Iron in PDB 5xmj: Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas

All present enzymatic activity of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas:
1.3.5.1;

The structure of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas, PDB code: 5xmj was solved by H.H.Guan, Y.C.Hsieh, P.R.Lin, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 3.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	112.136, 131.772, 195.428, 90.00, 94.22, 90.00
R / Rfree (%)	23.2 / 31.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 44;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas (pdb code 5xmj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 44 binding sites of Iron where determined in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas, PDB code: 5xmj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:25.3 occ:1.00 FE1 B:F3S301 0.0 25.3 1.0 SG B:CYS161 2.1 38.2 1.0 S2 B:F3S301 2.2 47.2 1.0 S1 B:F3S301 2.2 46.9 1.0 S3 B:F3S301 2.2 70.5 1.0 FE4 B:F3S301 2.5 54.8 1.0 FE3 B:F3S301 2.8 48.5 1.0 S4 B:F3S301 3.3 44.5 1.0 CB B:CYS161 3.4 53.4 1.0 OG1 B:THR163 4.0 55.7 1.0 CA B:CYS161 4.0 54.1 1.0 N B:LEU211 4.5 57.6 1.0 CB B:LEU211 4.6 61.3 1.0 SG B:CYS208 4.6 48.6 1.0 SG B:CYS214 4.6 85.0 1.0 CG B:LEU211 4.7 54.1 1.0 CB B:THR163 4.7 49.8 1.0 C B:CYS161 4.7 48.3 1.0 CD1 B:LEU211 4.8 48.6 1.0 N B:GLY162 4.9 46.3 1.0 CE2 B:PHE170 4.9 54.1 1.0 CZ B:PHE170 4.9 51.8 1.0 N B:THR163 4.9 55.7 1.0 N B:LEU212 5.0 64.5 1.0

Iron binding site 2 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:48.5 occ:1.00 FE3 B:F3S301 0.0 48.5 1.0 SG B:CYS208 2.1 48.6 1.0 S3 B:F3S301 2.2 70.5 1.0 S1 B:F3S301 2.2 46.9 1.0 S4 B:F3S301 2.2 44.5 1.0 FE4 B:F3S301 2.7 54.8 1.0 FE1 B:F3S301 2.8 25.3 1.0 CB B:CYS208 3.1 63.0 1.0 CD2 B:LEU228 3.5 35.1 1.0 CA B:CYS208 3.9 62.5 1.0 S2 B:F3S301 4.2 47.2 1.0 SG B:CYS161 4.3 38.2 1.0 CZ B:PHE170 4.4 51.8 1.0 N B:GLY210 4.4 67.6 1.0 C B:CYS208 4.6 62.8 1.0 SG B:CYS214 4.7 85.0 1.0 N B:MET209 4.7 69.7 1.0 CA B:GLY210 4.8 65.9 1.0 CG B:LEU228 4.9 46.9 1.0

Iron binding site 3 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:54.8 occ:1.00 FE4 B:F3S301 0.0 54.8 1.0 S4 B:F3S301 2.2 44.5 1.0 S3 B:F3S301 2.2 70.5 1.0 S2 B:F3S301 2.2 47.2 1.0 SG B:CYS214 2.3 85.0 1.0 FE1 B:F3S301 2.5 25.3 1.0 FE3 B:F3S301 2.7 48.5 1.0 CB B:CYS214 3.6 49.9 1.0 S1 B:F3S301 3.7 46.9 1.0 CD2 B:LEU228 4.0 35.1 1.0 N B:CYS214 4.0 49.3 1.0 SG B:CYS161 4.2 38.2 1.0 N B:LEU212 4.2 64.5 1.0 CA B:CYS214 4.4 50.1 1.0 CB B:ALA173 4.5 50.1 1.0 CA B:LEU212 4.5 62.5 1.0 N B:ALA213 4.5 57.1 1.0 SG B:CYS208 4.5 48.6 1.0 C B:LEU212 4.8 57.1 1.0 CB B:CYS161 5.0 53.4 1.0

Iron binding site 4 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:56.0 occ:1.00 FE1 B:SF4302 0.0 56.0 1.0 S2 B:SF4302 2.2 26.8 1.0 S3 B:SF4302 2.2 24.4 1.0 S4 B:SF4302 2.2 29.9 1.0 SG B:CYS157 2.3 48.0 1.0 FE4 B:SF4302 3.0 34.1 1.0 FE3 B:SF4302 3.0 53.9 1.0 FE2 B:SF4302 3.0 52.4 1.0 CB B:CYS157 3.3 54.1 1.0 CG2 B:VAL174 3.5 46.5 1.0 N B:CYS157 3.5 46.8 1.0 S1 B:SF4302 3.6 29.6 1.0 CA B:CYS157 4.0 51.0 1.0 SG B:CYS154 4.2 34.0 1.0 N B:CYS156 4.3 48.9 1.0 C B:CYS156 4.6 57.7 1.0 SG B:CYS151 4.8 50.6 1.0 N B:GLY155 4.8 43.3 1.0 CB B:VAL174 4.8 51.7 1.0 C B:CYS157 4.9 55.7 1.0 N B:VAL158 4.9 54.4 1.0 CA B:CYS156 4.9 56.4 1.0 C B:GLY155 4.9 52.6 1.0 CD1 B:LEU224 5.0 55.2 1.0

