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Iron in PDB 8k6j: Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A

Enzymatic activity of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A

All present enzymatic activity of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A:
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-H1147A (pdb code 8k6j). 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-H1147A, PDB code: 8k6j:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8k6j

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Iron binding site 1 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A


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-H1147A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:177.9
occ:1.00
 FE1 A:F3S602 0.0 177.9 1.0
S1 A:F3S602 2.2 165.2 1.0
S2 A:F3S602 2.2 164.0 1.0
SG A:CYS216 2.3 139.4 1.0
S3 A:F3S602 2.3 159.5 1.0
SG A:CYS226 2.3 104.5 1.0
FE4 A:F3S602 2.4 181.3 1.0
FE3 A:F3S602 2.6 159.7 1.0
CB A:CYS216 3.4 114.9 1.0
S4 A:F3S602 3.5 155.7 1.0
CB A:ALA230 3.6 89.2 1.0
CB A:CYS226 4.0 93.9 1.0
CD A:ARG205 4.2 108.9 1.0
CA A:CYS216 4.2 120.9 1.0
CG A:ARG205 4.3 105.8 1.0
C A:ALA230 4.3 103.6 1.0
CA A:ALA230 4.3 91.0 1.0
N A:MET231 4.4 110.9 1.0
N A:ALA230 4.5 107.3 1.0
NH1 A:ARG205 4.5 102.3 1.0
O A:ALA230 4.7 111.9 1.0
SG A:CYS222 4.8 124.3 1.0

Iron binding site 2 out of 6 in 8k6j

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Iron binding site 2 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A


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-H1147A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:159.7
occ:1.00
 FE3 A:F3S602 0.0 159.7 1.0
S4 A:F3S602 2.2 155.7 1.0
S3 A:F3S602 2.2 159.5 1.0
S1 A:F3S602 2.2 165.2 1.0
SG A:CYS222 2.3 124.3 1.0
FE1 A:F3S602 2.6 177.9 1.0
FE4 A:F3S602 2.7 181.3 1.0
SG A:CYS216 3.4 139.4 1.0
CB A:CYS222 3.5 104.4 1.0
SG A:CYS226 3.7 104.5 1.0
NH1 A:ARG205 3.7 102.3 1.0
N A:CYS222 3.8 115.9 1.0
CA A:CYS222 3.8 103.3 1.0
OG A:SER343 3.8 129.9 1.0
S2 A:F3S602 4.0 164.0 1.0
CD A:ARG205 4.0 108.9 1.0
CZ A:ARG205 4.4 105.7 1.0
NE A:ARG205 4.5 103.7 1.0
N A:ASN220 4.5 111.1 1.0
N A:ASN221 4.5 110.5 1.0
CA A:SER343 4.5 114.9 1.0
CB A:SER343 4.6 118.6 1.0
C A:ASN221 4.6 112.4 1.0
CB A:CYS226 4.7 93.9 1.0
CG A:ARG205 4.9 105.8 1.0
CA A:ASN220 4.9 101.8 1.0
CB A:CYS216 5.0 114.9 1.0

Iron binding site 3 out of 6 in 8k6j

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Iron binding site 3 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A


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-H1147A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:181.3
occ:1.00
 FE4 A:F3S602 0.0 181.3 1.0
S3 A:F3S602 2.2 159.5 1.0
S2 A:F3S602 2.2 164.0 1.0
S4 A:F3S602 2.3 155.7 1.0
SG A:CYS216 2.3 139.4 1.0
FE1 A:F3S602 2.4 177.9 1.0
FE3 A:F3S602 2.7 159.7 1.0
N A:ASN219 3.0 99.2 1.0
SG A:CYS226 3.3 104.5 1.0
CB A:ASN219 3.4 92.3 1.0
ND2 A:ASN219 3.6 106.8 1.0
CA A:ASN219 3.6 94.3 1.0
CG A:ASN219 3.8 103.0 1.0
N A:ASN220 3.9 111.1 1.0
S1 A:F3S602 3.9 165.2 1.0
C A:GLY218 3.9 106.8 1.0
N A:GLY218 3.9 111.1 1.0
CA A:GLY218 4.0 114.4 1.0
CB A:CYS216 4.1 114.9 1.0
C A:ASN219 4.2 105.3 1.0
N A:CYS217 4.6 117.5 1.0
CA A:CYS216 4.7 120.9 1.0
SG A:CYS222 4.8 124.3 1.0
C A:CYS217 4.8 106.5 1.0
OD1 A:ASN219 4.8 118.0 1.0
N A:ASN221 4.9 110.5 1.0
CB A:CYS226 4.9 93.9 1.0
C A:CYS216 4.9 123.3 1.0

