Iron in PDB 8xcm: Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q

The binding sites of Iron atom in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q (pdb code 8xcm). 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-N1146Q, PDB code: 8xcm:
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-N1146Q


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-N1146Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:136.6 occ:1.00 FE1 A:F3S602 0.0 136.6 1.0 S2 A:F3S602 2.3 155.1 1.0 S1 A:F3S602 2.3 134.8 1.0 S3 A:F3S602 2.3 156.0 1.0 SG A:CYS226 2.3 127.5 1.0 FE4 A:F3S602 2.6 154.8 1.0 FE3 A:F3S602 2.6 149.4 1.0 S4 A:F3S602 3.7 154.6 1.0 CB A:ALA230 3.8 109.0 1.0 CB A:CYS226 3.8 107.5 1.0 N A:ALA230 4.1 104.1 1.0 N A:MET231 4.3 100.1 1.0 CA A:ALA230 4.4 104.0 1.0 OD1 A:ASN219 4.4 116.4 1.0 CG A:MET231 4.4 105.8 1.0 CA A:CYS226 4.5 106.2 1.0 C A:ALA230 4.6 112.7 1.0 SG A:CYS216 4.6 131.8 1.0 NH1 A:ARG205 4.6 110.1 1.0 SG A:CYS222 4.8 131.1 1.0 CG1 A:ILE228 4.9 102.8 1.0 CD A:PRO227 4.9 116.2 1.0

Iron binding site 2 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q


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-N1146Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:149.4 occ:1.00 FE3 A:F3S602 0.0 149.4 1.0 S4 A:F3S602 2.3 154.6 1.0 S1 A:F3S602 2.3 134.8 1.0 S3 A:F3S602 2.3 156.0 1.0 SG A:CYS222 2.3 131.1 1.0 FE4 A:F3S602 2.6 154.8 1.0 FE1 A:F3S602 2.6 136.6 1.0 NH1 A:ARG205 3.5 110.1 1.0 CB A:CYS222 3.5 111.1 1.0 CA A:CYS222 3.7 102.5 1.0 N A:CYS222 3.7 113.4 1.0 S2 A:F3S602 3.9 155.1 1.0 C A:ASN221 4.4 111.4 1.0 CE A:MET231 4.4 101.5 1.0 N A:ASN221 4.5 100.5 1.0 SG A:CYS226 4.5 127.5 1.0 SG A:CYS216 4.5 131.8 1.0 CB A:SER343 4.5 127.9 1.0 N A:ASN220 4.6 103.8 1.0 CZ A:ARG205 4.6 112.8 1.0 CA A:SER343 4.6 126.8 1.0 CA A:ASN220 4.9 88.0 1.0 O A:ASN221 4.9 118.1 1.0

Iron binding site 3 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q


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-N1146Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:154.8 occ:1.00 FE4 A:F3S602 0.0 154.8 1.0 S3 A:F3S602 2.3 156.0 1.0 S2 A:F3S602 2.3 155.1 1.0 S4 A:F3S602 2.3 154.6 1.0 SG A:CYS216 2.3 131.8 1.0 FE3 A:F3S602 2.6 149.4 1.0 FE1 A:F3S602 2.6 136.6 1.0 CB A:CYS216 3.5 119.2 1.0 N A:GLY218 3.7 94.9 1.0 S1 A:F3S602 3.8 134.8 1.0 CA A:CYS216 3.9 114.4 1.0 CA A:GLY218 4.0 101.7 1.0 N A:ASN219 4.2 111.9 1.0 N A:CYS217 4.2 114.0 1.0 C A:CYS216 4.3 122.4 1.0 OD1 A:ASN219 4.3 116.4 1.0 NH1 A:ARG205 4.4 110.1 1.0 SG A:CYS222 4.5 131.1 1.0 CB A:ALA230 4.5 109.0 1.0 C A:GLY218 4.6 106.7 1.0 CD A:ARG205 4.7 114.7 1.0 O A:GLY342 4.8 123.1 1.0 C A:CYS217 4.8 106.1 1.0 SG A:CYS226 4.9 127.5 1.0