Iron binding site 5 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:52.4 occ:1.00 FE2 B:SF4302 0.0 52.4 1.0 S1 B:SF4302 2.1 29.6 1.0 S4 B:SF4302 2.1 29.9 1.0 S3 B:SF4302 2.2 24.4 1.0 SG B:CYS218 2.3 50.2 1.0 FE4 B:SF4302 3.0 34.1 1.0 FE1 B:SF4302 3.0 56.0 1.0 FE3 B:SF4302 3.0 53.9 1.0 CB B:CYS218 3.2 48.0 1.0 CG1 B:ILE222 3.6 59.8 1.0 S2 B:SF4302 3.7 26.8 1.0 CA B:CYS218 3.7 48.3 1.0 CD B:PRO219 3.9 49.2 1.0 C B:CYS218 4.3 41.2 1.0 N B:PRO219 4.3 36.8 1.0 CD1 B:ILE222 4.5 68.8 1.0 CD1 B:LEU224 4.5 55.2 1.0 SG B:CYS154 4.6 34.0 1.0 CG B:PRO219 4.7 58.1 1.0 CB B:ILE222 4.7 54.1 1.0 SG B:CYS157 4.7 48.0 1.0 N B:LYS220 4.8 51.9 1.0 CB B:CYS157 4.9 54.1 1.0 N B:ILE222 4.9 70.1 1.0

Iron binding site 6 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:53.9 occ:1.00 FE3 B:SF4302 0.0 53.9 1.0 S4 B:SF4302 2.1 29.9 1.0 S1 B:SF4302 2.2 29.6 1.0 S2 B:SF4302 2.2 26.8 1.0 SG B:CYS151 2.3 50.6 1.0 FE1 B:SF4302 3.0 56.0 1.0 FE2 B:SF4302 3.0 52.4 1.0 CB B:CYS151 3.1 61.2 1.0 FE4 B:SF4302 3.1 34.1 1.0 S3 B:SF4302 3.8 24.4 1.0 CG1 B:ILE222 3.9 59.8 1.0 CA B:CYS151 4.0 52.0 1.0 CG2 B:VAL174 4.2 46.5 1.0 N B:GLU153 4.3 52.3 1.0 N B:ILE152 4.4 53.2 1.0 CD1 B:ILE222 4.5 68.8 1.0 C B:CYS151 4.6 50.1 1.0 SG B:CYS157 4.7 48.0 1.0 CA B:GLU153 4.9 53.7 1.0 SG B:CYS218 4.9 50.2 1.0

Iron binding site 7 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:34.1 occ:1.00 FE4 B:SF4302 0.0 34.1 1.0 S1 B:SF4302 2.1 29.6 1.0 S2 B:SF4302 2.1 26.8 1.0 S3 B:SF4302 2.2 24.4 1.0 SG B:CYS154 2.3 34.0 1.0 FE1 B:SF4302 3.0 56.0 1.0 FE2 B:SF4302 3.0 52.4 1.0 FE3 B:SF4302 3.1 53.9 1.0 N B:CYS154 3.4 57.9 1.0 CB B:CYS154 3.5 46.6 1.0 S4 B:SF4302 3.7 29.9 1.0 N B:GLU153 3.8 52.3 1.0 CA B:CYS154 4.0 49.0 1.0 CG1 B:ILE152 4.1 52.8 1.0 SG B:CYS151 4.1 50.6 1.0 N B:GLY155 4.1 43.3 1.0 CA B:GLU153 4.3 53.7 1.0 CD B:PRO219 4.3 49.2 1.0 C B:GLU153 4.4 48.4 1.0 CG B:PRO219 4.4 58.1 1.0 C B:ILE152 4.5 57.5 1.0 N B:CYS156 4.5 48.9 1.0 N B:ILE152 4.6 53.2 1.0 C B:CYS154 4.6 45.2 1.0 SG B:CYS218 4.9 50.2 1.0 CA B:ILE152 4.9 52.5 1.0

Iron binding site 8 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:69.6 occ:1.00 FE1 B:FES303 0.0 69.6 1.0 SG B:CYS65 2.1 62.6 1.0 S1 B:FES303 2.2 60.6 1.0 S2 B:FES303 2.2 73.9 1.0 SG B:CYS77 2.3 55.7 1.0 CB B:CYS65 2.5 51.3 1.0 FE2 B:FES303 3.1 42.1 1.0 N B:CYS65 3.7 56.5 1.0 CA B:CYS65 3.7 47.6 1.0 CB B:CYS77 3.8 70.8 1.0 CA B:GLY60 4.1 62.6 1.0 SG B:CYS62 4.2 52.0 1.0 CD2 B:LEU75 4.4 46.9 1.0 N B:GLY60 4.5 52.4 1.0 N B:CYS77 4.5 68.8 1.0 CA B:CYS77 4.7 74.6 1.0 C B:GLY60 4.7 58.2 1.0 C B:CYS65 4.7 50.9 1.0 N B:GLY63 4.9 57.5 1.0 N B:SER64 4.9 43.1 1.0 CB B:LEU75 4.9 57.5 1.0 N B:HIS78 4.9 67.7 1.0 SG B:CYS57 4.9 58.6 1.0 C B:SER64 4.9 56.4 1.0

