Iron in PDB 7pkx: Crystal Structure of A Dyp-Type Peroxidase From Bacillus Subtilis in P3121 Space Group

The structure of Crystal Structure of A Dyp-Type Peroxidase From Bacillus Subtilis in P3121 Space Group, PDB code: 7pkx 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)	75.09 / 2.49
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.271, 95.271, 181.244, 90, 90, 120
R / Rfree (%)	19.3 / 19.3

The binding sites of Iron atom in the Crystal Structure of A Dyp-Type Peroxidase From Bacillus Subtilis in P3121 Space Group (pdb code 7pkx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of A Dyp-Type Peroxidase From Bacillus Subtilis in P3121 Space Group, PDB code: 7pkx:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of A Dyp-Type Peroxidase From Bacillus Subtilis in P3121 Space Group


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 Bacillus Subtilis in P3121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:57.2 occ:1.00 FE A:HEM501 0.0 57.2 1.0 NC A:HEM501 2.0 54.6 1.0 NB A:HEM501 2.0 54.8 1.0 NA A:HEM501 2.0 61.4 1.0 ND A:HEM501 2.1 65.9 1.0 NE2 A:HIS326 2.3 64.0 1.0 C1C A:HEM501 3.0 52.9 1.0 C4B A:HEM501 3.0 53.9 1.0 C4C A:HEM501 3.0 59.3 1.0 C1A A:HEM501 3.1 65.8 1.0 C4A A:HEM501 3.1 62.5 1.0 C1B A:HEM501 3.1 57.2 1.0 C1D A:HEM501 3.1 60.8 1.0 C4D A:HEM501 3.1 63.0 1.0 CE1 A:HIS326 3.1 66.5 1.0 CD2 A:HIS326 3.3 65.9 1.0 CHC A:HEM501 3.3 52.2 1.0 CHD A:HEM501 3.4 60.1 1.0 CHA A:HEM501 3.4 68.3 1.0 CHB A:HEM501 3.5 58.8 1.0 O A:HOH607 3.5 56.5 1.0 NE A:ARG339 4.0 58.8 1.0 C2C A:HEM501 4.2 53.5 1.0 C3C A:HEM501 4.2 61.2 1.0 C3B A:HEM501 4.3 59.4 1.0 C2A A:HEM501 4.3 66.1 1.0 ND1 A:HIS326 4.3 66.3 1.0 C3A A:HEM501 4.3 61.4 1.0 C2B A:HEM501 4.3 56.9 1.0 C2D A:HEM501 4.3 49.2 1.0 C3D A:HEM501 4.3 53.6 1.0 CG A:HIS326 4.4 65.3 1.0 NH2 A:ARG339 4.6 62.1 1.0 CZ A:ARG339 4.6 61.4 1.0 CD A:ARG339 4.7 54.7 1.0 CE2 A:PHE361 4.9 52.3 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Dyp-Type Peroxidase From Bacillus Subtilis in P3121 Space Group


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 Bacillus Subtilis in P3121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:58.9 occ:1.00 FE B:HEM501 0.0 58.9 1.0 NC B:HEM501 2.0 56.7 1.0 ND B:HEM501 2.0 55.7 1.0 NA B:HEM501 2.0 60.6 1.0 NB B:HEM501 2.0 57.0 1.0 NE2 B:HIS326 2.2 70.4 1.0 C1D B:HEM501 3.0 52.2 1.0 C4C B:HEM501 3.0 55.8 1.0 C4D B:HEM501 3.0 56.3 1.0 C1C B:HEM501 3.1 58.8 1.0 C1B B:HEM501 3.1 61.4 1.0 C4A B:HEM501 3.1 65.0 1.0 C1A B:HEM501 3.1 60.0 1.0 C4B B:HEM501 3.1 55.7 1.0 CE1 B:HIS326 3.1 71.4 1.0 CD2 B:HIS326 3.3 72.4 1.0 CHD B:HEM501 3.4 52.6 1.0 CHB B:HEM501 3.4 65.9 1.0 CHA B:HEM501 3.4 57.1 1.0 CHC B:HEM501 3.5 55.7 1.0 O B:HOH606 3.5 49.2 1.0 NE B:ARG339 4.1 56.7 1.0 C2D B:HEM501 4.2 52.7 1.0 C3D B:HEM501 4.2 56.2 1.0 C3C B:HEM501 4.2 58.9 1.0 C2C B:HEM501 4.3 58.2 1.0 ND1 B:HIS326 4.3 71.9 1.0 C2A B:HEM501 4.3 61.5 1.0 C3A B:HEM501 4.3 61.9 1.0 C2B B:HEM501 4.3 58.5 1.0 C3B B:HEM501 4.3 56.6 1.0 CG B:HIS326 4.4 72.4 1.0 NH2 B:ARG339 4.7 57.9 1.0 CZ B:ARG339 4.7 62.3 1.0 CD B:ARG339 4.7 52.1 1.0 CE2 B:PHE361 4.9 62.3 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