Iron binding site 4 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q


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-N1146Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:137.7 occ:1.00 FE C:HEC501 0.0 137.7 1.0 NC C:HEC501 2.0 122.6 1.0 ND C:HEC501 2.0 122.0 1.0 NA C:HEC501 2.0 121.5 1.0 NB C:HEC501 2.0 127.4 1.0 NE2 C:HIS347 2.1 120.3 1.0 CE1 C:HIS347 2.6 120.1 1.0 CE C:MET395 2.9 92.5 1.0 C4D C:HEC501 3.0 119.8 1.0 C1C C:HEC501 3.0 116.2 1.0 C4B C:HEC501 3.0 124.5 1.0 C1D C:HEC501 3.0 114.6 1.0 C1A C:HEC501 3.0 116.4 1.0 C1B C:HEC501 3.0 123.4 1.0 C4A C:HEC501 3.0 120.6 1.0 C4C C:HEC501 3.0 121.0 1.0 SD C:MET395 3.1 116.5 1.0 CD2 C:HIS347 3.3 109.5 1.0 CHD C:HEC501 3.4 115.5 1.0 CHA C:HEC501 3.4 116.6 1.0 CHC C:HEC501 3.4 117.4 1.0 CHB C:HEC501 3.4 118.7 1.0 ND1 C:HIS347 3.9 113.0 1.0 C3B C:HEC501 4.2 119.4 1.0 CG C:HIS347 4.2 106.3 1.0 C3C C:HEC501 4.2 119.3 1.0 C2B C:HEC501 4.2 120.1 1.0 C2D C:HEC501 4.3 113.7 1.0 C2A C:HEC501 4.3 114.1 1.0 C3D C:HEC501 4.3 118.8 1.0 C3A C:HEC501 4.3 117.1 1.0 C2C C:HEC501 4.3 110.1 1.0 CG C:MET395 4.8 123.7 1.0

Iron binding site 5 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q


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-N1146Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:148.6 occ:1.00 FE C:HEC502 0.0 148.6 1.0 NB C:HEC502 2.0 126.0 1.0 NC C:HEC502 2.0 126.7 1.0 NA C:HEC502 2.0 121.8 1.0 ND C:HEC502 2.0 128.7 1.0 NE2 C:HIS205 2.0 124.4 1.0 CE1 C:HIS205 2.9 121.7 1.0 SD C:MET267 3.0 122.5 1.0 C1B C:HEC502 3.0 126.0 1.0 C1D C:HEC502 3.0 124.2 1.0 C4B C:HEC502 3.0 123.3 1.0 C4A C:HEC502 3.0 123.7 1.0 C1C C:HEC502 3.0 120.5 1.0 C4D C:HEC502 3.0 125.8 1.0 C4C C:HEC502 3.0 125.8 1.0 C1A C:HEC502 3.1 120.0 1.0 CD2 C:HIS205 3.1 125.0 1.0 CHD C:HEC502 3.4 128.7 1.0 CHB C:HEC502 3.4 128.0 1.0 CHA C:HEC502 3.4 126.4 1.0 CHC C:HEC502 3.4 122.5 1.0 CG C:MET267 3.5 116.3 1.0 CE C:MET267 3.7 118.8 1.0 ND1 C:HIS205 4.0 121.7 1.0 CB C:MET267 4.2 120.2 1.0 CG C:HIS205 4.2 118.3 1.0 C3B C:HEC502 4.2 120.4 1.0 C2B C:HEC502 4.2 123.2 1.0 C3C C:HEC502 4.2 115.1 1.0 C2D C:HEC502 4.2 116.8 1.0 C3A C:HEC502 4.3 123.1 1.0 C3D C:HEC502 4.3 119.5 1.0 C2A C:HEC502 4.3 119.2 1.0 C2C C:HEC502 4.3 116.5 1.0 CA C:MET267 4.9 113.8 1.0

Iron binding site 6 out of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-N1146Q


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-N1146Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:144.1 occ:1.00 FE C:HEC503 0.0 144.1 1.0 NE2 C:HIS56 2.0 155.8 1.0 NB C:HEC503 2.0 147.6 1.0 NC C:HEC503 2.0 146.2 1.0 NA C:HEC503 2.0 147.5 1.0 ND C:HEC503 2.0 145.1 1.0 CE1 C:HIS56 2.6 150.6 1.0 SD C:MET118 2.9 148.1 1.0 C1D C:HEC503 3.0 144.8 1.0 C1B C:HEC503 3.0 149.1 1.0 C4A C:HEC503 3.0 147.4 1.0 C4B C:HEC503 3.0 144.2 1.0 C4C C:HEC503 3.0 145.3 1.0 C1C C:HEC503 3.0 146.1 1.0 C4D C:HEC503 3.0 146.2 1.0 C1A C:HEC503 3.1 146.6 1.0 CD2 C:HIS56 3.2 151.8 1.0 CHD C:HEC503 3.4 148.6 1.0 CE C:MET118 3.4 148.4 1.0 CHB C:HEC503 3.4 149.9 1.0 CHA C:HEC503 3.4 146.4 1.0 CHC C:HEC503 3.4 149.2 1.0 ND1 C:HIS56 3.9 145.8 1.0 CG C:HIS56 4.2 143.3 1.0 C2D C:HEC503 4.2 142.7 1.0 C3B C:HEC503 4.2 138.1 1.0 C2B C:HEC503 4.2 142.3 1.0 C3C C:HEC503 4.3 134.5 1.0 C3A C:HEC503 4.3 142.1 1.0 C2A C:HEC503 4.3 143.6 1.0 C3D C:HEC503 4.3 144.6 1.0 C2C C:HEC503 4.3 137.4 1.0 CG C:MET118 4.6 154.6 1.0 CD1 C:ILE83 4.8 159.4 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