Iron binding site 9 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:42.1 occ:1.00 FE2 B:FES303 0.0 42.1 1.0 SG B:CYS62 2.1 52.0 1.0 SG B:CYS57 2.2 58.6 1.0 S1 B:FES303 2.2 60.6 1.0 S2 B:FES303 2.2 73.9 1.0 FE1 B:FES303 3.1 69.6 1.0 N B:CYS57 3.3 56.1 1.0 CB B:CYS62 3.4 51.9 1.0 CB B:CYS57 3.6 49.6 1.0 N B:ARG58 3.8 57.4 1.0 SG B:CYS65 3.9 62.6 1.0 CA B:CYS57 3.9 54.6 1.0 N B:CYS62 4.1 51.6 1.0 SG B:CYS77 4.1 55.7 1.0 N B:GLY60 4.1 52.4 1.0 CB B:CYS56 4.1 49.2 1.0 N B:ILE61 4.3 54.6 1.0 N B:CYS56 4.3 47.8 1.0 C B:CYS57 4.3 59.2 1.0 CA B:CYS62 4.3 51.4 1.0 C B:CYS56 4.3 47.8 1.0 CA B:GLY60 4.3 62.6 1.0 N B:GLY63 4.3 57.5 1.0 CA B:CYS56 4.4 48.7 1.0 C B:GLY60 4.5 58.2 1.0 C B:ILE61 4.5 48.8 1.0 N B:ALA59 4.7 64.9 1.0 CA B:ARG58 4.7 51.2 1.0 N B:SER64 4.8 43.1 1.0 C B:CYS62 4.9 60.9 1.0 CA B:ILE61 5.0 53.5 1.0

Iron binding site 10 out of 44 in the Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Quinol:Fumarate Reductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:69.3 occ:1.00 FE C:HEM301 0.0 69.3 1.0 NC C:HEM301 2.0 94.4 1.0 NB C:HEM301 2.0 85.0 1.0 NA C:HEM301 2.0 77.4 1.0 NE2 C:HIS38 2.0 83.2 1.0 ND C:HEM301 2.2 78.5 1.0 NE2 C:HIS129 2.6 85.8 1.0 CD2 C:HIS38 2.6 91.3 1.0 C1C C:HEM301 2.9 96.2 1.0 C4B C:HEM301 3.0 88.9 1.0 C4A C:HEM301 3.0 84.0 1.0 C4C C:HEM301 3.0 87.3 1.0 C1B C:HEM301 3.0 84.7 1.0 C1A C:HEM301 3.1 80.3 1.0 C1D C:HEM301 3.1 85.9 1.0 C4D C:HEM301 3.2 79.7 1.0 CE1 C:HIS38 3.2 80.4 1.0 CHC C:HEM301 3.3 94.2 1.0 CE1 C:HIS129 3.4 87.7 1.0 CHB C:HEM301 3.4 87.8 1.0 CHD C:HEM301 3.4 82.5 1.0 CHA C:HEM301 3.5 80.1 1.0 CD2 C:HIS129 3.7 84.8 1.0 CG C:HIS38 3.9 88.2 1.0 ND1 C:HIS38 4.1 81.8 1.0 C2C C:HEM301 4.1 92.9 1.0 C3C C:HEM301 4.2 90.6 1.0 C3B C:HEM301 4.2 86.8 1.0 C3A C:HEM301 4.2 82.4 1.0 C2B C:HEM301 4.2 87.5 1.0 C2A C:HEM301 4.2 86.7 1.0 C2D C:HEM301 4.4 89.0 1.0 C3D C:HEM301 4.4 81.9 1.0 ND1 C:HIS129 4.6 90.0 1.0 CG2 C:VAL133 4.8 94.8 1.0 CG C:HIS129 4.8 81.2 1.0

H.H.Guan, Y.C.Hsieh, P.J.Lin, Y.C.Huang, M.Yoshimura, L.Y.Chen, S.K.Chen, P.Chuankhayan, C.C.Lin, N.C.Chen, A.Nakagawa, S.I.Chan, C.J.Chen. Structural Insights Into the Electron/Proton Transfer Pathways in the Quinol:Fumarate Reductase From Desulfovibrio Gigas. Sci Rep V. 8 14935 2018.
ISSN: ESSN 2045-2322
PubMed: 30297797
DOI: 10.1038/S41598-018-33193-5