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

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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-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

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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-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

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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-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

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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-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

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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-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

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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-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

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