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Iron in PDB 9jqa: Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions

Enzymatic activity of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions

All present enzymatic activity of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions:
1.1.99.11;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions (pdb code 9jqa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions, PDB code: 9jqa:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 9jqa

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Iron binding site 1 out of 5 in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:89.9
occ:1.00
 FE1 A:F3S602 0.0 89.9 1.0
S3 A:F3S602 2.3 65.7 1.0
S2 A:F3S602 2.3 67.8 1.0
S1 A:F3S602 2.3 62.6 1.0
SG A:CYS226 2.3 62.7 1.0
FE4 A:F3S602 2.6 91.2 1.0
FE3 A:F3S602 2.6 91.2 1.0
CB A:CYS226 3.2 56.9 1.0
S4 A:F3S602 3.8 69.5 1.0
CA A:CYS226 3.9 53.0 1.0
CB A:ASN219 4.1 52.5 1.0
CB A:ALA230 4.2 53.5 1.0
OD1 A:ASN219 4.4 60.1 1.0
CD A:PRO227 4.5 56.8 1.0
CG1 A:ILE228 4.6 57.9 1.0
N A:ALA230 4.6 61.1 1.0
CG A:MET231 4.6 60.1 1.0
N A:ASN219 4.7 52.8 1.0
C A:CYS226 4.7 62.5 1.0
CG A:ASN219 4.8 61.0 1.0
SD A:MET231 4.8 67.6 1.0
SG A:CYS216 4.8 58.1 1.0
SG A:CYS222 4.8 64.2 1.0
N A:PRO227 4.9 64.1 1.0
N A:MET231 4.9 70.4 1.0
CA A:ALA230 4.9 55.1 1.0
CA A:ASN219 4.9 48.9 1.0

Iron binding site 2 out of 5 in 9jqa

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Iron binding site 2 out of 5 in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:91.2
occ:1.00
 FE3 A:F3S602 0.0 91.2 1.0
S4 A:F3S602 2.3 69.5 1.0
S1 A:F3S602 2.3 62.6 1.0
S3 A:F3S602 2.3 65.7 1.0
SG A:CYS222 2.3 64.2 1.0
FE4 A:F3S602 2.6 91.2 1.0
FE1 A:F3S602 2.6 89.9 1.0
CB A:CYS222 3.5 58.0 1.0
N A:CYS222 3.5 60.8 1.0
CA A:CYS222 3.7 56.9 1.0
NE A:ARG205 3.8 61.9 1.0
S2 A:F3S602 3.9 67.8 1.0
N A:ASN220 4.1 61.3 1.0
N A:ASN221 4.1 59.9 1.0
SD A:MET231 4.3 67.6 1.0
CD A:ARG205 4.4 51.8 1.0
C A:ASN221 4.4 55.2 1.0
CZ A:ARG205 4.5 56.9 1.0
NH2 A:ARG205 4.6 55.4 1.0
SG A:CYS216 4.6 58.1 1.0
SG A:CYS226 4.6 62.7 1.0
CB A:SER343 4.7 62.0 1.0
CA A:ASN220 4.7 57.3 1.0
CB A:CYS226 4.7 56.9 1.0
CA A:SER343 4.7 59.5 1.0
N A:ASN219 4.8 52.8 1.0
C A:ASN219 4.9 58.6 1.0
C A:ASN220 4.9 66.9 1.0
CA A:ASN221 4.9 54.2 1.0
CB A:ASN219 4.9 52.5 1.0
CG A:MET231 5.0 60.1 1.0

Iron binding site 3 out of 5 in 9jqa

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Iron binding site 3 out of 5 in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:91.2
occ:1.00
 FE4 A:F3S602 0.0 91.2 1.0
S3 A:F3S602 2.3 65.7 1.0
S2 A:F3S602 2.3 67.8 1.0
S4 A:F3S602 2.3 69.5 1.0
SG A:CYS216 2.3 58.1 1.0
FE1 A:F3S602 2.6 89.9 1.0
FE3 A:F3S602 2.6 91.2 1.0
CB A:CYS216 3.6 58.2 1.0
S1 A:F3S602 3.8 62.6 1.0
N A:GLY218 3.9 56.7 1.0
N A:ASN219 3.9 52.8 1.0
CD A:ARG205 4.0 51.8 1.0
CA A:CYS216 4.0 56.5 1.0
CA A:GLY218 4.2 51.3 1.0
NE A:ARG205 4.2 61.9 1.0
N A:CYS217 4.3 60.0 1.0
CB A:ALA230 4.3 53.5 1.0
CG A:ARG205 4.5 59.9 1.0
C A:CYS216 4.5 59.4 1.0
C A:GLY218 4.5 55.6 1.0
SG A:CYS222 4.6 64.2 1.0
SG A:CYS226 4.7 62.7 1.0
CB A:ASN219 4.8 52.5 1.0
N A:ASN220 4.8 61.3 1.0
CA A:ASN219 4.9 48.9 1.0
C A:CYS217 4.9 63.9 1.0

