Iron in PDB 2fyn: Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex

All present enzymatic activity of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex:
1.10.2.2;

The structure of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex, PDB code: 2fyn was solved by L.Esser, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	351.300, 147.130, 160.830, 90.00, 103.94, 90.00
R / Rfree (%)	22.4 / 25.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Iron atom in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex (pdb code 2fyn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex, PDB code: 2fyn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.3 occ:1.00 FE A:HEM501 0.0 35.3 1.0 ND A:HEM501 2.0 37.7 1.0 NC A:HEM501 2.0 36.1 1.0 NE2 A:HIS212 2.0 34.1 1.0 NB A:HEM501 2.0 35.6 1.0 NA A:HEM501 2.0 41.2 1.0 NE2 A:HIS111 2.0 34.9 1.0 CE1 A:HIS212 3.0 36.7 1.0 CE1 A:HIS111 3.0 37.7 1.0 CD2 A:HIS212 3.0 37.2 1.0 CD2 A:HIS111 3.0 36.5 1.0 C1C A:HEM501 3.0 34.9 1.0 C4D A:HEM501 3.0 39.5 1.0 C1D A:HEM501 3.0 39.7 1.0 C4B A:HEM501 3.0 35.3 1.0 C1A A:HEM501 3.0 40.2 1.0 C4C A:HEM501 3.0 35.4 1.0 C1B A:HEM501 3.1 35.5 1.0 C4A A:HEM501 3.1 39.2 1.0 CHC A:HEM501 3.4 37.1 1.0 CHA A:HEM501 3.4 41.0 1.0 CHD A:HEM501 3.4 37.3 1.0 CHB A:HEM501 3.5 36.6 1.0 ND1 A:HIS212 4.1 39.1 1.0 ND1 A:HIS111 4.1 40.1 1.0 CG A:HIS212 4.1 39.3 1.0 CG A:HIS111 4.2 38.8 1.0 C2D A:HEM501 4.2 41.2 1.0 C3D A:HEM501 4.3 41.9 1.0 C2C A:HEM501 4.3 34.2 1.0 C3C A:HEM501 4.3 33.3 1.0 C3B A:HEM501 4.3 34.2 1.0 C2A A:HEM501 4.3 38.8 1.0 C2B A:HEM501 4.3 35.6 1.0 C3A A:HEM501 4.3 37.4 1.0

Iron binding site 2 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.2 occ:1.00 FE A:HEM502 0.0 31.2 1.0 ND A:HEM502 1.9 27.5 1.0 NC A:HEM502 1.9 30.2 1.0 NA A:HEM502 2.0 32.4 1.0 NE2 A:HIS198 2.0 27.2 1.0 NE2 A:HIS97 2.0 34.2 1.0 NB A:HEM502 2.0 32.3 1.0 C1D A:HEM502 2.9 30.9 1.0 C4C A:HEM502 2.9 29.7 1.0 CE1 A:HIS198 3.0 26.1 1.0 CE1 A:HIS97 3.0 34.6 1.0 C4D A:HEM502 3.0 25.7 1.0 C1A A:HEM502 3.0 31.3 1.0 CD2 A:HIS198 3.0 27.2 1.0 CD2 A:HIS97 3.0 32.8 1.0 C1C A:HEM502 3.0 33.2 1.0 C4A A:HEM502 3.0 33.3 1.0 C1B A:HEM502 3.1 34.5 1.0 C4B A:HEM502 3.1 30.5 1.0 CHD A:HEM502 3.3 30.5 1.0 CHA A:HEM502 3.4 29.7 1.0 CHB A:HEM502 3.4 34.4 1.0 CHC A:HEM502 3.4 32.0 1.0 ND1 A:HIS198 4.1 29.4 1.0 ND1 A:HIS97 4.1 35.1 1.0 CG A:HIS198 4.1 28.8 1.0 CG A:HIS97 4.1 35.3 1.0 C2D A:HEM502 4.2 26.9 1.0 C3C A:HEM502 4.2 33.2 1.0 C2A A:HEM502 4.2 32.5 1.0 C3D A:HEM502 4.2 24.4 1.0 C2C A:HEM502 4.2 33.9 1.0 C3A A:HEM502 4.2 32.0 1.0 C3B A:HEM502 4.3 32.6 1.0 C2B A:HEM502 4.4 33.3 1.0 CA A:GLY146 4.8 32.7 1.0 NE2 A:GLN58 4.9 42.1 1.0

