1 31.9 1.0 C1A C:HEM501 3.1 32.3 1.0 C4A C:HEM501 3.1 31.5 1.0 C1D C:HEM501 3.1 31.2 1.0 C1B C:HEM501 3.1 32.0 1.0 CE1 C:HIS326 3.2 33.6 1.0 CD2 C:HIS326 3.2 34.1 1.0 CHC C:HEM501 3.4 31.8 1.0 CHA C:HEM501 3.4 31.9 1.0 CHD C:HEM501 3.4 32.1 1.0 CHB C:HEM501 3.5 31.7 1.0 C2C C:HEM501 4.3 31.4 1.0 C3C C:HEM501 4.3 31.7 1.0 C3D C:HEM501 4.3 32.3 1.0 NH2 C:ARG339 4.3 42.6 1.0 ND1 C:HIS326 4.3 34.6 1.0 C2A C:HEM501 4.3 32.3 1.0 C2D C:HEM501 4.3 31.0 1.0 C3A C:HEM501 4.3 30.6 1.0 C3B C:HEM501 4.3 31.5 1.0 C2B C:HEM501 4.3 31.2 1.0 CG C:HIS326 4.3 35.3 1.0 NE C:ARG339 4.4 42.8 1.0 CZ C:ARG339 4.7 42.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Dyp-Type Peroxidase 5G5 Variant From Bacillus Subtilis


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 5G5 Variant From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:35.7 occ:1.00 FE D:HEM501 0.0 35.7 1.0 NC D:HEM501 2.0 37.1 1.0 ND D:HEM501 2.0 36.5 1.0 NB D:HEM501 2.1 36.5 1.0 NA D:HEM501 2.1 35.9 1.0 NE2 D:HIS326 2.2 39.0 1.0 C4C D:HEM501 3.0 36.6 1.0 C1C D:HEM501 3.0 36.9 1.0 C1D D:HEM501 3.1 37.9 1.0 C4B D:HEM501 3.1 35.9 1.0 C4D D:HEM501 3.1 37.5 1.0 C4A D:HEM501 3.1 34.6 1.0 C1B D:HEM501 3.1 34.8 1.0 C1A D:HEM501 3.1 37.1 1.0 CE1 D:HIS326 3.2 40.3 1.0 CD2 D:HIS326 3.3 39.8 1.0 CHD D:HEM501 3.4 37.5 1.0 O D:HOH719 3.4 48.8 1.0 CHC D:HEM501 3.4 35.8 1.0 CHA D:HEM501 3.4 37.9 1.0 CHB D:HEM501 3.4 34.8 1.0 NH2 D:ARG339 4.1 39.6 1.0 C3C D:HEM501 4.2 36.9 1.0 C2C D:HEM501 4.2 36.9 1.0 C2D D:HEM501 4.3 38.7 1.0 C3D D:HEM501 4.3 39.1 1.0 NE D:ARG339 4.3 41.8 1.0 C3A D:HEM501 4.3 34.8 1.0 ND1 D:HIS326 4.3 40.7 1.0 C2A D:HEM501 4.3 36.1 1.0 C2B D:HEM501 4.3 33.7 1.0 C3B D:HEM501 4.3 33.8 1.0 CG D:HIS326 4.4 40.1 1.0 CZ D:ARG339 4.5 40.8 1.0

C.F.Rodrigues, P.T.Borges, M.F.Scocozza, D.Silva, A.Taborda, V.Brissos, C.Frazao, L.O.Martins. Loops Around the Heme Pocket Have A Critical Role in the Function and Stability of Bs Dyp From Bacillus Subtilis . Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34639208
DOI: 10.3390/IJMS221910862