Iron binding site 4 out of 5 in 9jqa

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Iron binding site 4 out of 5 in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:89.7
occ:1.00
 FE C:HEC501 0.0 89.7 1.0
NB C:HEC501 2.0 74.4 1.0
NC C:HEC501 2.0 71.1 1.0
NA C:HEC501 2.0 69.3 1.0
ND C:HEC501 2.0 71.5 1.0
NE2 C:HIS347 2.0 64.9 1.0
SD C:MET395 2.8 70.1 1.0
CD2 C:HIS347 2.9 59.3 1.0
C4B C:HEC501 3.0 68.6 1.0
C1B C:HEC501 3.0 63.4 1.0
C1C C:HEC501 3.0 66.8 1.0
C1D C:HEC501 3.0 64.9 1.0
C4D C:HEC501 3.0 64.1 1.0
C4A C:HEC501 3.0 64.7 1.0
C4C C:HEC501 3.0 62.3 1.0
C1A C:HEC501 3.0 65.7 1.0
CE1 C:HIS347 3.1 61.8 1.0
CG C:MET395 3.2 56.6 1.0
CHD C:HEC501 3.4 64.4 1.0
CHB C:HEC501 3.4 63.5 1.0
CHA C:HEC501 3.4 63.3 1.0
CHC C:HEC501 3.4 61.8 1.0
CE C:MET395 3.7 60.1 1.0
CG C:HIS347 4.1 66.9 1.0
ND1 C:HIS347 4.2 69.1 1.0
C3B C:HEC501 4.2 75.6 1.0
C2B C:HEC501 4.2 65.5 1.0
C3C C:HEC501 4.2 71.1 1.0
C2D C:HEC501 4.2 67.4 1.0
C3D C:HEC501 4.3 68.5 1.0
C3A C:HEC501 4.3 68.4 1.0
C2C C:HEC501 4.3 67.9 1.0
C2A C:HEC501 4.3 68.2 1.0
CB C:MET395 4.3 62.9 1.0

Iron binding site 5 out of 5 in 9jqa

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Iron binding site 5 out of 5 in the Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Fructose Dehydrogenase Variant From Gluconobacter Japonicus Truncating Heme 1C and C-Terminal Hydrophobic Regions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:95.5
occ:1.00
 FE C:HEC502 0.0 95.5 1.0
NB C:HEC502 2.0 79.2 1.0
NC C:HEC502 2.0 76.3 1.0
NA C:HEC502 2.0 76.8 1.0
ND C:HEC502 2.0 80.7 1.0
NE2 C:HIS205 2.0 74.2 1.0
SD C:MET267 2.8 70.9 1.0
CD2 C:HIS205 2.9 71.0 1.0
C1B C:HEC502 3.0 75.1 1.0
C4B C:HEC502 3.0 72.7 1.0
C1D C:HEC502 3.0 76.6 1.0
C1C C:HEC502 3.0 76.0 1.0
C4A C:HEC502 3.0 72.9 1.0
C4D C:HEC502 3.0 74.5 1.0
C4C C:HEC502 3.0 74.9 1.0
C1A C:HEC502 3.0 73.2 1.0
CE C:MET267 3.1 64.2 1.0
CE1 C:HIS205 3.1 69.4 1.0
CHD C:HEC502 3.4 74.3 1.0
CHB C:HEC502 3.4 76.2 1.0
CHA C:HEC502 3.4 72.5 1.0
CHC C:HEC502 3.4 75.6 1.0
CG C:MET267 3.6 69.6 1.0
CG C:HIS205 4.1 68.8 1.0
ND1 C:HIS205 4.1 68.5 1.0
C3B C:HEC502 4.2 75.9 1.0
C2B C:HEC502 4.2 76.4 1.0
C2D C:HEC502 4.2 75.9 1.0
C3C C:HEC502 4.2 80.6 1.0
C3A C:HEC502 4.3 73.1 1.0
C3D C:HEC502 4.3 74.3 1.0
C2A C:HEC502 4.3 74.8 1.0
C2C C:HEC502 4.3 75.7 1.0
CB C:MET267 4.4 67.3 1.0
CA C:MET267 4.9 65.1 1.0

Reference:

T.Adachi, K.Ichikawa, T.Miyata, F.Makino, H.Tanaka, K.Namba, K.Sowa. Improved Direct Bioelectrochemical Fructose Oxidation with Surfactant-Free Heterotrimeric Fructose Dehydrogenase Variant Truncating Heme 1C and C-Terminal Hydrophobic Regions Acs Electrochem 2025.
DOI: 10.1021/ACSELECTROCHEM.5C00106
Page generated: Sat Aug 23 03:27:58 2025

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