Iron binding site 3 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:51.1 occ:1.00 FE B:HEM301 0.0 51.1 1.0 NC B:HEM301 1.9 48.7 1.0 NB B:HEM301 1.9 47.4 1.0 ND B:HEM301 2.0 47.8 1.0 NA B:HEM301 2.0 45.2 1.0 NE2 B:HIS40 2.0 53.1 1.0 SD B:MET185 2.1 56.1 1.0 CD2 B:HIS40 3.0 54.5 1.0 C4B B:HEM301 3.0 49.1 1.0 C1C B:HEM301 3.0 49.1 1.0 C4C B:HEM301 3.0 50.0 1.0 C1B B:HEM301 3.0 48.3 1.0 CE1 B:HIS40 3.0 51.4 1.0 C1D B:HEM301 3.0 47.9 1.0 C4A B:HEM301 3.0 44.8 1.0 C4D B:HEM301 3.0 45.6 1.0 C1A B:HEM301 3.0 42.1 1.0 CHC B:HEM301 3.3 47.7 1.0 CHD B:HEM301 3.4 46.7 1.0 CHB B:HEM301 3.4 46.6 1.0 CHA B:HEM301 3.4 40.5 1.0 CG B:MET185 3.5 64.1 1.0 CE B:MET185 3.5 58.0 1.0 ND1 B:HIS40 4.1 51.2 1.0 CG B:HIS40 4.1 53.6 1.0 CB B:MET185 4.1 67.2 1.0 C3C B:HEM301 4.2 54.4 1.0 C2C B:HEM301 4.2 50.8 1.0 C2B B:HEM301 4.2 50.3 1.0 C3B B:HEM301 4.2 52.8 1.0 C2D B:HEM301 4.2 48.0 1.0 C3A B:HEM301 4.3 42.3 1.0 C2A B:HEM301 4.3 42.0 1.0 C3D B:HEM301 4.3 48.9 1.0

Iron binding site 4 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:30.9 occ:1.00 FE1 C:FES200 0.0 30.9 1.0 S1 C:FES200 2.1 27.2 1.0 SG C:CYS129 2.2 31.1 1.0 SG C:CYS149 2.2 30.1 1.0 S2 C:FES200 2.3 32.5 1.0 FE2 C:FES200 2.6 34.5 1.0 CB C:CYS129 3.1 26.4 1.0 CB C:CYS149 3.1 27.7 1.0 CB C:HIS131 3.8 22.0 1.0 CB C:CYS151 4.3 38.7 1.0 ND1 C:HIS131 4.3 25.3 1.0 OG C:SER154 4.4 30.3 1.0 CB C:SER154 4.4 27.4 1.0 N C:HIS152 4.5 37.2 1.0 CA C:CYS129 4.5 28.8 1.0 CA C:CYS149 4.5 30.3 1.0 ND1 C:HIS152 4.5 27.6 1.0 CG C:HIS131 4.5 21.7 1.0 N C:LEU132 4.6 33.1 1.0 CB C:CYS134 4.6 29.3 1.0 N C:HIS131 4.7 28.3 1.0 CA C:HIS131 4.8 28.2 1.0 N C:CYS134 4.8 26.0 1.0 O C:CYS149 4.9 31.0 1.0 C C:CYS149 4.9 31.9 1.0 C C:CYS129 4.9 30.3 1.0

