Atomistry » Iron » PDB 8ire-8ji2 » 8jek
Atomistry »
  Iron »
    PDB 8ire-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: Sat Aug 10 06:51:47 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy