Iron in PDB 4zoh: Crystal Structure of Glyceraldehyde Oxidoreductase

The structure of Crystal Structure of Glyceraldehyde Oxidoreductase, PDB code: 4zoh was solved by H.Nishimasu, S.Fushinobu, T.Wakagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.40 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.431, 143.431, 235.509, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 24.2

The structure of Crystal Structure of Glyceraldehyde Oxidoreductase also contains other interesting chemical elements:

Molybdenum

(Mo)

1 atom

The binding sites of Iron atom in the Crystal Structure of Glyceraldehyde Oxidoreductase (pdb code 4zoh). 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 Glyceraldehyde Oxidoreductase, PDB code: 4zoh:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Glyceraldehyde Oxidoreductase


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 Glyceraldehyde Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:21.6 occ:1.00 FE1 C:FES201 0.0 21.6 1.0 SG C:CYS52 2.2 18.5 1.0 S2 C:FES201 2.2 21.1 1.0 S1 C:FES201 2.2 23.6 1.0 SG C:CYS47 2.3 24.4 1.0 FE2 C:FES201 2.8 20.7 1.0 CB C:CYS52 3.4 20.6 1.0 CB C:CYS47 3.5 22.1 1.0 N C:CYS47 3.5 18.9 1.0 N C:CYS52 3.5 24.3 1.0 N C:GLY53 3.8 18.2 1.0 CA C:CYS52 3.8 19.9 1.0 CA C:CYS47 3.9 22.4 1.0 O C:CYS47 4.0 24.0 1.0 C C:CYS47 4.2 22.1 1.0 N C:GLY46 4.2 22.4 1.0 C C:CYS52 4.2 19.2 1.0 C C:GLY46 4.2 20.9 1.0 O C:HOH307 4.3 30.4 1.0 SG C:CYS67 4.3 20.5 1.0 N C:ASN51 4.4 29.2 1.0 N C:ALA54 4.4 20.1 1.0 CA C:GLY46 4.5 21.6 1.0 CA C:SER50 4.6 25.4 1.0 N C:SER50 4.6 25.1 1.0 C C:ASN51 4.6 33.6 1.0 C C:SER50 4.6 27.3 1.0 SG C:CYS55 4.7 21.7 1.0 CA C:GLY53 4.8 18.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Glyceraldehyde Oxidoreductase


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 Glyceraldehyde Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:20.7 occ:1.00 FE2 C:FES201 0.0 20.7 1.0 S2 C:FES201 2.2 21.1 1.0 S1 C:FES201 2.2 23.6 1.0 SG C:CYS55 2.2 21.7 1.0 SG C:CYS67 2.3 20.5 1.0 FE1 C:FES201 2.8 21.6 1.0 CB C:CYS67 3.1 19.1 1.0 CB C:CYS55 3.3 18.8 1.0 O C:HOH307 4.0 30.4 1.0 N C:CYS55 4.2 18.1 1.0 N C:CYS67 4.2 17.0 1.0 CA C:CYS67 4.3 18.9 1.0 CB C:LYS65 4.3 20.6 1.0 CA C:CYS55 4.4 20.3 1.0 SG C:CYS52 4.5 18.5 1.0 SG C:CYS47 4.6 24.4 1.0 N C:GLY53 4.7 18.2 1.0 CA C:SER50 4.7 25.4 1.0 CG C:LYS65 4.8 18.1 1.0 N C:ALA54 4.8 20.1 1.0 CA C:LYS65 4.9 21.3 1.0 CA C:GLY53 5.0 18.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Glyceraldehyde Oxidoreductase


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 Glyceraldehyde Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:21.7 occ:1.00 FE1 C:FES202 0.0 21.7 1.0 S2 C:FES202 2.2 23.6 1.0 S1 C:FES202 2.2 21.7 1.0 SG C:CYS109 2.3 21.4 1.0 SG C:CYS141 2.3 20.5 1.0 FE2 C:FES202 2.8 22.6 1.0 CB C:CYS141 3.3 18.8 1.0 CB C:CYS109 3.4 17.5 1.0 CA C:CYS141 3.8 19.4 1.0 N C:CYS109 4.1 16.4 1.0 N C:ARG142 4.2 23.7 1.0 CA C:CYS109 4.4 17.1 1.0 CB C:CYS143 4.4 22.3 1.0 N C:CYS143 4.4 20.4 1.0 C C:CYS141 4.4 22.3 1.0 SG C:CYS143 4.5 24.9 1.0 O C:HOH347 4.5 22.4 1.0 CG2 C:THR144 4.6 17.7 1.0 SG C:CYS106 4.8 20.6 1.0 OG1 C:THR110 4.9 19.4 1.0 O C:LEU140 4.9 18.3 1.0 CA C:CYS143 5.0 21.5 1.0 N C:THR144 5.0 22.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Glyceraldehyde Oxidoreductase


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 Glyceraldehyde Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:22.6 occ:1.00 FE2 C:FES202 0.0 22.6 1.0 S1 C:FES202 2.1 21.7 1.0 S2 C:FES202 2.3 23.6 1.0 SG C:CYS143 2.3 24.9 1.0 SG C:CYS106 2.4 20.6 1.0 FE1 C:FES202 2.8 21.7 1.0 CB C:CYS143 3.2 22.3 1.0 CB C:CYS106 3.5 18.6 1.0 N C:CYS106 3.7 19.2 1.0 O A:HOH1061 3.7 14.8 1.0 N C:GLY107 3.9 20.9 1.0 CA C:CYS106 4.0 19.2 1.0 N C:CYS143 4.1 20.4 1.0 CA C:CYS143 4.3 21.5 1.0 C C:CYS106 4.3 20.0 1.0 N C:TYR108 4.4 19.4 1.0 SG C:CYS141 4.4 20.5 1.0 SG C:CYS109 4.7 21.4 1.0 C C:GLN105 4.7 19.5 1.0 CB C:GLN105 4.8 18.8 1.0 N C:ARG142 4.8 23.7 1.0 N C:CYS109 4.9 16.4 1.0 N C:GLN105 4.9 17.7 1.0

T.Wakagi, H.Nishimasu, M.Miyake, S.Fushinobu. Archaeal Mo-Containing Glyceraldehyde Oxidoreductase Isozymes Exhibit Diverse Substrate Specificities Through Unique Subunit Assemblies. Plos One V. 11 47333.
ISSN: ESSN 1932-6203
PubMed: 26808202
DOI: 10.1371/JOURNAL.PONE.0147333