Iron in PDB 7w2j: Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus

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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus (pdb code 7w2j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus, PDB code: 7w2j:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:18.0 occ:1.00 FE1 A:F3S602 0.0 18.0 1.0 SG A:CYS226 1.2 8.8 1.0 S1 A:F3S602 2.2 18.0 1.0 S2 A:F3S602 2.2 18.0 1.0 S3 A:F3S602 2.3 18.0 1.0 FE4 A:F3S602 2.5 18.0 1.0 FE3 A:F3S602 2.6 18.0 1.0 CB A:CYS226 2.7 8.8 1.0 SG A:CYS222 3.2 8.2 1.0 CA A:CYS226 3.9 8.8 1.0 S4 A:F3S602 4.0 18.0 1.0 N A:MET231 4.1 8.1 1.0 CB A:ALA230 4.1 25.3 1.0 CB A:MET231 4.3 8.1 1.0 N A:ALA230 4.5 25.3 1.0 C A:CYS226 4.6 8.8 1.0 CB A:CYS222 4.6 8.2 1.0 CG A:MET231 4.7 8.1 1.0 CA A:ALA230 4.7 25.3 1.0 SG A:CYS216 4.7 25.3 1.0 C A:ALA230 4.8 25.3 1.0 CB A:ASN219 4.8 6.6 1.0 CA A:MET231 4.9 8.1 1.0 CA A:CYS222 4.9 8.2 1.0 CG1 A:ILE228 4.9 11.6 1.0 CD A:PRO227 4.9 9.2 1.0

Iron binding site 2 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:18.0 occ:1.00 FE3 A:F3S602 0.0 18.0 1.0 SG A:CYS222 1.2 8.2 1.0 S3 A:F3S602 2.2 18.0 1.0 S4 A:F3S602 2.2 18.0 1.0 S1 A:F3S602 2.3 18.0 1.0 FE4 A:F3S602 2.4 18.0 1.0 FE1 A:F3S602 2.6 18.0 1.0 CB A:CYS222 2.9 8.2 1.0 SG A:CYS226 3.3 8.8 1.0 S2 A:F3S602 3.5 18.0 1.0 CA A:CYS222 3.5 8.2 1.0 N A:CYS222 3.7 8.2 1.0 N A:ASN220 3.8 6.1 1.0 N A:ASN221 4.2 6.8 1.0 CB A:CYS226 4.3 8.8 1.0 C A:ASN221 4.4 6.8 1.0 CA A:ASN220 4.4 6.1 1.0 OG A:SER343 4.4 9.8 1.0 CB A:ASN219 4.4 6.6 1.0 N A:ASN219 4.5 6.6 1.0 SG A:CYS216 4.5 25.3 1.0 C A:ASN219 4.6 6.6 1.0 C A:ASN220 4.7 6.1 1.0 NH2 A:ARG205 4.7 7.0 1.0 CA A:ASN219 4.7 6.6 1.0 CB A:SER343 4.9 9.8 1.0 CA A:ASN221 4.9 6.8 1.0 O A:ASN221 4.9 6.8 1.0 C A:CYS222 5.0 8.2 1.0 CZ A:ARG205 5.0 7.0 1.0

Iron binding site 3 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:18.0 occ:1.00 FE4 A:F3S602 0.0 18.0 1.0 S2 A:F3S602 2.2 18.0 1.0 S3 A:F3S602 2.2 18.0 1.0 S4 A:F3S602 2.2 18.0 1.0 SG A:CYS216 2.3 25.3 1.0 FE3 A:F3S602 2.4 18.0 1.0 FE1 A:F3S602 2.5 18.0 1.0 SG A:CYS222 3.1 8.2 1.0 CB A:CYS216 3.4 25.3 1.0 SG A:CYS226 3.7 8.8 1.0 S1 A:F3S602 3.8 18.0 1.0 CA A:CYS216 4.1 25.3 1.0 CB A:ALA230 4.2 25.3 1.0 CG A:ARG205 4.3 7.0 1.0 N A:GLY218 4.6 8.1 1.0 N A:CYS217 4.6 10.1 1.0 N A:ASN219 4.6 6.6 1.0 C A:CYS216 4.7 25.3 1.0 CB A:CYS222 4.9 8.2 1.0 N A:MET231 5.0 8.1 1.0 CA A:GLY218 5.0 8.1 1.0

