Atomistry » Iron » PDB 8irg-8ji2 » 8jek
Atomistry »
  Iron »
    PDB 8irg-8ji2 »
      8jek »

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

Go back to Iron Binding Sites List in 8jek
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

Go back to Iron Binding Sites List in 8jek
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

Go back to Iron Binding Sites List in 8jek
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

Go back to Iron Binding Sites List in 8jek
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

Go back to Iron Binding Sites List in 8jek
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

Go back to Iron Binding Sites List in 8jek
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: Thu Aug 7 18:41:31 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy