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Iron in PDB 8jej: Cryo-Em Structure of Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus

Enzymatic activity of Cryo-Em Structure of Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus

All present enzymatic activity of Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus (pdb code 8jej). 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus, PDB code: 8jej:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8jej

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Iron binding site 1 out of 6 in the Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:38.0
occ:1.00
 FE1 A:F3S602 0.0 38.0 1.0
S3 A:F3S602 2.3 22.9 1.0
S1 A:F3S602 2.3 20.6 1.0
S2 A:F3S602 2.3 15.8 1.0
SG A:CYS226 2.3 17.2 1.0
FE4 A:F3S602 2.6 42.2 1.0
FE3 A:F3S602 2.6 38.7 1.0
CB A:CYS226 3.4 17.6 1.0
S4 A:F3S602 3.8 20.7 1.0
CA A:CYS226 4.1 11.6 1.0
CB A:ASN219 4.2 16.1 1.0
CB A:ALA230 4.2 6.3 1.0
CD A:PRO227 4.3 17.4 1.0
OD1 A:ASN219 4.5 26.3 1.0
CG1 A:ILE228 4.5 19.9 1.0
N A:ALA230 4.7 10.7 1.0
N A:ASN219 4.7 14.9 1.0
CG A:MET231 4.8 15.2 1.0
SD A:MET231 4.8 26.1 1.0
SG A:CYS216 4.8 25.7 1.0
SG A:CYS222 4.8 22.0 1.0
CG A:ASN219 4.8 23.1 1.0
C A:CYS226 4.9 22.2 1.0
CA A:ALA230 4.9 12.6 1.0
N A:PRO227 4.9 21.6 1.0
CA A:ASN219 5.0 15.4 1.0

Iron binding site 2 out of 6 in 8jej

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Iron binding site 2 out of 6 in the Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:38.7
occ:1.00
 FE3 A:F3S602 0.0 38.7 1.0
S4 A:F3S602 2.3 20.7 1.0
S1 A:F3S602 2.3 20.6 1.0
S3 A:F3S602 2.3 22.9 1.0
SG A:CYS222 2.3 22.0 1.0
FE1 A:F3S602 2.6 38.0 1.0
FE4 A:F3S602 2.6 42.2 1.0
CB A:CYS222 3.5 17.4 1.0
N A:CYS222 3.8 21.0 1.0
NH1 A:ARG205 3.8 14.7 1.0
CA A:CYS222 3.8 13.9 1.0
S2 A:F3S602 3.9 15.8 1.0
SD A:MET231 4.3 26.1 1.0
N A:ASN220 4.3 16.0 1.0
N A:ASN221 4.4 12.0 1.0
CD A:ARG205 4.4 17.4 1.0
SG A:CYS226 4.5 17.2 1.0
SG A:CYS216 4.6 25.7 1.0
C A:ASN221 4.6 10.5 1.0
CZ A:ARG205 4.6 21.5 1.0
CB A:SER343 4.6 21.9 1.0
CA A:SER343 4.8 23.2 1.0
N A:ASN219 4.8 14.9 1.0
CA A:ASN220 4.8 19.1 1.0
CB A:CYS226 4.8 17.6 1.0
NE A:ARG205 4.9 25.4 1.0
CB A:ASN219 5.0 16.1 1.0
C A:ASN219 5.0 23.8 1.0

Iron binding site 3 out of 6 in 8jej

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Iron binding site 3 out of 6 in the Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:42.2
occ:1.00
 FE4 A:F3S602 0.0 42.2 1.0
S3 A:F3S602 2.3 22.9 1.0
S4 A:F3S602 2.3 20.7 1.0
S2 A:F3S602 2.3 15.8 1.0
SG A:CYS216 2.3 25.7 1.0
FE1 A:F3S602 2.6 38.0 1.0
FE3 A:F3S602 2.6 38.7 1.0
CB A:CYS216 3.4 20.8 1.0
S1 A:F3S602 3.8 20.6 1.0
N A:GLY218 3.9 24.8 1.0
CA A:CYS216 3.9 16.3 1.0
CD A:ARG205 4.0 17.4 1.0
N A:ASN219 4.0 14.9 1.0
CA A:GLY218 4.3 18.9 1.0
CB A:ALA230 4.3 6.3 1.0
N A:CYS217 4.4 26.6 1.0
CG A:ARG205 4.4 25.7 1.0
C A:CYS216 4.4 20.0 1.0
C A:GLY218 4.6 23.1 1.0
SG A:CYS222 4.7 22.0 1.0
SG A:CYS226 4.7 17.2 1.0
CB A:ASN219 4.9 16.1 1.0
NH1 A:ARG205 4.9 14.7 1.0
N A:ASN220 5.0 16.0 1.0
CA A:ASN219 5.0 15.4 1.0

