Iron in PDB 6nhg: Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex

All present enzymatic activity of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex:
1.10.2.2;

The structure of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex, PDB code: 6nhg was solved by D.Xia, F.Zhou, L.Esser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.87 / 2.80
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	154.181, 154.181, 598.180, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 28.9

The binding sites of Iron atom in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex (pdb code 6nhg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex, PDB code: 6nhg:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1001 b:0.9 occ:1.00 FE C:HEM1001 0.0 0.9 1.0 NE2 C:HIS182 2.0 95.5 1.0 NE2 C:HIS83 2.0 95.4 1.0 NA C:HEM1001 2.0 0.8 1.0 ND C:HEM1001 2.0 0.8 1.0 NB C:HEM1001 2.1 0.5 1.0 NC C:HEM1001 2.1 0.5 1.0 CE1 C:HIS83 2.9 0.4 1.0 CE1 C:HIS182 2.9 94.9 1.0 HE1 C:HIS83 3.0 1.0 1.0 C1A C:HEM1001 3.1 0.2 1.0 C4A C:HEM1001 3.1 0.8 1.0 CD2 C:HIS182 3.1 96.2 1.0 C4D C:HEM1001 3.1 0.3 1.0 C1B C:HEM1001 3.1 0.4 1.0 C1D C:HEM1001 3.1 0.2 1.0 C4B C:HEM1001 3.1 0.2 1.0 C4C C:HEM1001 3.1 0.3 1.0 C1C C:HEM1001 3.1 0.3 1.0 CD2 C:HIS83 3.1 96.8 1.0 HE1 C:HIS182 3.1 0.5 1.0 HD2 C:HIS182 3.3 0.1 1.0 HD2 C:HIS83 3.3 0.9 1.0 CHA C:HEM1001 3.4 0.0 1.0 CHB C:HEM1001 3.4 0.6 1.0 CHD C:HEM1001 3.4 0.9 1.0 CHC C:HEM1001 3.4 0.6 1.0 ND1 C:HIS83 4.1 0.2 1.0 ND1 C:HIS182 4.1 95.2 1.0 CG C:HIS182 4.2 96.0 1.0 CG C:HIS83 4.2 96.2 1.0 HA3 C:GLY130 4.2 0.9 1.0 C3A C:HEM1001 4.3 1.0 1.0 C2A C:HEM1001 4.3 1.0 1.0 C3D C:HEM1001 4.3 0.1 1.0 C2D C:HEM1001 4.3 0.5 1.0 C2B C:HEM1001 4.3 0.1 1.0 C3B C:HEM1001 4.3 0.5 1.0 C3C C:HEM1001 4.3 0.6 1.0 C2C C:HEM1001 4.3 0.9 1.0 HHA C:HEM1001 4.4 0.7 1.0 HHB C:HEM1001 4.4 0.8 1.0 HHD C:HEM1001 4.4 0.7 1.0 HHC C:HEM1001 4.4 0.8 1.0 HA2 C:GLY48 4.6 0.8 1.0 HA3 C:GLY48 4.6 0.8 1.0 HA2 C:GLY130 4.6 0.9 1.0 HD12 C:LEU133 4.7 0.4 1.0 HE21 C:GLN44 4.8 0.2 1.0 CA C:GLY130 4.9 99.7 1.0

Iron binding site 2 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1002 b:72.1 occ:1.00 FE C:HEM1002 0.0 72.1 1.0 ND C:HEM1002 2.0 75.2 1.0 NE2 C:HIS196 2.0 73.6 1.0 NE2 C:HIS97 2.0 75.3 1.0 NA C:HEM1002 2.1 82.9 1.0 NC C:HEM1002 2.1 71.3 1.0 NB C:HEM1002 2.1 71.0 1.0 CE1 C:HIS196 3.0 73.6 1.0 CE1 C:HIS97 3.0 75.0 1.0 CD2 C:HIS196 3.0 73.5 1.0 C4D C:HEM1002 3.0 71.7 1.0 C1D C:HEM1002 3.0 84.8 1.0 C4C C:HEM1002 3.0 84.5 1.0 C1A C:HEM1002 3.1 82.7 1.0 C1C C:HEM1002 3.1 76.9 1.0 C4B C:HEM1002 3.1 70.9 1.0 CD2 C:HIS97 3.1 98.8 1.0 C4A C:HEM1002 3.1 78.4 1.0 C1B C:HEM1002 3.1 78.5 1.0 HE1 C:HIS196 3.1 84.9 1.0 HE1 C:HIS97 3.1 89.6 1.0 HD2 C:HIS196 3.2 84.8 1.0 HD2 C:HIS97 3.3 0.2 1.0 CHA C:HEM1002 3.4 71.7 1.0 CHD C:HEM1002 3.4 89.7 1.0 CHC C:HEM1002 3.4 87.7 1.0 CHB C:HEM1002 3.5 84.4 1.0 ND1 C:HIS196 4.1 73.4 1.0 CG C:HIS196 4.1 73.3 1.0 ND1 C:HIS97 4.1 75.8 1.0 CG C:HIS97 4.2 76.8 1.0 C3C C:HEM1002 4.2 86.8 1.0 C3D C:HEM1002 4.2 71.9 1.0 C2C C:HEM1002 4.2 83.6 1.0 C2D C:HEM1002 4.3 92.7 1.0 HH22 C:ARG100 4.3 0.9 1.0 C2A C:HEM1002 4.3 71.5 1.0 C3A C:HEM1002 4.3 71.3 1.0 C3B C:HEM1002 4.3 88.5 1.0 C2B C:HEM1002 4.3 82.1 1.0 HHA C:HEM1002 4.4 86.7 1.0 HHD C:HEM1002 4.4 0.2 1.0 HHC C:HEM1002 4.4 0.9 1.0 HHB C:HEM1002 4.5 1.0 1.0 HD12 C:LEU37 4.6 90.6 1.0 HA2 C:GLY34 4.9 0.9 1.0 NH2 C:ARG100 5.0 95.2 1.0 HH21 C:ARG100 5.0 0.9 1.0 HD13 C:LEU37 5.0 90.6 1.0 HD12 C:LEU119 5.0 88.3 1.0

