Atomistry » Iron » PDB 8ji3-8k6k » 8k6k
Atomistry »
  Iron »
    PDB 8ji3-8k6k »
      8k6k »

Iron in PDB 8k6k: Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A

Enzymatic activity of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A

All present enzymatic activity of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A:
1.1.99.11;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A (pdb code 8k6k). 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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A, PDB code: 8k6k:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8k6k

Go back to Iron Binding Sites List in 8k6k
Iron binding site 1 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A


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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:102.4
occ:1.00
 FE1 A:F3S602 0.0 102.4 1.0
S3 A:F3S602 2.3 79.4 1.0
S1 A:F3S602 2.3 78.0 1.0
S2 A:F3S602 2.3 74.1 1.0
SG A:CYS226 2.3 68.7 1.0
FE4 A:F3S602 2.6 105.0 1.0
FE3 A:F3S602 2.6 102.5 1.0
CB A:CYS226 3.6 64.8 1.0
S4 A:F3S602 3.8 85.5 1.0
CA A:CYS226 4.2 58.3 1.0
CB A:ASN219 4.2 62.2 1.0
CB A:ALA230 4.3 55.2 1.0
CG A:MET231 4.3 59.0 1.0
ND2 A:ASN219 4.4 64.4 1.0
CD A:PRO227 4.4 59.6 1.0
CG1 A:ILE228 4.6 64.2 1.0
N A:ALA230 4.7 60.9 1.0
N A:ASN219 4.7 51.6 1.0
SG A:CYS216 4.7 67.3 1.0
SG A:CYS222 4.8 73.9 1.0
CG A:ASN219 4.8 67.5 1.0
SD A:MET231 4.9 74.2 1.0
N A:MET231 4.9 73.7 1.0
CA A:ALA230 4.9 53.8 1.0
C A:CYS226 5.0 69.1 1.0

Iron binding site 2 out of 6 in 8k6k

Go back to Iron Binding Sites List in 8k6k
Iron binding site 2 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A


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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:102.5
occ:1.00
 FE3 A:F3S602 0.0 102.5 1.0
S4 A:F3S602 2.3 85.5 1.0
S3 A:F3S602 2.3 79.4 1.0
S1 A:F3S602 2.3 78.0 1.0
SG A:CYS222 2.3 73.9 1.0
FE1 A:F3S602 2.6 102.4 1.0
FE4 A:F3S602 2.6 105.0 1.0
CB A:CYS222 3.6 60.9 1.0
N A:CYS222 3.7 70.7 1.0
NH1 A:ARG205 3.7 55.9 1.0
CA A:CYS222 3.8 59.3 1.0
S2 A:F3S602 3.9 74.1 1.0
N A:ASN220 4.1 66.9 1.0
N A:ASN221 4.1 56.5 1.0
C A:ASN221 4.4 63.8 1.0
SG A:CYS226 4.5 68.7 1.0
CD A:ARG205 4.6 60.7 1.0
SD A:MET231 4.6 74.2 1.0
SG A:CYS216 4.6 67.3 1.0
CZ A:ARG205 4.6 57.8 1.0
CB A:SER343 4.6 69.8 1.0
CA A:ASN220 4.6 63.4 1.0
CA A:SER343 4.7 71.2 1.0
N A:ASN219 4.7 51.6 1.0
CG A:MET231 4.8 59.0 1.0
CB A:ASN219 4.8 62.2 1.0
C A:ASN219 4.8 65.2 1.0
C A:ASN220 4.9 70.2 1.0
CA A:ASN221 4.9 57.3 1.0
NE A:ARG205 5.0 66.6 1.0

Iron binding site 3 out of 6 in 8k6k

Go back to Iron Binding Sites List in 8k6k
Iron binding site 3 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A