Iron binding site 5 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:34.5 occ:1.00 FE2 C:FES200 0.0 34.5 1.0 ND1 C:HIS152 2.2 27.6 1.0 ND1 C:HIS131 2.2 25.3 1.0 S2 C:FES200 2.2 32.5 1.0 S1 C:FES200 2.2 27.2 1.0 FE1 C:FES200 2.6 30.9 1.0 CG C:HIS152 3.0 27.0 1.0 CG C:HIS131 3.0 21.7 1.0 CB C:HIS152 3.2 31.4 1.0 CB C:HIS131 3.2 22.0 1.0 CE1 C:HIS152 3.2 27.1 1.0 CE1 C:HIS131 3.2 21.3 1.0 N C:HIS152 3.6 37.2 1.0 CA C:HIS152 3.9 35.2 1.0 CB C:CYS151 4.0 38.7 1.0 N C:LEU132 4.1 33.1 1.0 CD2 C:HIS152 4.2 27.3 1.0 CD2 C:HIS131 4.2 24.1 1.0 NE2 C:HIS152 4.3 24.1 1.0 NE2 C:HIS131 4.3 21.7 1.0 SG C:CYS129 4.3 31.1 1.0 CB C:LEU132 4.3 23.5 1.0 C C:CYS151 4.4 38.5 1.0 SG C:CYS149 4.4 30.1 1.0 CA C:HIS131 4.5 28.2 1.0 CG C:LEU132 4.7 21.6 1.0 C C:HIS131 4.7 32.4 1.0 C C:HIS152 4.8 37.6 1.0 CA C:LEU132 4.8 31.3 1.0 CA C:CYS151 4.8 37.4 1.0 CD1 C:LEU132 4.9 21.2 1.0 OG C:SER154 4.9 30.3 1.0

Iron binding site 6 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:40.7 occ:1.00 FE D:HEM501 0.0 40.7 1.0 NA D:HEM501 1.9 42.6 1.0 NB D:HEM501 2.0 42.4 1.0 ND D:HEM501 2.0 45.2 1.0 NC D:HEM501 2.0 41.5 1.0 NE2 D:HIS111 2.0 36.5 1.0 NE2 D:HIS212 2.0 40.1 1.0 CE1 D:HIS212 3.0 39.5 1.0 C4A D:HEM501 3.0 44.6 1.0 C1A D:HEM501 3.0 44.1 1.0 CD2 D:HIS111 3.0 37.5 1.0 CE1 D:HIS111 3.0 37.0 1.0 C1B D:HEM501 3.0 44.4 1.0 CD2 D:HIS212 3.0 40.7 1.0 C4C D:HEM501 3.0 42.3 1.0 C4D D:HEM501 3.0 45.7 1.0 C1D D:HEM501 3.0 45.7 1.0 C1C D:HEM501 3.0 41.0 1.0 C4B D:HEM501 3.0 40.4 1.0 CHB D:HEM501 3.4 44.4 1.0 CHA D:HEM501 3.4 45.4 1.0 CHD D:HEM501 3.4 45.5 1.0 CHC D:HEM501 3.4 40.9 1.0 ND1 D:HIS212 4.1 39.2 1.0 ND1 D:HIS111 4.1 35.9 1.0 CG D:HIS111 4.1 36.7 1.0 CG D:HIS212 4.2 39.0 1.0 C3A D:HEM501 4.2 47.4 1.0 C2A D:HEM501 4.2 47.7 1.0 C3C D:HEM501 4.3 42.1 1.0 C2C D:HEM501 4.3 41.0 1.0 C2B D:HEM501 4.3 42.7 1.0 C3D D:HEM501 4.3 45.6 1.0 C2D D:HEM501 4.3 45.9 1.0 C3B D:HEM501 4.3 41.6 1.0

