Iron in PDB 5zm3: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B, PDB code: 5zm3 was solved by Y.Nakashima, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 2.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.642, 73.340, 86.971, 75.97, 71.35, 89.68
R / Rfree (%)	21.3 / 27.4

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B (pdb code 5zm3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B, PDB code: 5zm3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:20.8 occ:1.00 OD1 A:ASP137 2.1 18.8 1.0 NE2 A:HIS213 2.2 16.5 1.0 O A:HOH402 2.3 19.9 1.0 O2 A:AKG302 2.3 22.4 1.0 NE2 A:HIS135 2.4 13.7 1.0 O5 A:AKG302 2.5 23.8 1.0 CE1 A:HIS213 3.0 14.6 1.0 CG A:ASP137 3.0 18.5 1.0 C1 A:AKG302 3.1 24.6 1.0 C2 A:AKG302 3.1 23.5 1.0 OD2 A:ASP137 3.1 18.9 1.0 CD2 A:HIS135 3.2 16.1 1.0 CE1 A:HIS135 3.3 14.3 1.0 CD2 A:HIS213 3.3 14.4 1.0 C25 A:9FR303 4.1 17.1 1.0 ND1 A:HIS213 4.1 15.4 1.0 O1 A:AKG302 4.2 20.4 1.0 CG A:HIS213 4.3 13.1 1.0 ND1 A:HIS135 4.4 14.5 1.0 CG A:HIS135 4.4 14.3 1.0 CB A:ASP137 4.4 16.7 1.0 C3 A:AKG302 4.5 19.6 1.0 O A:HOH479 4.8 22.1 1.0 CA A:ASP137 4.9 13.6 1.0

Iron binding site 2 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:18.6 occ:1.00 OD1 B:ASP137 2.1 13.9 1.0 O B:HOH426 2.1 20.3 1.0 NE2 B:HIS213 2.1 17.9 1.0 O1 B:AKG302 2.2 20.2 1.0 NE2 B:HIS135 2.3 14.7 1.0 O5 B:AKG302 2.3 23.6 1.0 C1 B:AKG302 2.9 20.0 1.0 CE1 B:HIS213 2.9 15.9 1.0 C2 B:AKG302 3.0 22.9 1.0 CG B:ASP137 3.0 15.2 1.0 CD2 B:HIS135 3.1 18.0 1.0 CD2 B:HIS213 3.2 16.4 1.0 CE1 B:HIS135 3.3 18.0 1.0 OD2 B:ASP137 3.3 16.2 1.0 C25 B:9FR303 4.0 18.9 1.0 ND1 B:HIS213 4.1 14.6 1.0 O2 B:AKG302 4.1 21.8 1.0 CG B:HIS213 4.3 14.8 1.0 CG B:HIS135 4.3 17.1 1.0 O B:HOH456 4.3 27.1 1.0 ND1 B:HIS135 4.4 17.2 1.0 CB B:ASP137 4.4 16.0 1.0 C3 B:AKG302 4.5 19.5 1.0 CA B:ASP137 4.7 17.2 1.0 OE1 B:GLN132 4.7 20.9 1.0 N B:ASP137 4.9 15.1 1.0

Iron binding site 3 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:23.4 occ:1.00 O C:HOH413 1.9 20.8 1.0 O1 C:AKG302 2.1 22.7 1.0 NE2 C:HIS213 2.2 19.6 1.0 OD1 C:ASP137 2.2 22.0 1.0 NE2 C:HIS135 2.3 17.6 1.0 O5 C:AKG302 2.5 27.7 1.0 C1 C:AKG302 2.8 24.5 1.0 C2 C:AKG302 3.0 26.6 1.0 CE1 C:HIS213 3.1 19.7 1.0 CD2 C:HIS213 3.2 18.5 1.0 CG C:ASP137 3.2 19.4 1.0 CD2 C:HIS135 3.2 16.4 1.0 CE1 C:HIS135 3.2 18.6 1.0 OD2 C:ASP137 3.5 19.4 1.0 O2 C:AKG302 4.0 20.6 1.0 C25 C:9FR303 4.2 20.6 1.0 ND1 C:HIS213 4.2 17.3 1.0 CG C:HIS213 4.3 17.8 1.0 ND1 C:HIS135 4.3 16.7 1.0 CG C:HIS135 4.4 16.9 1.0 C3 C:AKG302 4.5 23.1 1.0 O C:HOH492 4.5 22.3 1.0 CB C:ASP137 4.6 19.7 1.0 OE1 C:GLN132 4.7 19.8 1.0 C08 C:9FR303 4.9 20.7 1.0 CA C:ASP137 4.9 17.5 1.0

Iron binding site 4 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Anda with Preandiloid B within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:23.6 occ:1.00 O D:HOH404 1.8 23.4 1.0 NE2 D:HIS213 2.1 18.2 1.0 NE2 D:HIS135 2.3 19.3 1.0 O2 D:AKG302 2.3 24.9 1.0 OD1 D:ASP137 2.3 21.3 1.0 O5 D:AKG302 2.3 25.8 1.0 CE1 D:HIS213 2.9 16.7 1.0 C1 D:AKG302 3.0 25.0 1.0 C2 D:AKG302 3.0 28.1 1.0 CD2 D:HIS213 3.2 17.7 1.0 CD2 D:HIS135 3.2 19.9 1.0 CE1 D:HIS135 3.2 20.7 1.0 CG D:ASP137 3.3 21.4 1.0 OD2 D:ASP137 3.5 23.8 1.0 ND1 D:HIS213 4.0 16.0 1.0 C25 D:9FR303 4.0 23.3 1.0 O1 D:AKG302 4.1 22.2 1.0 CG D:HIS213 4.2 17.9 1.0 ND1 D:HIS135 4.3 18.6 1.0 CG D:HIS135 4.3 17.7 1.0 C3 D:AKG302 4.4 24.8 1.0 O D:HOH436 4.6 28.3 1.0 CB D:ASP137 4.6 21.0 1.0 OE1 D:GLN132 4.9 21.2 1.0 CA D:ASP137 4.9 20.4 1.0

Y.Nakashima, T.Mitsuhashi, Y.Matsuda, M.Senda, H.Sato, M.Yamazaki, M.Uchiyama, T.Senda, I.Abe. Structural and Computational Bases For Dramatic Skeletal Rearrangement in Anditomin Biosynthesis. J. Am. Chem. Soc. V. 140 9743 2018.
ISSN: ESSN 1520-5126
PubMed: 29972643
DOI: 10.1021/JACS.8B06084