Iron binding site 4 out of 6 in 8k6j

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A


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-H1147A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:133.1
occ:1.00
 FE C:HEC501 0.0 133.1 1.0
NE2 C:HIS347 2.0 112.8 1.0
NC C:HEC501 2.0 116.6 1.0
NA C:HEC501 2.0 117.1 1.0
NB C:HEC501 2.0 116.9 1.0
ND C:HEC501 2.0 116.8 1.0
CE1 C:HIS347 2.6 109.5 1.0
SD C:MET395 2.8 100.1 1.0
C1D C:HEC501 3.0 113.9 1.0
C1B C:HEC501 3.0 114.2 1.0
C4A C:HEC501 3.0 113.2 1.0
C4B C:HEC501 3.0 116.7 1.0
C1C C:HEC501 3.0 114.6 1.0
C4C C:HEC501 3.0 115.8 1.0
C1A C:HEC501 3.0 115.8 1.0
C4D C:HEC501 3.1 117.5 1.0
CD2 C:HIS347 3.2 107.3 1.0
CHD C:HEC501 3.4 115.4 1.0
CHB C:HEC501 3.4 115.1 1.0
CHA C:HEC501 3.4 116.0 1.0
CHC C:HEC501 3.4 115.9 1.0
CE C:MET395 3.7 102.6 1.0
ND1 C:HIS347 3.8 110.0 1.0
CG C:HIS347 4.2 105.6 1.0
C2D C:HEC501 4.2 110.8 1.0
C3B C:HEC501 4.2 114.7 1.0
C2B C:HEC501 4.2 114.4 1.0
C3C C:HEC501 4.2 112.5 1.0
C3A C:HEC501 4.2 110.1 1.0
C2A C:HEC501 4.3 114.7 1.0
C2C C:HEC501 4.3 111.5 1.0
C3D C:HEC501 4.3 114.5 1.0
CG C:MET395 4.5 114.6 1.0

Iron binding site 5 out of 6 in 8k6j

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Iron binding site 5 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A


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-H1147A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:147.2
occ:1.00
 FE C:HEC502 0.0 147.2 1.0
NE2 C:HIS205 1.9 120.0 1.0
NC C:HEC502 2.0 120.1 1.0
NB C:HEC502 2.0 121.6 1.0
NA C:HEC502 2.0 122.3 1.0
ND C:HEC502 2.0 121.5 1.0
CD2 C:HIS205 2.7 115.5 1.0
SD C:MET267 2.8 113.4 1.0
C1D C:HEC502 3.0 121.7 1.0
C1B C:HEC502 3.0 118.3 1.0
C4A C:HEC502 3.0 121.5 1.0
C4C C:HEC502 3.0 118.3 1.0
C4B C:HEC502 3.0 117.4 1.0
C1C C:HEC502 3.0 117.7 1.0
C4D C:HEC502 3.0 116.2 1.0
C1A C:HEC502 3.0 115.3 1.0
CE1 C:HIS205 3.1 117.7 1.0
CHD C:HEC502 3.4 122.5 1.0
CHB C:HEC502 3.4 120.3 1.0
CHA C:HEC502 3.4 114.6 1.0
CHC C:HEC502 3.5 117.3 1.0
CE C:MET267 3.5 105.2 1.0
CG C:HIS205 3.9 110.9 1.0
ND1 C:HIS205 4.1 117.3 1.0
C3C C:HEC502 4.2 109.7 1.0
C3B C:HEC502 4.2 113.6 1.0
C2B C:HEC502 4.2 116.6 1.0
C2D C:HEC502 4.2 118.3 1.0
C3A C:HEC502 4.3 119.7 1.0
C2A C:HEC502 4.3 114.7 1.0
C3D C:HEC502 4.3 113.9 1.0
C2C C:HEC502 4.3 113.0 1.0
CG C:MET267 4.5 112.5 1.0

Iron binding site 6 out of 6 in 8k6j

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Iron binding site 6 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A


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-H1147A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:153.8
occ:1.00
 FE C:HEC503 0.0 153.8 1.0
NC C:HEC503 2.0 137.1 1.0
NA C:HEC503 2.0 138.6 1.0
NB C:HEC503 2.0 140.6 1.0
ND C:HEC503 2.0 136.1 1.0
NE2 C:HIS56 2.1 137.0 1.0
CE1 C:HIS56 2.6 135.4 1.0
SD C:MET118 2.9 139.9 1.0
C1D C:HEC503 3.0 135.5 1.0
C1B C:HEC503 3.0 136.5 1.0
C4A C:HEC503 3.0 139.0 1.0
C4C C:HEC503 3.0 134.9 1.0
C4B C:HEC503 3.0 136.8 1.0
C4D C:HEC503 3.0 138.8 1.0
C1A C:HEC503 3.0 137.7 1.0
C1C C:HEC503 3.0 135.9 1.0
CD2 C:HIS56 3.3 134.9 1.0
CHD C:HEC503 3.4 137.0 1.0
CHB C:HEC503 3.4 138.5 1.0
CG C:MET118 3.4 131.6 1.0
CHA C:HEC503 3.4 140.3 1.0
CHC C:HEC503 3.5 135.3 1.0
ND1 C:HIS56 3.8 133.7 1.0
CG C:HIS56 4.2 130.5 1.0
CE C:MET118 4.2 135.6 1.0
C2D C:HEC503 4.2 135.2 1.0
C3C C:HEC503 4.2 130.4 1.0
C3B C:HEC503 4.2 133.7 1.0
C2B C:HEC503 4.2 133.8 1.0
C3A C:HEC503 4.3 136.7 1.0
C2A C:HEC503 4.3 135.2 1.0
C3D C:HEC503 4.3 134.8 1.0
C2C C:HEC503 4.3 130.8 1.0
CB C:MET118 4.8 128.3 1.0
CD1 C:ILE83 4.8 157.8 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: Thu Aug 7 18:53:40 2025

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