Iron binding site 7 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:30.7 occ:1.00 FE D:HEM502 0.0 30.7 1.0 NA D:HEM502 1.9 27.6 1.0 ND D:HEM502 1.9 32.5 1.0 NE2 D:HIS97 2.0 35.3 1.0 NB D:HEM502 2.0 29.1 1.0 NC D:HEM502 2.0 30.0 1.0 NE2 D:HIS198 2.0 30.4 1.0 CE1 D:HIS97 2.9 36.9 1.0 CD2 D:HIS97 3.0 34.5 1.0 CE1 D:HIS198 3.0 30.5 1.0 C4A D:HEM502 3.0 29.9 1.0 C1D D:HEM502 3.0 34.0 1.0 C1A D:HEM502 3.0 29.1 1.0 C4D D:HEM502 3.0 31.8 1.0 C4C D:HEM502 3.0 31.7 1.0 C1B D:HEM502 3.0 29.4 1.0 C4B D:HEM502 3.0 31.2 1.0 C1C D:HEM502 3.0 32.5 1.0 CD2 D:HIS198 3.1 28.0 1.0 CHB D:HEM502 3.4 30.2 1.0 CHD D:HEM502 3.4 33.5 1.0 CHA D:HEM502 3.4 29.3 1.0 CHC D:HEM502 3.4 33.3 1.0 ND1 D:HIS97 4.0 38.4 1.0 CG D:HIS97 4.1 36.6 1.0 ND1 D:HIS198 4.1 30.0 1.0 CG D:HIS198 4.2 25.7 1.0 C2D D:HEM502 4.2 32.5 1.0 C3A D:HEM502 4.2 29.0 1.0 C2A D:HEM502 4.2 29.4 1.0 C3D D:HEM502 4.2 32.6 1.0 C3C D:HEM502 4.3 34.7 1.0 C2B D:HEM502 4.3 32.5 1.0 C2C D:HEM502 4.3 34.0 1.0 C3B D:HEM502 4.3 32.0 1.0 CA D:GLY146 4.7 33.0 1.0 NE2 D:GLN58 4.9 32.9 1.0

Iron binding site 8 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:50.5 occ:1.00 FE E:HEM301 0.0 50.5 1.0 NC E:HEM301 1.9 51.6 1.0 ND E:HEM301 2.0 52.9 1.0 NB E:HEM301 2.0 48.1 1.0 NE2 E:HIS40 2.0 67.8 1.0 NA E:HEM301 2.0 52.1 1.0 SD E:MET185 2.1 52.2 1.0 C4C E:HEM301 2.9 52.4 1.0 CD2 E:HIS40 3.0 72.0 1.0 CE1 E:HIS40 3.0 68.9 1.0 C1C E:HEM301 3.0 52.3 1.0 C1D E:HEM301 3.0 54.1 1.0 C4B E:HEM301 3.0 49.4 1.0 C1B E:HEM301 3.0 48.5 1.0 C4D E:HEM301 3.1 54.5 1.0 C4A E:HEM301 3.1 51.4 1.0 C1A E:HEM301 3.1 51.1 1.0 CHD E:HEM301 3.3 52.2 1.0 CHC E:HEM301 3.4 48.2 1.0 CHB E:HEM301 3.4 51.3 1.0 CE E:MET185 3.5 53.1 1.0 CHA E:HEM301 3.5 50.9 1.0 CG E:MET185 3.5 57.9 1.0 ND1 E:HIS40 4.1 71.4 1.0 CG E:HIS40 4.1 69.9 1.0 CB E:MET185 4.1 60.3 1.0 C3C E:HEM301 4.2 54.2 1.0 C2C E:HEM301 4.2 51.8 1.0 C2B E:HEM301 4.2 50.1 1.0 C3B E:HEM301 4.2 53.2 1.0 C2D E:HEM301 4.3 57.4 1.0 C3D E:HEM301 4.3 58.3 1.0 C3A E:HEM301 4.3 47.7 1.0 C2A E:HEM301 4.3 47.8 1.0

