Iron in PDB 8xcn: Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A

The binding sites of Iron atom in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A (pdb code 8xcn). 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-N1190A, PDB code: 8xcn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A


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-N1190A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:113.9 occ:1.00 FE1 A:F3S602 0.0 113.9 1.0 S3 A:F3S602 2.2 97.5 1.0 S1 A:F3S602 2.2 115.5 1.0 S2 A:F3S602 2.3 124.5 1.0 SG A:CYS226 2.3 87.4 1.0 FE4 A:F3S602 2.5 106.1 1.0 FE3 A:F3S602 2.6 97.9 1.0 CB A:CYS226 2.8 64.4 1.0 S4 A:F3S602 3.8 110.4 1.0 CA A:CYS226 3.9 72.1 1.0 ND2 A:ASN219 4.1 75.2 1.0 CB A:ASN219 4.2 71.3 1.0 CD A:PRO227 4.6 67.3 1.0 CG A:ASN219 4.6 77.0 1.0 CB A:ALA230 4.7 72.3 1.0 C A:CYS226 4.8 75.2 1.0 N A:ASN219 4.8 81.8 1.0 SG A:CYS216 4.8 88.5 1.0 CB A:ILE228 4.8 77.7 1.0 SG A:CYS222 4.9 83.6 1.0 N A:CYS226 4.9 78.0 1.0 N A:PRO227 5.0 63.5 1.0 SD A:MET231 5.0 73.6 1.0 N A:CYS217 5.0 82.7 1.0

Iron binding site 2 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A


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-N1190A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:97.9 occ:1.00 FE3 A:F3S602 0.0 97.9 1.0 S1 A:F3S602 2.3 115.5 1.0 S4 A:F3S602 2.3 110.4 1.0 S3 A:F3S602 2.3 97.5 1.0 SG A:CYS222 2.3 83.6 1.0 FE4 A:F3S602 2.6 106.1 1.0 FE1 A:F3S602 2.6 113.9 1.0 N A:CYS222 3.4 84.0 1.0 CB A:CYS222 3.5 75.0 1.0 CA A:CYS222 3.7 72.8 1.0 S2 A:F3S602 3.9 124.5 1.0 NH1 A:ARG205 4.1 64.8 1.0 CB A:CYS226 4.1 64.4 1.0 C A:ASN221 4.1 80.5 1.0 CD A:ARG205 4.2 75.4 1.0 N A:ASN221 4.3 78.5 1.0 OG A:SER343 4.4 93.7 1.0 SG A:CYS216 4.5 88.5 1.0 O A:ASN221 4.5 76.9 1.0 SG A:CYS226 4.6 87.4 1.0 N A:ASN220 4.6 79.3 1.0 CZ A:ARG205 4.8 62.5 1.0 NE A:ARG205 4.8 69.0 1.0 N A:ASN219 4.9 81.8 1.0 CB A:ASN219 4.9 71.3 1.0 CA A:SER343 5.0 84.3 1.0 CA A:ASN221 5.0 75.0 1.0

Iron binding site 3 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A


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-N1190A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:106.1 occ:1.00 FE4 A:F3S602 0.0 106.1 1.0 S2 A:F3S602 2.3 124.5 1.0 S4 A:F3S602 2.3 110.4 1.0 S3 A:F3S602 2.3 97.5 1.0 SG A:CYS216 2.3 88.5 1.0 FE1 A:F3S602 2.5 113.9 1.0 FE3 A:F3S602 2.6 97.9 1.0 CB A:CYS216 3.1 69.9 1.0 CA A:CYS216 3.6 76.1 1.0 N A:CYS217 3.7 82.7 1.0 S1 A:F3S602 3.7 115.5 1.0 CD A:ARG205 3.8 75.4 1.0 N A:GLY218 3.8 75.8 1.0 C A:CYS216 4.0 83.6 1.0 N A:ASN219 4.1 81.8 1.0 SG A:CYS222 4.4 83.6 1.0 CA A:GLY218 4.4 81.7 1.0 CG A:ARG205 4.5 69.8 1.0 SG A:CYS226 4.6 87.4 1.0 CB A:ALA230 4.7 72.3 1.0 OG A:SER343 4.7 93.7 1.0 C A:CYS217 4.7 67.4 1.0 CA A:CYS217 4.7 68.5 1.0 C A:GLY218 4.8 86.2 1.0 N A:CYS216 4.9 80.4 1.0 CB A:ASN219 4.9 71.3 1.0 NE A:ARG205 4.9 69.0 1.0