Iron binding site 3 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1001 b:0.9 occ:1.00 FE D:HEC1001 0.0 0.9 1.0 NE2 D:HIS41 2.0 0.6 1.0 NC D:HEC1001 2.1 0.1 1.0 NB D:HEC1001 2.1 0.5 1.0 NA D:HEC1001 2.1 0.7 1.0 ND D:HEC1001 2.1 0.5 1.0 SD D:MET160 2.2 0.2 1.0 CE1 D:HIS41 3.0 1.0 1.0 CD2 D:HIS41 3.0 0.6 1.0 C4B D:HEC1001 3.1 0.8 1.0 C1C D:HEC1001 3.1 0.6 1.0 C4C D:HEC1001 3.1 0.9 1.0 C4A D:HEC1001 3.1 0.0 1.0 C1D D:HEC1001 3.1 0.6 1.0 C1B D:HEC1001 3.1 0.3 1.0 C1A D:HEC1001 3.1 0.3 1.0 C4D D:HEC1001 3.1 0.0 1.0 HE1 D:HIS41 3.2 0.2 1.0 HD2 D:HIS41 3.2 0.3 1.0 CE D:MET160 3.4 0.7 1.0 CHC D:HEC1001 3.4 0.3 1.0 HG3 D:MET160 3.4 0.9 1.0 CHD D:HEC1001 3.4 0.1 1.0 CHB D:HEC1001 3.5 0.8 1.0 CHA D:HEC1001 3.5 0.3 1.0 CG D:MET160 3.5 0.4 1.0 HE1 D:MET160 3.5 0.7 1.0 HE2 D:MET160 3.5 0.7 1.0 HB2 D:MET160 3.9 0.9 1.0 ND1 D:HIS41 4.1 0.9 1.0 HB3 D:PRO110 4.1 0.6 1.0 CG D:HIS41 4.1 0.3 1.0 HE3 D:MET160 4.2 0.7 1.0 HG2 D:MET160 4.2 0.9 1.0 CB D:MET160 4.3 0.5 1.0 C3B D:HEC1001 4.3 0.2 1.0 C2B D:HEC1001 4.3 0.0 1.0 C2C D:HEC1001 4.3 0.8 1.0 C3A D:HEC1001 4.3 0.4 1.0 C2A D:HEC1001 4.3 0.1 1.0 C3C D:HEC1001 4.3 0.5 1.0 C2D D:HEC1001 4.3 0.9 1.0 C3D D:HEC1001 4.3 0.2 1.0 HHC D:HEC1001 4.4 0.7 1.0 HHD D:HEC1001 4.4 0.9 1.0 HHB D:HEC1001 4.4 0.0 1.0 HHA D:HEC1001 4.4 0.5 1.0 HG3 D:PRO163 4.5 0.3 1.0 HB3 D:MET160 4.6 0.9 1.0 HB2 D:CYS40 4.8 0.9 1.0 HD2 D:PRO111 5.0 0.7 1.0

