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Iron in PDB 8jek: Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus

Enzymatic activity of Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus

All present enzymatic activity of Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus:
1.1.99.11;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus (pdb code 8jek). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus, PDB code: 8jek:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8jek

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Iron binding site 1 out of 6 in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:37.5
occ:1.00
 FE1 A:F3S602 0.0 37.5 1.0
S3 A:F3S602 2.3 26.2 1.0
S1 A:F3S602 2.3 29.3 1.0
S2 A:F3S602 2.3 20.3 1.0
SG A:CYS226 2.3 27.3 1.0
FE4 A:F3S602 2.6 36.9 1.0
FE3 A:F3S602 2.6 41.4 1.0
CB A:CYS226 3.4 22.6 1.0
S4 A:F3S602 3.8 22.1 1.0
CA A:CYS226 4.2 19.0 1.0
CB A:ASN219 4.3 20.0 1.0
CB A:ALA230 4.4 18.3 1.0
CD A:PRO227 4.5 18.7 1.0
CG1 A:ILE228 4.7 28.3 1.0
SD A:MET231 4.7 38.9 1.0
OD1 A:ASN219 4.7 25.9 1.0
N A:ALA230 4.7 24.2 1.0
SG A:CYS216 4.8 34.0 1.0
CG A:MET231 4.8 25.8 1.0
SG A:CYS222 4.8 28.2 1.0
N A:ASN219 4.8 22.7 1.0
CA A:ALA230 4.9 2.5 1.0
C A:ALA230 4.9 26.1 1.0
C A:CYS226 4.9 28.8 1.0
CB A:MET231 5.0 24.9 1.0
CG A:ASN219 5.0 24.9 1.0

Iron binding site 2 out of 6 in 8jek

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Iron binding site 2 out of 6 in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:41.4
occ:1.00
 FE3 A:F3S602 0.0 41.4 1.0
S4 A:F3S602 2.3 22.1 1.0
S1 A:F3S602 2.3 29.3 1.0
S3 A:F3S602 2.3 26.2 1.0
SG A:CYS222 2.3 28.2 1.0
FE4 A:F3S602 2.6 36.9 1.0
FE1 A:F3S602 2.6 37.5 1.0
CB A:CYS222 3.6 24.1 1.0
N A:CYS222 3.7 35.4 1.0
NH1 A:ARG205 3.8 20.8 1.0
CA A:CYS222 3.8 16.1 1.0
S2 A:F3S602 3.9 20.3 1.0
N A:ASN220 4.1 21.9 1.0
N A:ASN221 4.2 20.7 1.0
SD A:MET231 4.4 38.9 1.0
C A:ASN221 4.4 27.5 1.0
CD A:ARG205 4.6 20.9 1.0
SG A:CYS226 4.6 27.3 1.0
CA A:ASN220 4.6 23.2 1.0
CB A:SER343 4.6 25.1 1.0
CZ A:ARG205 4.6 22.7 1.0
SG A:CYS216 4.6 34.0 1.0
CA A:SER343 4.7 28.4 1.0
C A:ASN220 4.8 28.1 1.0
N A:ASN219 4.8 22.7 1.0
C A:ASN219 4.9 22.6 1.0
CB A:CYS226 4.9 22.6 1.0
NE A:ARG205 4.9 21.7 1.0
CA A:ASN221 4.9 16.6 1.0
CB A:ASN219 5.0 20.0 1.0

Iron binding site 3 out of 6 in 8jek

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Iron binding site 3 out of 6 in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:36.9
occ:1.00
 FE4 A:F3S602 0.0 36.9 1.0
S3 A:F3S602 2.3 26.2 1.0
S4 A:F3S602 2.3 22.1 1.0
S2 A:F3S602 2.3 20.3 1.0
SG A:CYS216 2.3 34.0 1.0
FE1 A:F3S602 2.6 37.5 1.0
FE3 A:F3S602 2.6 41.4 1.0
CB A:CYS216 3.4 27.1 1.0
S1 A:F3S602 3.8 29.3 1.0
N A:GLY218 4.0 35.8 1.0
CA A:CYS216 4.0 23.5 1.0
N A:ASN219 4.0 22.7 1.0
CD A:ARG205 4.0 20.9 1.0
CA A:GLY218 4.3 31.2 1.0
N A:CYS217 4.4 32.3 1.0
CG A:ARG205 4.4 28.0 1.0
C A:CYS216 4.5 34.4 1.0
CB A:ALA230 4.6 18.3 1.0
SG A:CYS222 4.6 28.2 1.0
C A:GLY218 4.6 24.0 1.0
NH1 A:ARG205 4.8 20.8 1.0
SG A:CYS226 4.8 27.3 1.0
N A:ASN220 4.8 21.9 1.0
CB A:ASN219 4.8 20.0 1.0
CA A:ASN219 4.9 19.9 1.0

