Iron in PDB 1ntk: Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1

All present enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1:
1.10.2.2;

The structure of Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1, PDB code: 1ntk was solved by X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.-A.Yu, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.60
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	153.785, 153.785, 592.498, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1 (pdb code 1ntk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1, PDB code: 1ntk:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1


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 Mitochondrial Cytochrome BC1 in Complex with Antimycin A1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe381 b:36.0 occ:1.00 FE C:HEM381 0.0 36.0 1.0 ND C:HEM381 2.0 40.5 1.0 NB C:HEM381 2.0 43.4 1.0 NC C:HEM381 2.0 42.1 1.0 NE2 C:HIS182 2.0 11.1 1.0 NE2 C:HIS83 2.1 17.7 1.0 NA C:HEM381 2.1 42.0 1.0 CE1 C:HIS182 2.9 14.5 1.0 CE1 C:HIS83 2.9 20.6 1.0 C4D C:HEM381 3.0 43.1 1.0 C1D C:HEM381 3.0 43.3 1.0 C4C C:HEM381 3.0 42.1 1.0 C1B C:HEM381 3.1 43.5 1.0 C4B C:HEM381 3.1 44.6 1.0 CD2 C:HIS182 3.1 14.6 1.0 C1C C:HEM381 3.1 41.0 1.0 C1A C:HEM381 3.1 41.3 1.0 C4A C:HEM381 3.1 42.8 1.0 CD2 C:HIS83 3.2 18.8 1.0 CHA C:HEM381 3.6 43.1 1.0 CHD C:HEM381 3.6 43.4 1.0 CHB C:HEM381 3.6 44.0 1.0 CHC C:HEM381 3.7 40.8 1.0 ND1 C:HIS182 4.0 16.7 1.0 C3D C:HEM381 4.1 43.5 1.0 C2D C:HEM381 4.1 44.5 1.0 ND1 C:HIS83 4.1 24.9 1.0 C3C C:HEM381 4.1 41.3 1.0 C2C C:HEM381 4.2 40.3 1.0 CG C:HIS182 4.2 18.0 1.0 C3B C:HEM381 4.2 46.3 1.0 C2B C:HEM381 4.2 46.0 1.0 CG C:HIS83 4.2 23.9 1.0 C2A C:HEM381 4.4 40.4 1.0 C3A C:HEM381 4.4 41.6 1.0 CA C:GLY48 4.8 26.5 1.0 CA C:GLY130 4.9 35.6 1.0 OE1 C:GLN44 5.0 34.5 1.0

Iron binding site 2 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1


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 Mitochondrial Cytochrome BC1 in Complex with Antimycin A1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe382 b:28.6 occ:1.00 FE C:HEM382 0.0 28.6 1.0 ND C:HEM382 2.0 30.9 1.0 NB C:HEM382 2.0 31.6 1.0 NC C:HEM382 2.0 32.9 1.0 NA C:HEM382 2.1 30.6 1.0 NE2 C:HIS196 2.2 25.6 1.0 NE2 C:HIS97 2.3 21.0 1.0 C4C C:HEM382 3.0 34.2 1.0 C1C C:HEM382 3.0 32.8 1.0 CE1 C:HIS196 3.0 26.0 1.0 C4D C:HEM382 3.0 31.2 1.0 CD2 C:HIS97 3.1 22.4 1.0 C1D C:HEM382 3.1 34.7 1.0 C1B C:HEM382 3.1 30.1 1.0 C4B C:HEM382 3.1 30.8 1.0 C4A C:HEM382 3.1 31.9 1.0 C1A C:HEM382 3.1 29.7 1.0 CD2 C:HIS196 3.2 24.4 1.0 CE1 C:HIS97 3.5 22.4 1.0 CHA C:HEM382 3.6 30.8 1.0 CHD C:HEM382 3.6 36.5 1.0 CHC C:HEM382 3.6 34.6 1.0 CHB C:HEM382 3.6 31.0 1.0 C3C C:HEM382 4.0 33.5 1.0 C2C C:HEM382 4.0 34.1 1.0 ND1 C:HIS196 4.1 27.8 1.0 C3D C:HEM382 4.2 31.3 1.0 C2D C:HEM382 4.2 34.2 1.0 C2B C:HEM382 4.2 32.0 1.0 C3B C:HEM382 4.2 31.7 1.0 CG C:HIS196 4.3 29.1 1.0 CG C:HIS97 4.3 26.1 1.0 C3A C:HEM382 4.3 31.4 1.0 C2A C:HEM382 4.3 30.9 1.0 ND1 C:HIS97 4.4 26.9 1.0