Iron binding site 4 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1001 b:75.8 occ:0.25 FE1 E:FES1001 0.0 75.8 0.2 S1 E:FES1001 2.2 76.7 0.2 S2 E:FES1001 2.2 76.1 0.2 SG E:CYS158 2.3 70.9 0.2 SG E:CYS139 2.3 71.2 0.2 HB3 E:CYS139 2.7 85.3 0.2 HB3 E:HIS141 2.9 90.4 0.2 CB E:CYS139 2.9 70.5 0.2 FE2 E:FES1001 3.1 76.9 0.2 HB2 E:CYS139 3.1 85.3 0.2 HB2 E:CYS144 3.3 87.2 0.2 CB E:CYS158 3.5 71.0 0.2 HB3 E:CYS158 3.5 85.9 0.2 HB2 E:CYS160 3.6 87.8 0.2 HB2 E:CYS158 3.6 85.9 0.2 HB2 E:HIS141 3.7 90.4 0.2 CB E:HIS141 3.7 74.8 0.2 H E:HIS141 3.8 89.6 0.2 H E:LEU142 3.8 92.5 0.2 H E:CYS144 3.9 87.2 0.2 H E:HIS161 4.1 90.5 0.2 CB E:CYS144 4.2 72.1 0.2 H E:GLY143 4.3 86.0 0.2 HB2 E:SER163 4.3 85.4 0.2 CA E:CYS139 4.4 70.2 0.2 CB E:CYS160 4.4 72.6 0.2 HB3 E:CYS160 4.5 87.8 0.2 N E:HIS141 4.5 74.1 0.2 ND1 E:HIS141 4.6 75.5 0.2 OG E:SER163 4.6 70.9 0.2 N E:LEU142 4.6 76.6 0.2 CG E:HIS141 4.6 75.2 0.2 N E:CYS144 4.6 72.1 0.2 CA E:HIS141 4.7 74.4 0.2 SG E:CYS144 4.7 72.8 0.2 HB2 E:HIS161 4.7 91.4 0.2 HH E:TYR165 4.7 83.0 0.2 H E:CYS160 4.7 87.5 0.2 C E:CYS139 4.8 70.4 0.2 HA E:CYS139 4.8 85.0 0.2 HB3 E:CYS144 4.8 87.2 0.2 CA E:CYS158 4.9 70.7 0.2 HG3 E:PRO146 4.9 86.3 0.2 N E:HIS161 4.9 74.8 0.2 CA E:CYS144 4.9 71.7 0.2 ND1 E:HIS161 5.0 75.2 0.2 H E:GLY162 5.0 87.7 0.2 CB E:SER163 5.0 70.6 0.2

Iron binding site 5 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1001 b:76.9 occ:0.25 FE2 E:FES1001 0.0 76.9 0.2 ND1 E:HIS161 2.1 75.2 0.2 ND1 E:HIS141 2.1 75.5 0.2 S1 E:FES1001 2.2 76.7 0.2 S2 E:FES1001 2.2 76.1 0.2 HB2 E:HIS161 2.5 91.4 0.2 HB3 E:HIS141 2.7 90.4 0.2 CG E:HIS161 3.0 75.5 0.2 CG E:HIS141 3.0 75.2 0.2 FE1 E:FES1001 3.1 75.8 0.2 CE1 E:HIS141 3.1 75.8 0.2 CB E:HIS161 3.2 75.6 0.2 CE1 E:HIS161 3.2 75.2 0.2 CB E:HIS141 3.3 74.8 0.2 HE1 E:HIS141 3.4 91.7 0.2 HE1 E:HIS161 3.5 90.9 0.2 H E:HIS161 3.5 90.5 0.2 HB2 E:HIS141 3.6 90.4 0.2 HB3 E:CYS160 3.8 87.8 0.2 N E:HIS161 3.9 74.8 0.2 HB3 E:HIS161 3.9 91.4 0.2 HB2 E:CYS160 3.9 87.8 0.2 H E:LEU142 4.1 92.5 0.2 CA E:HIS161 4.1 75.5 0.2 HB2 E:LEU142 4.2 92.9 0.2 CD2 E:HIS141 4.2 75.4 0.2 CD2 E:HIS161 4.2 75.8 0.2 NE2 E:HIS141 4.2 75.8 0.2 NE2 E:HIS161 4.2 75.6 0.2 HG E:LEU142 4.3 93.3 0.2 CB E:CYS160 4.3 72.6 0.2 N E:LEU142 4.5 76.6 0.2 CA E:HIS141 4.6 74.4 0.2 SG E:CYS158 4.6 70.9 0.2 HD12 E:LEU142 4.6 93.7 0.2 HG2 E:PRO175 4.7 82.5 0.2 HD13 E:LEU142 4.7 93.7 0.2 C E:CYS160 4.8 73.5 0.2 C E:HIS141 4.8 74.3 0.2 SG E:CYS139 4.8 71.2 0.2 C E:HIS161 4.8 75.6 0.2 H E:GLY162 4.9 87.7 0.2 HA E:HIS161 4.9 91.2 0.2 CG E:LEU142 4.9 77.2 0.2 CB E:LEU142 4.9 76.8 0.2 CD1 E:LEU142 5.0 77.5 0.2 HD2 E:HIS161 5.0 91.6 0.2 HD2 E:HIS141 5.0 91.1 0.2

L.Esser, F.Zhou, C.A.Yu, D.Xia. Crystal Structure of Bacterial CYTOCHROMEBC1IN Complex with Azoxystrobin Reveals A Conformational Switch of the Rieske Iron-Sulfur Protein Subunit. J.Biol.Chem. V. 294 12007 2019.
ISSN: ESSN 1083-351X
PubMed: 31182483
DOI: 10.1074/JBC.RA119.008381