Iron in PDB 5c2i: Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx)

The structure of Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx), PDB code: 5c2i was solved by T.Yoshida, Y.Amano, H.Tsuge, Y.Sugano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.73 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.734, 132.601, 176.528, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.9

The binding sites of Iron atom in the Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx) (pdb code 5c2i). 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 Anabaena Sp. Dyp-Type Peroxidese (Anapx), PDB code: 5c2i:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx)


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 Anabaena Sp. Dyp-Type Peroxidese (Anapx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:15.1 occ:1.00 FE A:HEM501 0.0 15.1 1.0 ND A:HEM501 1.9 13.7 1.0 NA A:HEM501 2.0 13.4 1.0 NC A:HEM501 2.0 14.1 1.0 NB A:HEM501 2.1 13.9 1.0 NE2 A:HIS331 2.1 16.2 1.0 O A:HOH716 2.3 20.8 1.0 C4D A:HEM501 2.9 13.4 1.0 C1D A:HEM501 2.9 14.4 1.0 C4B A:HEM501 3.0 14.7 1.0 C1B A:HEM501 3.0 15.2 1.0 C1A A:HEM501 3.0 13.2 1.0 C4A A:HEM501 3.0 13.6 1.0 C4C A:HEM501 3.0 14.6 1.0 C1C A:HEM501 3.1 14.8 1.0 CE1 A:HIS331 3.1 15.7 1.0 CD2 A:HIS331 3.1 16.7 1.0 CHA A:HEM501 3.4 13.3 1.0 CHD A:HEM501 3.4 14.5 1.0 CHB A:HEM501 3.4 13.5 1.0 CHC A:HEM501 3.4 13.8 1.0 NH1 A:ARG365 4.1 14.7 1.0 NE2 A:HIS204 4.1 23.1 1.0 C2D A:HEM501 4.2 14.2 1.0 C3D A:HEM501 4.2 13.8 1.0 C3C A:HEM501 4.2 15.3 1.0 ND1 A:HIS331 4.2 15.8 1.0 C2A A:HEM501 4.2 14.1 1.0 C3A A:HEM501 4.2 13.1 1.0 C2C A:HEM501 4.2 14.4 1.0 C2B A:HEM501 4.2 15.0 1.0 C3B A:HEM501 4.3 14.6 1.0 CG A:HIS331 4.3 15.9 1.0 CD2 A:HIS204 4.8 23.7 1.0 CD A:ARG365 4.9 15.1 1.0 CZ A:ARG365 5.0 14.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx)


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 Anabaena Sp. Dyp-Type Peroxidese (Anapx) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:21.9 occ:1.00 FE B:HEM501 0.0 21.9 1.0 ND B:HEM501 1.9 20.2 1.0 NA B:HEM501 2.0 18.8 1.0 NC B:HEM501 2.0 19.8 1.0 NB B:HEM501 2.1 21.6 1.0 NE2 B:HIS331 2.2 23.1 1.0 O B:HOH675 2.5 21.4 1.0 C1D B:HEM501 2.9 20.4 1.0 C4D B:HEM501 2.9 19.7 1.0 C4A B:HEM501 3.0 18.5 1.0 C1A B:HEM501 3.0 18.0 1.0 C1B B:HEM501 3.0 20.8 1.0 C4C B:HEM501 3.0 20.6 1.0 C4B B:HEM501 3.1 19.6 1.0 CD2 B:HIS331 3.1 23.4 1.0 C1C B:HEM501 3.1 18.8 1.0 CE1 B:HIS331 3.1 24.4 1.0 CHB B:HEM501 3.4 18.6 1.0 CHD B:HEM501 3.4 19.4 1.0 CHA B:HEM501 3.4 19.9 1.0 CHC B:HEM501 3.5 18.9 1.0 NH1 B:ARG365 4.1 22.8 1.0 C3A B:HEM501 4.1 18.0 1.0 NE2 B:HIS204 4.2 27.0 1.0 C2D B:HEM501 4.2 22.1 1.0 C2A B:HEM501 4.2 18.6 1.0 C3D B:HEM501 4.2 20.7 1.0 C3C B:HEM501 4.2 19.9 1.0 ND1 B:HIS331 4.2 24.2 1.0 C2C B:HEM501 4.3 21.1 1.0 CG B:HIS331 4.3 24.2 1.0 C2B B:HEM501 4.3 20.2 1.0 C3B B:HEM501 4.3 20.1 1.0 CD2 B:HIS204 4.8 27.1 1.0 CZ B:ARG365 5.0 23.0 1.0 CD B:ARG365 5.0 21.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx)


