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Iron in PDB 4zoh: Crystal Structure of Glyceraldehyde Oxidoreductase

Protein crystallography data

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

Other elements in 4zoh:

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

Molybdenum (Mo) 1 atom

Iron Binding Sites:

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 4zoh

Go back to Iron Binding Sites List in 4zoh
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 4zoh

Go back to Iron Binding Sites List in 4zoh
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 4zoh

Go back to Iron Binding Sites List in 4zoh
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 4zoh

Go back to Iron Binding Sites List in 4zoh
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

Reference:

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
Page generated: Sun Dec 13 15:55:02 2020

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