Iron binding site 4 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A


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-N1190A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:68.3 occ:1.00 FE C:HEC501 0.0 68.3 1.0 NC C:HEC501 2.0 84.0 1.0 NA C:HEC501 2.0 85.4 1.0 NB C:HEC501 2.1 68.2 1.0 ND C:HEC501 2.1 78.8 1.0 NE2 C:HIS347 2.1 60.4 1.0 SD C:MET395 3.0 86.4 1.0 C4C C:HEC501 3.0 80.8 1.0 C4A C:HEC501 3.0 84.5 1.0 C1A C:HEC501 3.1 77.6 1.0 C1D C:HEC501 3.1 74.4 1.0 CD2 C:HIS347 3.1 66.1 1.0 C1C C:HEC501 3.1 85.3 1.0 C1B C:HEC501 3.1 76.9 1.0 C4B C:HEC501 3.1 75.9 1.0 C4D C:HEC501 3.1 79.4 1.0 CE1 C:HIS347 3.1 63.0 1.0 CHD C:HEC501 3.4 74.7 1.0 CHB C:HEC501 3.4 78.4 1.0 CHA C:HEC501 3.4 77.4 1.0 CHC C:HEC501 3.5 81.9 1.0 CE C:MET395 3.7 73.9 1.0 CG C:MET395 4.0 80.2 1.0 ND1 C:HIS347 4.2 67.2 1.0 CG C:HIS347 4.2 69.4 1.0 C2A C:HEC501 4.2 68.9 1.0 C3A C:HEC501 4.2 75.4 1.0 C3C C:HEC501 4.3 76.3 1.0 C2C C:HEC501 4.3 80.2 1.0 C2D C:HEC501 4.3 67.2 1.0 C3B C:HEC501 4.3 79.7 1.0 C2B C:HEC501 4.3 83.5 1.0 C3D C:HEC501 4.3 72.1 1.0 CB C:MET395 4.5 81.4 1.0

Iron binding site 5 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A


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-N1190A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:99.6 occ:1.00 FE C:HEC502 0.0 99.6 1.0 NE2 C:HIS205 1.8 92.7 1.0 NA C:HEC502 2.0 84.0 1.0 NC C:HEC502 2.0 86.0 1.0 ND C:HEC502 2.1 75.6 1.0 NB C:HEC502 2.1 81.9 1.0 CE1 C:HIS205 2.5 91.0 1.0 SD C:MET267 3.0 61.5 1.0 C4C C:HEC502 3.0 84.3 1.0 C1D C:HEC502 3.0 77.7 1.0 C4A C:HEC502 3.0 82.3 1.0 CD2 C:HIS205 3.0 87.2 1.0 C1B C:HEC502 3.1 81.3 1.0 C1A C:HEC502 3.1 81.8 1.0 C4D C:HEC502 3.1 78.9 1.0 C1C C:HEC502 3.1 84.8 1.0 C4B C:HEC502 3.1 78.1 1.0 CE C:MET267 3.2 66.9 1.0 CHD C:HEC502 3.4 86.9 1.0 CHB C:HEC502 3.4 82.8 1.0 CHA C:HEC502 3.4 83.2 1.0 CHC C:HEC502 3.5 81.4 1.0 ND1 C:HIS205 3.7 88.4 1.0 CG C:HIS205 4.0 81.2 1.0 C2D C:HEC502 4.3 69.1 1.0 C3A C:HEC502 4.3 80.8 1.0 C2B C:HEC502 4.3 78.6 1.0 C2A C:HEC502 4.3 84.0 1.0 C3C C:HEC502 4.3 71.8 1.0 C2C C:HEC502 4.3 78.5 1.0 C3D C:HEC502 4.3 72.8 1.0 C3B C:HEC502 4.3 76.4 1.0 CG C:MET267 4.4 66.8 1.0 CB C:MET267 4.9 71.1 1.0

Iron binding site 6 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1190A


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-N1190A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:127.6 occ:1.00 FE C:HEC503 0.0 127.6 1.0 NB C:HEC503 2.0 111.5 1.0 NC C:HEC503 2.1 114.1 1.0 NA C:HEC503 2.1 113.8 1.0 ND C:HEC503 2.1 113.4 1.0 NE2 C:HIS56 2.2 108.8 1.0 CE1 C:HIS56 2.6 108.1 1.0 C4C C:HEC503 3.1 113.3 1.0 C1D C:HEC503 3.1 110.4 1.0 C1B C:HEC503 3.1 113.3 1.0 C4A C:HEC503 3.1 113.3 1.0 C1A C:HEC503 3.1 113.5 1.0 C4B C:HEC503 3.1 108.1 1.0 C1C C:HEC503 3.1 111.4 1.0 C4D C:HEC503 3.1 114.4 1.0 SD C:MET118 3.3 82.6 1.0 CHD C:HEC503 3.4 110.3 1.0 CHB C:HEC503 3.4 114.4 1.0 CHA C:HEC503 3.5 115.0 1.0 CE C:MET118 3.5 98.9 1.0 CHC C:HEC503 3.5 109.2 1.0 CD2 C:HIS56 3.6 108.1 1.0 ND1 C:HIS56 3.9 109.4 1.0 C3C C:HEC503 4.3 111.1 1.0 C3A C:HEC503 4.3 113.3 1.0 C2B C:HEC503 4.3 111.5 1.0 C2A C:HEC503 4.3 113.9 1.0 C3B C:HEC503 4.3 109.3 1.0 C2D C:HEC503 4.3 112.2 1.0 C2C C:HEC503 4.3 111.4 1.0 C3D C:HEC503 4.3 114.1 1.0 CG C:HIS56 4.4 106.4 1.0 CG C:MET118 4.5 86.4 1.0 CB C:MET118 4.6 87.7 1.0 CD1 C:ILE83 5.0 123.5 1.0

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