Iron in PDB 8zyb: A-Kg Dependent Oxygenase

The structure of A-Kg Dependent Oxygenase, PDB code: 8zyb was solved by A.Fan, S.Fan, M.Wu, Z.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.57 / 2.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	368.944, 78.254, 81.912, 90, 98.02, 90
R / Rfree (%)	20.3 / 25.7

The binding sites of Iron atom in the A-Kg Dependent Oxygenase (pdb code 8zyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the A-Kg Dependent Oxygenase, PDB code: 8zyb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:44.4 occ:1.00 NE2 F:HIS64 2.0 67.2 1.0 NE2 E:HIS126 2.1 46.5 1.0 NE2 E:HIS203 2.1 41.2 1.0 OD1 E:ASP128 2.2 36.9 1.0 CE1 F:HIS64 2.9 69.6 1.0 CE1 E:HIS126 2.9 42.6 1.0 CG E:ASP128 3.0 47.3 1.0 CD2 F:HIS64 3.1 65.3 1.0 CD2 E:HIS203 3.1 36.3 1.0 CE1 E:HIS203 3.1 42.3 1.0 OD2 E:ASP128 3.2 58.2 1.0 CD2 E:HIS126 3.3 35.0 1.0 ND1 F:HIS64 4.0 69.4 1.0 ND1 E:HIS126 4.1 30.7 1.0 CG F:HIS64 4.1 66.7 1.0 ND1 E:HIS203 4.2 35.2 1.0 CG E:HIS203 4.2 38.9 1.0 CG E:HIS126 4.3 37.1 1.0 CB E:ASP128 4.5 27.1 1.0 OE1 E:GLN123 4.9 50.0 1.0 CA E:ASP128 4.9 38.7 1.0 N E:ASP128 5.0 42.1 1.0

Iron binding site 2 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:49.5 occ:1.00 NE2 A:HIS203 2.1 43.5 1.0 NE2 A:HIS126 2.1 48.8 1.0 OD1 A:ASP128 2.4 50.2 1.0 CE1 A:HIS126 2.8 53.7 1.0 CE1 A:HIS203 3.0 55.5 1.0 CD2 A:HIS203 3.1 50.7 1.0 CG A:ASP128 3.2 47.6 1.0 CD2 A:HIS126 3.3 51.7 1.0 OD2 A:ASP128 3.4 49.5 1.0 ND1 A:HIS126 4.1 39.8 1.0 ND1 A:HIS203 4.2 55.8 1.0 CG A:HIS203 4.2 53.7 1.0 CG A:HIS126 4.3 54.4 1.0 CB A:ASP128 4.7 46.2 1.0

Iron binding site 3 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:48.2 occ:1.00 NE2 B:HIS126 2.1 66.5 1.0 NE2 B:HIS203 2.1 59.6 1.0 OD1 B:ASP128 2.4 50.3 1.0 NE2 H:HIS64 2.5 140.7 1.0 CE1 B:HIS126 2.8 68.1 1.0 CE1 B:HIS203 3.0 52.6 1.0 CD2 B:HIS203 3.1 46.7 1.0 CG B:ASP128 3.2 53.8 1.0 OD2 B:ASP128 3.2 66.5 1.0 CD2 H:HIS64 3.2 143.7 1.0 CD2 B:HIS126 3.3 56.8 1.0 CE1 H:HIS64 3.5 138.3 1.0 ND1 B:HIS126 4.0 67.3 1.0 ND1 B:HIS203 4.1 50.2 1.0 CG B:HIS203 4.2 47.8 1.0 CG B:HIS126 4.3 63.6 1.0 CG H:HIS64 4.4 143.1 1.0 ND1 H:HIS64 4.5 139.6 1.0 CB B:ASP128 4.6 38.9 1.0 OE1 B:GLN123 4.8 58.5 1.0

Iron binding site 4 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:54.1 occ:1.00 NE2 C:HIS203 2.1 51.9 1.0 OD1 C:ASP128 2.3 52.9 1.0 NE2 C:HIS126 2.3 58.6 1.0 CE1 C:HIS126 3.0 67.7 1.0 CE1 C:HIS203 3.0 53.7 1.0 CG C:ASP128 3.1 53.7 1.0 CD2 C:HIS203 3.2 44.4 1.0 OD2 C:ASP128 3.2 54.9 1.0 CD2 C:HIS126 3.5 59.4 1.0 ND1 C:HIS203 4.1 48.6 1.0 ND1 C:HIS126 4.2 53.5 1.0 CG C:HIS203 4.2 47.5 1.0 CG C:HIS126 4.5 54.5 1.0 CB C:ASP128 4.6 50.5 1.0 OE1 C:GLN123 4.9 57.5 1.0