Iron binding site 4 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:5.6 occ:1.00 FE C:HEC501 0.0 5.6 1.0 NA C:HEC501 2.0 5.6 1.0 NC C:HEC501 2.0 5.6 1.0 NB C:HEC501 2.0 5.6 1.0 ND C:HEC501 2.1 5.6 1.0 CE1 C:HIS347 2.7 4.0 1.0 SD C:MET395 2.8 2.9 1.0 C1A C:HEC501 3.0 5.6 1.0 C4A C:HEC501 3.0 5.6 1.0 C4C C:HEC501 3.0 5.6 1.0 C1B C:HEC501 3.0 5.6 1.0 C1C C:HEC501 3.0 5.6 1.0 C4B C:HEC501 3.1 5.6 1.0 C4D C:HEC501 3.1 5.6 1.0 C1D C:HEC501 3.1 5.6 1.0 CHA C:HEC501 3.4 5.6 1.0 CHD C:HEC501 3.4 5.6 1.0 NE2 C:HIS347 3.4 4.0 1.0 CHC C:HEC501 3.4 5.6 1.0 CHB C:HEC501 3.4 5.6 1.0 CE C:MET395 3.4 2.9 1.0 ND1 C:HIS347 3.7 4.0 1.0 CG C:MET395 4.0 2.9 1.0 C2A C:HEC501 4.2 5.6 1.0 C3A C:HEC501 4.2 5.6 1.0 C3C C:HEC501 4.2 5.6 1.0 C2B C:HEC501 4.3 5.6 1.0 C2C C:HEC501 4.3 5.6 1.0 C3B C:HEC501 4.3 5.6 1.0 C2D C:HEC501 4.3 5.6 1.0 C3D C:HEC501 4.3 5.6 1.0 CD2 C:HIS347 4.7 4.0 1.0 CB C:MET395 4.8 2.9 1.0 CG C:HIS347 4.8 4.0 1.0

Iron binding site 5 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:10.0 occ:1.00 FE C:HEC502 0.0 10.0 1.0 NB C:HEC502 2.0 10.0 1.0 NC C:HEC502 2.0 10.0 1.0 NA C:HEC502 2.0 10.0 1.0 ND C:HEC502 2.1 10.0 1.0 NE2 C:HIS205 2.6 13.5 1.0 SD C:MET267 2.8 7.7 1.0 C1D C:HEC502 3.0 10.0 1.0 C4C C:HEC502 3.0 10.0 1.0 C1B C:HEC502 3.0 10.0 1.0 C4A C:HEC502 3.0 10.0 1.0 C4B C:HEC502 3.1 10.0 1.0 C1A C:HEC502 3.1 10.0 1.0 C1C C:HEC502 3.1 10.0 1.0 C4D C:HEC502 3.1 10.0 1.0 CHD C:HEC502 3.3 10.0 1.0 CD2 C:HIS205 3.3 13.5 1.0 CHB C:HEC502 3.4 10.0 1.0 CG C:MET267 3.4 7.7 1.0 CHA C:HEC502 3.4 10.0 1.0 CHC C:HEC502 3.5 10.0 1.0 CE1 C:HIS205 3.6 13.5 1.0 CE C:MET267 4.1 7.7 1.0 C2D C:HEC502 4.2 10.0 1.0 C2B C:HEC502 4.2 10.0 1.0 C3C C:HEC502 4.2 10.0 1.0 C3B C:HEC502 4.3 10.0 1.0 C3A C:HEC502 4.3 10.0 1.0 C2A C:HEC502 4.3 10.0 1.0 C2C C:HEC502 4.3 10.0 1.0 C3D C:HEC502 4.3 10.0 1.0 CG C:HIS205 4.5 13.5 1.0 ND1 C:HIS205 4.5 13.5 1.0 CB C:MET267 4.9 7.7 1.0