Iron binding site 3 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1


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 Mitochondrial Cytochrome BC1 in Complex with Antimycin A1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe242 b:31.4 occ:1.00 FE D:HEM242 0.0 31.4 1.0 NC D:HEM242 2.0 31.4 1.0 ND D:HEM242 2.0 31.6 1.0 NB D:HEM242 2.0 30.4 1.0 NA D:HEM242 2.1 31.5 1.0 NE2 D:HIS41 2.3 32.6 1.0 SD D:MET160 3.0 29.6 1.0 C1D D:HEM242 3.0 32.0 1.0 C4D D:HEM242 3.0 31.6 1.0 C4C D:HEM242 3.0 32.0 1.0 C1C D:HEM242 3.1 33.0 1.0 C1B D:HEM242 3.1 28.6 1.0 C4B D:HEM242 3.1 30.0 1.0 C4A D:HEM242 3.1 30.8 1.0 C1A D:HEM242 3.1 32.0 1.0 CE1 D:HIS41 3.2 32.8 1.0 CD2 D:HIS41 3.3 33.4 1.0 CG D:MET160 3.3 31.3 1.0 CHD D:HEM242 3.6 32.2 1.0 CHA D:HEM242 3.6 32.5 1.0 CE D:MET160 3.6 29.7 1.0 CHB D:HEM242 3.6 29.3 1.0 CHC D:HEM242 3.6 32.9 1.0 C2D D:HEM242 4.1 32.5 1.0 C3D D:HEM242 4.1 32.7 1.0 C3C D:HEM242 4.1 32.1 1.0 C2C D:HEM242 4.1 32.5 1.0 C2B D:HEM242 4.2 27.6 1.0 C3B D:HEM242 4.2 28.8 1.0 CB D:MET160 4.2 32.4 1.0 ND1 D:HIS41 4.3 33.6 1.0 C3A D:HEM242 4.4 31.0 1.0 CG D:HIS41 4.4 32.8 1.0 C2A D:HEM242 4.4 30.7 1.0 CB D:PRO110 4.6 37.6 1.0

Iron binding site 4 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1


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 Mitochondrial Cytochrome BC1 in Complex with Antimycin A1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe197 b:48.3 occ:1.00 FE1 E:FES197 0.0 48.3 1.0 SG E:CYS158 2.1 32.5 1.0 S1 E:FES197 2.2 48.9 1.0 S2 E:FES197 2.2 48.0 1.0 FE2 E:FES197 2.7 50.1 1.0 SG E:CYS139 2.8 28.3 1.0 CB E:CYS158 3.3 32.9 1.0 CB E:CYS139 3.5 29.1 1.0 CB E:CYS144 3.9 32.1 1.0 CB E:CYS160 4.0 33.4 1.0 ND1 E:HIS161 4.3 30.4 1.0 CB E:HIS141 4.3 28.7 1.0 N E:HIS161 4.4 32.7 1.0 OG E:SER163 4.5 29.1 1.0 CA E:CYS158 4.6 32.9 1.0 N E:CYS144 4.6 31.7 1.0 N E:LEU142 4.6 29.0 1.0 N E:CYS160 4.6 33.5 1.0 SG E:CYS144 4.6 32.6 1.0 O E:CYS158 4.7 32.9 1.0 C E:CYS158 4.7 33.1 1.0 CB E:SER163 4.7 29.4 1.0 CA E:CYS160 4.7 33.4 1.0 ND1 E:HIS141 4.8 27.0 1.0 CA E:CYS144 4.8 32.0 1.0 SG E:CYS160 4.8 35.5 1.0 CA E:CYS139 5.0 29.2 1.0

Iron binding site 5 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 in Complex with Antimycin A1


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 Mitochondrial Cytochrome BC1 in Complex with Antimycin A1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe197 b:50.1 occ:1.00 FE2 E:FES197 0.0 50.1 1.0 ND1 E:HIS161 2.0 30.4 1.0 S2 E:FES197 2.2 48.0 1.0 S1 E:FES197 2.2 48.9 1.0 ND1 E:HIS141 2.4 27.0 1.0 FE1 E:FES197 2.7 48.3 1.0 CG E:HIS161 2.9 31.0 1.0 CE1 E:HIS161 3.0 30.7 1.0 CB E:HIS161 3.2 32.0 1.0 CG E:HIS141 3.3 28.1 1.0 CE1 E:HIS141 3.4 27.1 1.0 CB E:HIS141 3.5 28.7 1.0 N E:HIS161 3.7 32.7 1.0 CA E:HIS161 4.0 32.0 1.0 CD2 E:HIS161 4.1 30.6 1.0 N E:LEU142 4.1 29.0 1.0 NE2 E:HIS161 4.1 31.3 1.0 CB E:CYS160 4.2 33.4 1.0 CB E:LEU142 4.2 29.1 1.0 CG E:LEU142 4.3 28.0 1.0 C E:CYS160 4.4 33.1 1.0 CD1 E:LEU142 4.5 26.2 1.0 CD2 E:HIS141 4.5 27.8 1.0 NE2 E:HIS141 4.5 27.5 1.0 CG E:PRO175 4.5 34.3 1.0 SG E:CYS139 4.6 28.3 1.0 CA E:HIS141 4.7 28.7 1.0 SG E:CYS158 4.7 32.5 1.0 CA E:LEU142 4.7 29.2 1.0 C E:HIS141 4.7 28.8 1.0 CA E:CYS160 4.8 33.4 1.0 C E:HIS161 4.8 31.6 1.0 OG E:SER163 4.9 29.1 1.0

X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.-A.Yu, D.Xia. Structural Basis For the Quinone Reduction in the Bc(1) Complex: A Comparative Analysis of Crystal Structures of Mitochondrial Cytochrome Bc(1) with Bound Substrate and Inhibitors at the Q(I) Site Biochemistry V. 42 9067 2003.
ISSN: ISSN 0006-2960
PubMed: 12885240
DOI: 10.1021/BI0341814