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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:105.0
occ:1.00
 FE4 A:F3S602 0.0 105.0 1.0
S3 A:F3S602 2.3 79.4 1.0
S4 A:F3S602 2.3 85.5 1.0
S2 A:F3S602 2.3 74.1 1.0
SG A:CYS216 2.3 67.3 1.0
FE1 A:F3S602 2.6 102.4 1.0
FE3 A:F3S602 2.6 102.5 1.0
CB A:CYS216 3.4 68.0 1.0
S1 A:F3S602 3.8 78.0 1.0
N A:GLY218 3.8 66.5 1.0
N A:ASN219 3.9 51.6 1.0
CA A:CYS216 4.0 66.7 1.0
CD A:ARG205 4.1 60.7 1.0
CA A:GLY218 4.2 62.6 1.0
N A:CYS217 4.2 73.4 1.0
C A:CYS216 4.4 72.9 1.0
C A:GLY218 4.5 62.9 1.0
CG A:ARG205 4.5 60.3 1.0
SG A:CYS222 4.6 73.9 1.0
CB A:ALA230 4.6 55.2 1.0
SG A:CYS226 4.7 68.7 1.0
CB A:ASN219 4.8 62.2 1.0
NH1 A:ARG205 4.8 55.9 1.0
N A:ASN220 4.8 66.9 1.0
CA A:ASN219 4.8 49.7 1.0
C A:CYS217 4.9 69.9 1.0

Iron binding site 4 out of 6 in 8k6k

Go back to Iron Binding Sites List in 8k6k
Iron binding site 4 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A


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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:99.2
occ:1.00
 FE C:HEC501 0.0 99.2 1.0
NE2 C:HIS347 2.1 73.7 1.0
NC C:HEC501 2.1 81.1 1.0
NA C:HEC501 2.1 73.8 1.0
NB C:HEC501 2.1 80.8 1.0
ND C:HEC501 2.1 77.5 1.0
CE1 C:HIS347 2.9 65.1 1.0
SD C:MET395 2.9 96.9 1.0
C4C C:HEC501 3.1 73.3 1.0
C4B C:HEC501 3.1 78.6 1.0
C4A C:HEC501 3.1 71.1 1.0
C1A C:HEC501 3.1 74.0 1.0
C4D C:HEC501 3.1 74.5 1.0
C1D C:HEC501 3.1 75.5 1.0
C1B C:HEC501 3.1 71.7 1.0
C1C C:HEC501 3.1 73.8 1.0
CD2 C:HIS347 3.2 69.6 1.0
CE C:MET395 3.2 58.0 1.0
CHA C:HEC501 3.4 77.1 1.0
CHB C:HEC501 3.4 72.7 1.0
CHD C:HEC501 3.4 73.3 1.0
CHC C:HEC501 3.4 73.5 1.0
CG C:MET395 3.5 66.7 1.0
ND1 C:HIS347 4.1 63.1 1.0
CG C:HIS347 4.3 69.1 1.0
C3C C:HEC501 4.4 77.9 1.0
C3B C:HEC501 4.4 68.8 1.0
C3A C:HEC501 4.4 79.0 1.0
C2A C:HEC501 4.4 75.5 1.0
C3D C:HEC501 4.4 73.8 1.0
C2D C:HEC501 4.4 75.9 1.0
C2C C:HEC501 4.4 76.2 1.0
C2B C:HEC501 4.4 74.0 1.0
CB C:MET395 4.7 71.9 1.0

Iron binding site 5 out of 6 in 8k6k

Go back to Iron Binding Sites List in 8k6k
Iron binding site 5 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A