Iron binding site 6 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:28.3 occ:1.00 FE C:HEC503 0.0 28.3 1.0 NC C:HEC503 2.0 28.3 1.0 ND C:HEC503 2.0 28.3 1.0 NB C:HEC503 2.0 28.3 1.0 NA C:HEC503 2.1 28.3 1.0 NE2 C:HIS56 2.6 21.2 1.0 CE C:MET118 2.8 28.0 1.0 C1D C:HEC503 3.0 28.3 1.0 C4C C:HEC503 3.0 28.3 1.0 C1B C:HEC503 3.0 28.3 1.0 C4A C:HEC503 3.1 28.3 1.0 C1C C:HEC503 3.1 28.3 1.0 C4D C:HEC503 3.1 28.3 1.0 C4B C:HEC503 3.1 28.3 1.0 C1A C:HEC503 3.1 28.3 1.0 CE1 C:HIS56 3.2 21.2 1.0 CHD C:HEC503 3.3 28.3 1.0 CHB C:HEC503 3.4 28.3 1.0 CHC C:HEC503 3.5 28.3 1.0 CHA C:HEC503 3.5 28.3 1.0 SD C:MET118 3.6 28.0 1.0 CD2 C:HIS56 3.7 21.2 1.0 C3C C:HEC503 4.2 28.3 1.0 C2D C:HEC503 4.2 28.3 1.0 C2C C:HEC503 4.2 28.3 1.0 C2B C:HEC503 4.3 28.3 1.0 C3A C:HEC503 4.3 28.3 1.0 C3D C:HEC503 4.3 28.3 1.0 C3B C:HEC503 4.3 28.3 1.0 C2A C:HEC503 4.3 28.3 1.0 ND1 C:HIS56 4.4 21.2 1.0 CG C:MET118 4.5 28.0 1.0 CG C:HIS56 4.6 21.2 1.0 CD1 C:ILE83 4.7 31.9 1.0

Iron binding site 7 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:17.7 occ:1.00 FE1 D:F3S602 0.0 17.7 1.0 SG D:CYS226 1.2 8.3 1.0 S1 D:F3S602 2.2 17.7 1.0 S2 D:F3S602 2.2 17.7 1.0 S3 D:F3S602 2.3 17.7 1.0 FE4 D:F3S602 2.5 17.7 1.0 FE3 D:F3S602 2.6 17.7 1.0 CB D:CYS226 2.7 8.3 1.0 SG D:CYS222 3.2 9.3 1.0 CA D:CYS226 3.9 8.3 1.0 S4 D:F3S602 4.0 17.7 1.0 N D:MET231 4.1 8.3 1.0 CB D:ALA230 4.1 25.3 1.0 CB D:MET231 4.3 8.3 1.0 N D:ALA230 4.5 25.3 1.0 C D:CYS226 4.6 8.3 1.0 CB D:CYS222 4.6 9.3 1.0 CG D:MET231 4.7 8.3 1.0 CA D:ALA230 4.7 25.3 1.0 SG D:CYS216 4.7 12.5 1.0 C D:ALA230 4.8 25.3 1.0 CB D:ASN219 4.8 25.3 1.0 CA D:MET231 4.9 8.3 1.0 CA D:CYS222 4.9 9.3 1.0 CG1 D:ILE228 4.9 10.8 1.0 CD D:PRO227 4.9 8.9 1.0

Iron binding site 8 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:17.7 occ:1.00 FE3 D:F3S602 0.0 17.7 1.0 SG D:CYS222 1.2 9.3 1.0 S3 D:F3S602 2.2 17.7 1.0 S4 D:F3S602 2.2 17.7 1.0 S1 D:F3S602 2.3 17.7 1.0 FE4 D:F3S602 2.4 17.7 1.0 FE1 D:F3S602 2.6 17.7 1.0 CB D:CYS222 2.9 9.3 1.0 SG D:CYS226 3.3 8.3 1.0 S2 D:F3S602 3.5 17.7 1.0 CA D:CYS222 3.5 9.3 1.0 N D:CYS222 3.7 9.3 1.0 N D:ASN220 3.8 11.2 1.0 N D:ASN221 4.2 6.0 1.0 CB D:CYS226 4.3 8.3 1.0 C D:ASN221 4.4 6.0 1.0 CA D:ASN220 4.4 11.2 1.0 OG D:SER343 4.4 11.9 1.0 CB D:ASN219 4.4 25.3 1.0 N D:ASN219 4.5 25.3 1.0 SG D:CYS216 4.5 12.5 1.0 C D:ASN219 4.6 25.3 1.0 C D:ASN220 4.7 11.2 1.0 NH2 D:ARG205 4.7 7.0 1.0 CA D:ASN219 4.7 25.3 1.0 CB D:SER343 4.9 11.9 1.0 CA D:ASN221 4.9 6.0 1.0 O D:ASN221 4.9 6.0 1.0 C D:CYS222 5.0 9.3 1.0 CZ D:ARG205 5.0 7.0 1.0