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 Anabaena Sp. Dyp-Type Peroxidese (Anapx) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:17.8 occ:1.00 FE C:HEM501 0.0 17.8 1.0 ND C:HEM501 2.0 17.9 1.0 NA C:HEM501 2.0 16.5 1.0 NB C:HEM501 2.1 17.1 1.0 NC C:HEM501 2.1 17.8 1.0 NE2 C:HIS331 2.2 17.3 1.0 O C:HOH644 2.5 21.7 1.0 C4B C:HEM501 3.0 17.3 1.0 C4D C:HEM501 3.0 18.2 1.0 C1D C:HEM501 3.0 18.0 1.0 C1B C:HEM501 3.0 17.6 1.0 C4A C:HEM501 3.0 16.6 1.0 C1A C:HEM501 3.0 17.2 1.0 C4C C:HEM501 3.0 18.4 1.0 C1C C:HEM501 3.1 16.7 1.0 CE1 C:HIS331 3.1 17.4 1.0 CD2 C:HIS331 3.1 17.1 1.0 CHB C:HEM501 3.4 17.0 1.0 CHC C:HEM501 3.4 16.0 1.0 CHD C:HEM501 3.4 17.7 1.0 CHA C:HEM501 3.4 16.9 1.0 NH1 C:ARG365 4.1 18.4 1.0 NE2 C:HIS204 4.2 21.9 1.0 ND1 C:HIS331 4.2 18.2 1.0 C3A C:HEM501 4.2 16.9 1.0 C2A C:HEM501 4.3 16.9 1.0 C2C C:HEM501 4.3 18.4 1.0 C3C C:HEM501 4.3 18.4 1.0 CG C:HIS331 4.3 17.7 1.0 C2B C:HEM501 4.3 17.2 1.0 C2D C:HEM501 4.3 17.3 1.0 C3B C:HEM501 4.3 16.3 1.0 C3D C:HEM501 4.3 16.1 1.0 CD2 C:HIS204 4.8 23.0 1.0 CD C:ARG365 4.9 17.4 1.0 CZ C:ARG365 4.9 18.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Anabaena Sp. Dyp-Type Peroxidese (Anapx)


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 Anabaena Sp. Dyp-Type Peroxidese (Anapx) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:23.8 occ:1.00 FE D:HEM501 0.0 23.8 1.0 ND D:HEM501 1.9 20.9 1.0 NA D:HEM501 1.9 20.8 1.0 NC D:HEM501 2.0 22.4 1.0 NB D:HEM501 2.1 23.8 1.0 NE2 D:HIS331 2.2 24.1 1.0 O D:HOH702 2.5 27.0 1.0 C1D D:HEM501 2.9 20.0 1.0 C4D D:HEM501 3.0 19.6 1.0 C4A D:HEM501 3.0 21.3 1.0 C1A D:HEM501 3.0 20.3 1.0 C4C D:HEM501 3.0 22.4 1.0 C1B D:HEM501 3.0 21.7 1.0 C4B D:HEM501 3.0 22.8 1.0 C1C D:HEM501 3.1 21.4 1.0 CE1 D:HIS331 3.1 25.1 1.0 CD2 D:HIS331 3.2 24.6 1.0 CHD D:HEM501 3.3 21.4 1.0 CHB D:HEM501 3.4 21.4 1.0 CHA D:HEM501 3.4 18.7 1.0 CHC D:HEM501 3.5 20.8 1.0 NH1 D:ARG365 4.1 22.9 1.0 C3A D:HEM501 4.2 20.3 1.0 C2A D:HEM501 4.2 19.4 1.0 NE2 D:HIS204 4.2 34.0 1.0 C2D D:HEM501 4.2 20.6 1.0 C3C D:HEM501 4.2 22.5 1.0 C3D D:HEM501 4.2 20.4 1.0 C2B D:HEM501 4.2 23.5 1.0 ND1 D:HIS331 4.3 25.7 1.0 C2C D:HEM501 4.3 22.0 1.0 C3B D:HEM501 4.3 21.7 1.0 CG D:HIS331 4.3 25.3 1.0 CD2 D:HIS204 4.9 32.6 1.0 CD D:ARG365 4.9 22.3 1.0 CZ D:ARG365 5.0 22.5 1.0

T.Yoshida, H.J.Ogola, Y.Amano, T.Hisabori, H.Ashida, Y.Sawa, H.Tsuge, Y.Sugano. Anabaena Sp. Dyp-Type Peroxidase Is A Tetramer Consisting of Two Asymmetric Dimers. Proteins V. 84 31 2016.
ISSN: ESSN 1097-0134
PubMed: 26492416
DOI: 10.1002/PROT.24952