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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:100.4
occ:1.00
 FE C:HEC502 0.0 100.4 1.0
NE2 C:HIS205 2.1 74.5 1.0
NC C:HEC502 2.1 77.8 1.0
NB C:HEC502 2.1 77.9 1.0
NA C:HEC502 2.1 76.3 1.0
ND C:HEC502 2.1 80.1 1.0
SD C:MET267 2.9 66.8 1.0
CE1 C:HIS205 2.9 71.8 1.0
C4C C:HEC502 3.1 76.0 1.0
C1A C:HEC502 3.1 69.2 1.0
C4B C:HEC502 3.1 74.9 1.0
C4D C:HEC502 3.1 73.8 1.0
C4A C:HEC502 3.1 74.3 1.0
C1B C:HEC502 3.1 73.4 1.0
C1D C:HEC502 3.1 81.1 1.0
C1C C:HEC502 3.1 74.5 1.0
CD2 C:HIS205 3.2 75.2 1.0
CHA C:HEC502 3.4 73.8 1.0
CHB C:HEC502 3.4 78.5 1.0
CHD C:HEC502 3.4 78.1 1.0
CHC C:HEC502 3.4 74.7 1.0
CG C:MET267 3.7 67.1 1.0
CE C:MET267 3.7 69.9 1.0
ND1 C:HIS205 4.1 69.0 1.0
CB C:MET267 4.1 65.2 1.0
CG C:HIS205 4.2 72.6 1.0
C3C C:HEC502 4.4 76.6 1.0
C3B C:HEC502 4.4 76.2 1.0
C2A C:HEC502 4.4 72.6 1.0
C3A C:HEC502 4.4 75.5 1.0
C3D C:HEC502 4.4 73.5 1.0
C2D C:HEC502 4.4 77.1 1.0
C2B C:HEC502 4.4 77.2 1.0
C2C C:HEC502 4.4 74.2 1.0
CA C:MET267 4.9 68.0 1.0

Iron binding site 6 out of 6 in 8k6k

Go back to Iron Binding Sites List in 8k6k
Iron binding site 6 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A


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 Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:112.4
occ:1.00
 FE C:HEC503 0.0 112.4 1.0
NA C:HEC503 2.1 94.6 1.0
NC C:HEC503 2.1 99.6 1.0
NB C:HEC503 2.1 93.0 1.0
ND C:HEC503 2.1 93.8 1.0
NE2 C:HIS56 2.1 100.1 1.0
CE1 C:HIS56 2.7 96.6 1.0
SD C:MET118 2.8 80.2 1.0
C4A C:HEC503 3.1 92.7 1.0
C4C C:HEC503 3.1 97.6 1.0
C1B C:HEC503 3.1 95.3 1.0
C1D C:HEC503 3.1 90.1 1.0
C1A C:HEC503 3.1 92.9 1.0
C1C C:HEC503 3.1 95.6 1.0
C4B C:HEC503 3.1 88.4 1.0
C4D C:HEC503 3.1 96.5 1.0
CD2 C:HIS56 3.4 95.0 1.0
CE C:MET118 3.4 85.8 1.0
CHB C:HEC503 3.4 98.0 1.0
CHC C:HEC503 3.5 90.1 1.0
CHD C:HEC503 3.5 93.4 1.0
CHA C:HEC503 3.5 95.0 1.0
ND1 C:HIS56 4.0 90.8 1.0
CG C:MET118 4.2 94.6 1.0
CG C:HIS56 4.3 86.6 1.0
C3C C:HEC503 4.4 92.5 1.0
C3B C:HEC503 4.4 90.4 1.0
C3A C:HEC503 4.4 94.3 1.0
C2A C:HEC503 4.4 93.9 1.0
C2D C:HEC503 4.4 92.1 1.0
C2B C:HEC503 4.4 95.7 1.0
C3D C:HEC503 4.4 95.4 1.0
C2C C:HEC503 4.5 92.0 1.0
CB C:MET118 5.0 85.8 1.0

Reference:

E.Fukawa, Y.Suzuki, T.Adachi, T.Miyata, F.Makino, H.Tanaka, K.Namba, K.Sowa, Y.Kitazumi, O.Shirai. Structural and Electrochemical Elucidation of Biocatalytic Mechanisms in Direct Electron Transfer-Type D-Fructose Dehydrogenase. Electrochim Acta V. 490 2024.
DOI: 10.1016/J.ELECTACTA.2024.144271
Page generated: Sat Aug 10 07:26:57 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