Iron binding site 4 out of 6 in 8jej

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:47.6
occ:1.00
 FE C:HEC501 0.0 47.6 1.0
NC C:HEC501 2.0 35.0 1.0
NA C:HEC501 2.0 22.9 1.0
ND C:HEC501 2.0 30.0 1.0
NB C:HEC501 2.0 30.6 1.0
NE2 C:HIS347 2.2 8.2 1.0
SD C:MET395 2.8 21.4 1.0
C1D C:HEC501 3.0 18.6 1.0
C4C C:HEC501 3.0 19.2 1.0
C4A C:HEC501 3.0 20.8 1.0
C1B C:HEC501 3.0 26.2 1.0
C4D C:HEC501 3.0 27.2 1.0
C1C C:HEC501 3.0 22.4 1.0
C4B C:HEC501 3.0 27.5 1.0
C1A C:HEC501 3.0 22.9 1.0
CD2 C:HIS347 3.1 12.2 1.0
CE1 C:HIS347 3.3 15.8 1.0
CHD C:HEC501 3.3 18.4 1.0
CHB C:HEC501 3.4 28.6 1.0
CHA C:HEC501 3.4 23.4 1.0
CHC C:HEC501 3.4 17.2 1.0
CE C:MET395 3.6 17.9 1.0
CG C:MET395 3.8 15.9 1.0
C2D C:HEC501 4.2 27.6 1.0
C3C C:HEC501 4.2 29.7 1.0
C3A C:HEC501 4.2 29.9 1.0
C3B C:HEC501 4.2 25.9 1.0
C2B C:HEC501 4.3 26.0 1.0
C2A C:HEC501 4.3 30.9 1.0
CG C:HIS347 4.3 27.4 1.0
C3D C:HEC501 4.3 28.1 1.0
C2C C:HEC501 4.3 25.6 1.0
ND1 C:HIS347 4.3 24.1 1.0
CB C:MET395 4.4 11.4 1.0

Iron binding site 5 out of 6 in 8jej

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Iron binding site 5 out of 6 in the Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:58.7
occ:1.00
 FE C:HEC502 0.0 58.7 1.0
NB C:HEC502 2.0 34.7 1.0
NC C:HEC502 2.0 30.6 1.0
NA C:HEC502 2.0 30.0 1.0
ND C:HEC502 2.0 41.1 1.0
NE2 C:HIS205 2.3 21.2 1.0
SD C:MET267 2.8 28.1 1.0
C1D C:HEC502 3.0 31.3 1.0
C1B C:HEC502 3.0 27.1 1.0
C4B C:HEC502 3.0 25.5 1.0
C4A C:HEC502 3.0 23.3 1.0
C1C C:HEC502 3.0 31.3 1.0
C4C C:HEC502 3.0 24.9 1.0
C1A C:HEC502 3.0 23.4 1.0
C4D C:HEC502 3.0 27.8 1.0
CD2 C:HIS205 3.1 29.0 1.0
CHD C:HEC502 3.4 23.7 1.0
CE C:MET267 3.4 10.9 1.0
CHB C:HEC502 3.4 22.6 1.0
CE1 C:HIS205 3.4 28.4 1.0
CHC C:HEC502 3.4 26.1 1.0
CHA C:HEC502 3.4 22.5 1.0
CG C:MET267 3.6 22.6 1.0
C3B C:HEC502 4.2 32.2 1.0
C2B C:HEC502 4.2 28.0 1.0
C2D C:HEC502 4.2 30.6 1.0
C3C C:HEC502 4.2 32.3 1.0
C3A C:HEC502 4.3 32.9 1.0
C2A C:HEC502 4.3 25.9 1.0
C3D C:HEC502 4.3 31.0 1.0
C2C C:HEC502 4.3 30.4 1.0
CG C:HIS205 4.4 36.0 1.0
ND1 C:HIS205 4.5 43.5 1.0
CB C:MET267 4.5 27.0 1.0

Iron binding site 6 out of 6 in 8jej

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Iron binding site 6 out of 6 in the Cryo-Em Structure of Na-Dithionite Reduced 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 Na-Dithionite Reduced Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:77.1
occ:1.00
 FE C:HEC503 0.0 77.1 1.0
NC C:HEC503 2.0 58.2 1.0
NB C:HEC503 2.0 55.5 1.0
NA C:HEC503 2.0 60.2 1.0
ND C:HEC503 2.0 57.9 1.0
NE2 C:HIS56 2.3 52.3 1.0
SD C:MET118 2.9 45.0 1.0
C1B C:HEC503 3.0 54.9 1.0
CE1 C:HIS56 3.0 53.7 1.0
C1D C:HEC503 3.0 53.0 1.0
C4A C:HEC503 3.0 58.2 1.0
C1C C:HEC503 3.0 54.0 1.0
C4C C:HEC503 3.0 53.2 1.0
C4B C:HEC503 3.1 51.6 1.0
C4D C:HEC503 3.1 57.1 1.0
C1A C:HEC503 3.1 57.0 1.0
CHD C:HEC503 3.4 53.9 1.0
CHB C:HEC503 3.4 57.8 1.0
CHC C:HEC503 3.4 51.6 1.0
CHA C:HEC503 3.4 54.2 1.0
CD2 C:HIS56 3.5 58.4 1.0
CE C:MET118 3.8 49.9 1.0
CG C:MET118 4.0 53.1 1.0
CB C:MET118 4.1 50.8 1.0
C2B C:HEC503 4.2 58.0 1.0
ND1 C:HIS56 4.2 59.3 1.0
C2D C:HEC503 4.2 55.8 1.0
C3C C:HEC503 4.3 52.6 1.0
C3A C:HEC503 4.3 55.7 1.0
C3B C:HEC503 4.3 56.3 1.0
C2A C:HEC503 4.3 58.5 1.0
C2C C:HEC503 4.3 53.8 1.0
C3D C:HEC503 4.3 58.5 1.0
CG C:HIS56 4.5 58.1 1.0
CA C:MET118 4.9 46.6 1.0
CG1 C:ILE83 4.9 69.9 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: Thu Dec 28 06:03:09 2023

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