Iron binding site 4 out of 6 in 8jek

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Iron binding site 4 out of 6 in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:69.2
occ:1.00
 FE C:HEC501 0.0 69.2 1.0
NC C:HEC501 2.0 36.2 1.0
NB C:HEC501 2.0 43.6 1.0
NA C:HEC501 2.0 32.1 1.0
ND C:HEC501 2.0 37.8 1.0
NE2 C:HIS347 2.1 20.6 1.0
SD C:MET395 2.8 24.5 1.0
CE1 C:HIS347 2.9 17.4 1.0
C1B C:HEC501 3.0 35.0 1.0
C1D C:HEC501 3.0 35.8 1.0
C1C C:HEC501 3.0 31.0 1.0
C4A C:HEC501 3.0 31.5 1.0
C4D C:HEC501 3.0 33.7 1.0
C4C C:HEC501 3.0 31.1 1.0
C4B C:HEC501 3.0 33.5 1.0
C1A C:HEC501 3.1 35.9 1.0
CD2 C:HIS347 3.2 23.8 1.0
CHD C:HEC501 3.4 34.7 1.0
CHB C:HEC501 3.4 34.1 1.0
CHA C:HEC501 3.4 34.7 1.0
CHC C:HEC501 3.5 25.2 1.0
CG C:MET395 3.9 24.1 1.0
CE C:MET395 4.0 23.5 1.0
ND1 C:HIS347 4.1 15.1 1.0
CG C:HIS347 4.2 27.7 1.0
C3B C:HEC501 4.2 32.7 1.0
C3C C:HEC501 4.2 39.6 1.0
C2B C:HEC501 4.2 35.7 1.0
C3A C:HEC501 4.3 37.2 1.0
C2D C:HEC501 4.3 35.7 1.0
C2A C:HEC501 4.3 39.6 1.0
C2C C:HEC501 4.3 34.9 1.0
C3D C:HEC501 4.3 31.7 1.0
CB C:MET395 4.6 27.9 1.0

Iron binding site 5 out of 6 in 8jek

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Iron binding site 5 out of 6 in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:68.5
occ:1.00
 FE C:HEC502 0.0 68.5 1.0
NB C:HEC502 2.0 41.4 1.0
NC C:HEC502 2.0 38.4 1.0
ND C:HEC502 2.0 41.0 1.0
NA C:HEC502 2.0 43.4 1.0
NE2 C:HIS205 2.1 35.6 1.0
SD C:MET267 2.9 32.7 1.0
C1D C:HEC502 3.0 39.2 1.0
C1B C:HEC502 3.0 31.1 1.0
C4B C:HEC502 3.0 38.4 1.0
C4D C:HEC502 3.0 31.5 1.0
C1C C:HEC502 3.0 41.2 1.0
C4A C:HEC502 3.0 36.2 1.0
C4C C:HEC502 3.1 33.2 1.0
C1A C:HEC502 3.1 36.5 1.0
CE1 C:HIS205 3.1 35.0 1.0
CD2 C:HIS205 3.1 37.3 1.0
CHD C:HEC502 3.4 32.3 1.0
CHB C:HEC502 3.4 30.1 1.0
CHA C:HEC502 3.4 32.2 1.0
CHC C:HEC502 3.4 35.7 1.0
CG C:MET267 3.7 28.8 1.0
CE C:MET267 3.8 26.7 1.0
ND1 C:HIS205 4.2 40.9 1.0
CG C:HIS205 4.2 40.5 1.0
C2D C:HEC502 4.2 34.7 1.0
C3B C:HEC502 4.2 39.2 1.0
C2B C:HEC502 4.2 36.1 1.0
C3C C:HEC502 4.3 36.4 1.0
C3D C:HEC502 4.3 34.6 1.0
C3A C:HEC502 4.3 39.1 1.0
C2A C:HEC502 4.3 32.9 1.0
C2C C:HEC502 4.3 40.3 1.0
CB C:MET267 4.4 27.0 1.0

Iron binding site 6 out of 6 in 8jek

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Iron binding site 6 out of 6 in the Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of K-Ferricyanide Oxidized Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:76.1
occ:1.00
 FE C:HEC503 0.0 76.1 1.0
NC C:HEC503 2.0 59.4 1.0
NA C:HEC503 2.0 60.4 1.0
NB C:HEC503 2.0 59.3 1.0
ND C:HEC503 2.0 60.9 1.0
NE2 C:HIS56 2.1 64.7 1.0
SD C:MET118 2.8 51.1 1.0
CE1 C:HIS56 2.9 62.6 1.0
C1D C:HEC503 3.0 57.0 1.0
C1B C:HEC503 3.0 60.1 1.0
C4A C:HEC503 3.0 59.4 1.0
C4C C:HEC503 3.0 61.2 1.0
C1C C:HEC503 3.0 59.9 1.0
C4B C:HEC503 3.0 56.5 1.0
C1A C:HEC503 3.0 60.5 1.0
C4D C:HEC503 3.0 64.2 1.0
CD2 C:HIS56 3.3 63.0 1.0
CHD C:HEC503 3.4 59.9 1.0
CHB C:HEC503 3.4 61.9 1.0
CHA C:HEC503 3.4 62.1 1.0
CHC C:HEC503 3.5 59.2 1.0
CE C:MET118 3.9 58.1 1.0
ND1 C:HIS56 4.1 63.9 1.0
C3C C:HEC503 4.2 61.1 1.0
C2D C:HEC503 4.2 59.7 1.0
C3B C:HEC503 4.2 59.1 1.0
C2B C:HEC503 4.2 61.3 1.0
C3A C:HEC503 4.3 62.3 1.0
C2A C:HEC503 4.3 62.9 1.0
C3D C:HEC503 4.3 63.4 1.0
C2C C:HEC503 4.3 62.3 1.0
CG C:HIS56 4.3 60.2 1.0
CG C:MET118 4.4 62.1 1.0
CB C:MET118 4.9 54.0 1.0

Reference:

Y.Suzuki, F.Makino, T.Miyata, H.Tanaka, K.Namba, K.Kano, K.Sowa, Y.Kitazumi, O.Shirai. Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis By Membrane-Bound D-Fructose Dehydrogenase with Structural Bioelectrochemistry. Acs Catalysis V. 13 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C03769
Page generated: Sat Aug 10 06:51:47 2024

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