Iron binding site 5 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:53.6 occ:1.00 NE2 D:HIS126 2.1 74.1 1.0 NE2 D:HIS203 2.1 53.2 1.0 OD1 D:ASP128 2.3 65.4 1.0 CE1 D:HIS126 2.9 73.4 1.0 CE1 D:HIS203 3.0 60.9 1.0 CG D:ASP128 3.0 64.2 1.0 CD2 D:HIS203 3.0 55.1 1.0 OD2 D:ASP128 3.1 66.3 1.0 CD2 D:HIS126 3.1 67.0 1.0 ND1 D:HIS203 4.0 59.1 1.0 CG D:HIS203 4.1 55.8 1.0 ND1 D:HIS126 4.1 56.6 1.0 CG D:HIS126 4.2 55.4 1.0 CB D:ASP128 4.5 53.5 1.0 OE1 D:GLN123 4.7 65.0 1.0 N D:ASP128 4.9 59.6 1.0 CA D:ASP128 5.0 64.4 1.0

Iron binding site 6 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe301 b:55.0 occ:1.00 O F:HOH412 1.9 47.1 1.0 NE2 F:HIS126 2.1 36.5 1.0 NE2 F:HIS203 2.1 54.3 1.0 OD1 F:ASP128 2.5 43.6 1.0 CE1 F:HIS126 2.8 46.5 1.0 CE1 F:HIS203 3.0 52.9 1.0 CD2 F:HIS203 3.1 44.1 1.0 CD2 F:HIS126 3.2 47.9 1.0 CG F:ASP128 3.3 42.2 1.0 OD2 F:ASP128 3.4 51.9 1.0 ND1 F:HIS126 4.0 45.0 1.0 ND1 F:HIS203 4.1 52.0 1.0 CG F:HIS203 4.2 53.6 1.0 CG F:HIS126 4.2 41.3 1.0 CB F:ASP128 4.7 43.6 1.0 OE1 F:GLN123 4.8 77.3 1.0

Iron binding site 7 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe301 b:66.8 occ:1.00 NE2 G:HIS126 2.3 66.8 1.0 NE2 G:HIS203 2.3 65.2 1.0 OD1 G:ASP128 2.6 59.3 1.0 CE1 G:HIS126 2.8 73.2 1.0 CD2 G:HIS203 3.2 60.1 1.0 CE1 G:HIS203 3.4 73.4 1.0 CG G:ASP128 3.4 58.0 1.0 OD2 G:ASP128 3.5 65.0 1.0 CD2 G:HIS126 3.6 64.0 1.0 ND1 G:HIS126 4.1 59.6 1.0 CG G:HIS203 4.4 64.1 1.0 ND1 G:HIS203 4.4 65.2 1.0 CG G:HIS126 4.5 58.8 1.0 CB G:ASP128 4.9 50.3 1.0 OE1 G:GLN123 5.0 99.9 1.0

Iron binding site 8 out of 8 in the A-Kg Dependent Oxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A-Kg Dependent Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:144.4 occ:1.00 NE2 H:HIS203 2.2 102.4 1.0 NE2 H:HIS126 2.3 102.5 1.0 OD1 H:ASP128 2.5 104.3 1.0 CE1 H:HIS203 2.9 104.9 1.0 CE1 H:HIS126 2.9 111.7 1.0 CD2 H:HIS203 3.3 102.0 1.0 CG H:ASP128 3.4 101.4 1.0 OD2 H:ASP128 3.5 96.7 1.0 CD2 H:HIS126 3.5 105.2 1.0 ND1 H:HIS203 4.1 104.0 1.0 ND1 H:HIS126 4.2 102.1 1.0 CG H:HIS203 4.3 98.9 1.0 CG H:HIS126 4.5 106.0 1.0 CB H:ASP128 4.8 87.8 1.0

A.Fan, S.Fan, M.Wu, Z.Sun. A-Kg Dependent Oxygenase To Be Published.