Iron binding site 9 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe200 b:31.2 occ:1.00 FE1 F:FES200 0.0 31.2 1.0 S1 F:FES200 2.1 32.8 1.0 S2 F:FES200 2.2 36.7 1.0 SG F:CYS129 2.2 34.1 1.0 SG F:CYS149 2.2 33.5 1.0 FE2 F:FES200 2.7 32.8 1.0 CB F:CYS129 3.0 26.0 1.0 CB F:CYS149 3.1 31.3 1.0 CB F:HIS131 3.9 24.9 1.0 CB F:CYS151 4.2 36.9 1.0 CA F:CYS129 4.4 29.4 1.0 CB F:CYS134 4.4 37.9 1.0 ND1 F:HIS131 4.5 27.2 1.0 ND1 F:HIS152 4.5 37.9 1.0 CA F:CYS149 4.5 32.4 1.0 N F:HIS152 4.5 43.2 1.0 N F:LEU132 4.6 32.9 1.0 N F:CYS134 4.6 31.7 1.0 OG F:SER154 4.7 26.9 1.0 CG F:HIS131 4.7 24.7 1.0 N F:HIS131 4.7 27.8 1.0 CB F:SER154 4.7 29.5 1.0 O F:CYS149 4.7 30.4 1.0 CA F:HIS131 4.8 29.4 1.0 C F:CYS149 4.8 33.0 1.0 C F:CYS129 4.8 30.2 1.0 SG F:CYS134 4.9 45.3 1.0 N F:GLY133 5.0 36.4 1.0 N F:CYS151 5.0 34.8 1.0 CA F:CYS151 5.0 38.8 1.0 CA F:CYS134 5.0 36.4 1.0

Iron binding site 10 out of 30 in the Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure Analysis of the Double Mutant Rhodobacter Sphaeroides BC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe200 b:32.8 occ:1.00 FE2 F:FES200 0.0 32.8 1.0 ND1 F:HIS152 2.1 37.9 1.0 ND1 F:HIS131 2.1 27.2 1.0 S2 F:FES200 2.2 36.7 1.0 S1 F:FES200 2.2 32.8 1.0 FE1 F:FES200 2.7 31.2 1.0 CG F:HIS131 3.0 24.7 1.0 CG F:HIS152 3.0 40.3 1.0 CB F:HIS131 3.1 24.9 1.0 CE1 F:HIS152 3.2 42.1 1.0 CB F:HIS152 3.2 39.7 1.0 CE1 F:HIS131 3.2 22.3 1.0 N F:HIS152 3.7 43.2 1.0 N F:LEU132 4.0 32.9 1.0 CA F:HIS152 4.0 42.5 1.0 CB F:CYS151 4.1 36.9 1.0 CD2 F:HIS131 4.2 22.1 1.0 CD2 F:HIS152 4.2 40.3 1.0 NE2 F:HIS152 4.2 43.5 1.0 SG F:CYS129 4.3 34.1 1.0 CB F:LEU132 4.3 31.6 1.0 NE2 F:HIS131 4.3 22.1 1.0 C F:CYS151 4.4 40.8 1.0 CA F:HIS131 4.4 29.4 1.0 SG F:CYS149 4.5 33.5 1.0 CG F:LEU132 4.5 32.5 1.0 C F:HIS131 4.6 32.7 1.0 CA F:LEU132 4.7 33.9 1.0 C F:HIS152 4.8 42.6 1.0 CD1 F:LEU132 4.8 31.4 1.0 CA F:CYS151 4.8 38.8 1.0 OG F:SER154 5.0 26.9 1.0

L.Esser, X.Gong, S.Yang, L.Yu, C.A.Yu, D.Xia. Surface-Modulated Motion Switch: Capture and Release of Iron-Sulfur Protein in the Cytochrome BC1 Complex. Proc.Natl.Acad.Sci.Usa V. 103 13045 2006.
ISSN: ISSN 0027-8424
PubMed: 16924113
DOI: 10.1073/PNAS.0601149103