Iron binding site 9 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:17.7 occ:1.00 FE4 D:F3S602 0.0 17.7 1.0 S2 D:F3S602 2.2 17.7 1.0 S3 D:F3S602 2.2 17.7 1.0 S4 D:F3S602 2.2 17.7 1.0 SG D:CYS216 2.3 12.5 1.0 FE3 D:F3S602 2.4 17.7 1.0 FE1 D:F3S602 2.5 17.7 1.0 SG D:CYS222 3.1 9.3 1.0 CB D:CYS216 3.4 12.5 1.0 SG D:CYS226 3.7 8.3 1.0 S1 D:F3S602 3.8 17.7 1.0 CA D:CYS216 4.1 12.5 1.0 CB D:ALA230 4.2 25.3 1.0 CG D:ARG205 4.3 7.0 1.0 N D:GLY218 4.6 13.1 1.0 N D:CYS217 4.6 9.2 1.0 N D:ASN219 4.6 25.3 1.0 C D:CYS216 4.7 12.5 1.0 CB D:CYS222 4.9 9.3 1.0 N D:MET231 5.0 8.3 1.0 CA D:GLY218 5.0 13.1 1.0

Iron binding site 10 out of 12 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:7.6 occ:1.00 FE F:HEC501 0.0 7.6 1.0 NA F:HEC501 2.0 7.6 1.0 NC F:HEC501 2.0 7.6 1.0 NB F:HEC501 2.0 7.6 1.0 ND F:HEC501 2.1 7.6 1.0 CE1 F:HIS347 2.7 6.8 1.0 SD F:MET395 2.8 3.0 1.0 C1A F:HEC501 3.0 7.6 1.0 C4A F:HEC501 3.0 7.6 1.0 C4C F:HEC501 3.0 7.6 1.0 C1B F:HEC501 3.0 7.6 1.0 C1C F:HEC501 3.0 7.6 1.0 C4B F:HEC501 3.1 7.6 1.0 C4D F:HEC501 3.1 7.6 1.0 C1D F:HEC501 3.1 7.6 1.0 CHA F:HEC501 3.4 7.6 1.0 CHD F:HEC501 3.4 7.6 1.0 CHC F:HEC501 3.4 7.6 1.0 NE2 F:HIS347 3.4 6.8 1.0 CHB F:HEC501 3.4 7.6 1.0 CE F:MET395 3.4 3.0 1.0 ND1 F:HIS347 3.7 6.8 1.0 CG F:MET395 4.0 3.0 1.0 C2A F:HEC501 4.2 7.6 1.0 C3A F:HEC501 4.2 7.6 1.0 C3C F:HEC501 4.2 7.6 1.0 C2B F:HEC501 4.3 7.6 1.0 C2C F:HEC501 4.3 7.6 1.0 C3B F:HEC501 4.3 7.6 1.0 C2D F:HEC501 4.3 7.6 1.0 C3D F:HEC501 4.3 7.6 1.0 CD2 F:HIS347 4.7 6.8 1.0 CB F:MET395 4.8 3.0 1.0 CG F:HIS347 4.8 6.8 1.0

Y.Suzuki, F.Makino, T.Miyata, H.Tanaka, K.Namba, K.Kano, K.Sowa, Y.Kitazumi, O.Shirai. (Tentative Title) Elucidation of Electron Transfer Mechanism of Membrane-Bound Fructose Dehydrotenase From Gluconobacter Japonicus To Be Published.