Iron in PDB 2qjp: Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited

All present enzymatic activity of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited:
1.10.2.2;

The structure of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited, PDB code: 2qjp 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)	17.98 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	135.061, 146.520, 141.003, 90.00, 110.21, 90.00
R / Rfree (%)	24.4 / 27.7

The structure of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited also contains other interesting chemical elements:

Strontium

(Sr)

6 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited (pdb code 2qjp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited, PDB code: 2qjp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:64.4 occ:1.00 FE A:HEM501 0.0 64.4 1.0 NA A:HEM501 2.0 64.6 1.0 ND A:HEM501 2.0 63.5 1.0 NC A:HEM501 2.0 64.2 1.0 NE2 A:HIS212 2.0 61.3 1.0 NB A:HEM501 2.0 64.9 1.0 NE2 A:HIS111 2.0 65.4 1.0 CE1 A:HIS212 3.0 61.0 1.0 CD2 A:HIS111 3.0 64.4 1.0 CE1 A:HIS111 3.0 65.8 1.0 CD2 A:HIS212 3.0 61.1 1.0 C1A A:HEM501 3.0 65.5 1.0 C4A A:HEM501 3.0 65.0 1.0 C1D A:HEM501 3.0 63.2 1.0 C4D A:HEM501 3.0 63.5 1.0 C4C A:HEM501 3.0 64.2 1.0 C1B A:HEM501 3.1 65.1 1.0 C1C A:HEM501 3.1 64.9 1.0 C4B A:HEM501 3.1 65.1 1.0 CHA A:HEM501 3.4 65.0 1.0 CHD A:HEM501 3.4 64.2 1.0 CHB A:HEM501 3.4 65.0 1.0 CHC A:HEM501 3.4 65.2 1.0 ND1 A:HIS212 4.1 61.1 1.0 ND1 A:HIS111 4.1 65.1 1.0 CG A:HIS212 4.1 61.4 1.0 CG A:HIS111 4.1 64.3 1.0 C3A A:HEM501 4.2 65.5 1.0 C2A A:HEM501 4.2 66.2 1.0 C3D A:HEM501 4.3 63.2 1.0 C2D A:HEM501 4.3 62.9 1.0 C2C A:HEM501 4.3 65.3 1.0 C3C A:HEM501 4.3 64.3 1.0 C2B A:HEM501 4.3 65.0 1.0 C3B A:HEM501 4.3 65.3 1.0

Iron binding site 2 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE A:HEM502 0.0 50.5 1.0 NC A:HEM502 2.0 47.9 1.0 ND A:HEM502 2.0 48.8 1.0 NB A:HEM502 2.0 48.7 1.0 NA A:HEM502 2.0 49.7 1.0 NE2 A:HIS97 2.0 50.1 1.0 NE2 A:HIS198 2.0 45.5 1.0 CE1 A:HIS198 3.0 45.1 1.0 CE1 A:HIS97 3.0 50.4 1.0 CD2 A:HIS97 3.0 50.8 1.0 C4C A:HEM502 3.0 46.9 1.0 CD2 A:HIS198 3.0 45.7 1.0 C1D A:HEM502 3.0 47.8 1.0 C1C A:HEM502 3.0 47.0 1.0 C1B A:HEM502 3.0 47.6 1.0 C4B A:HEM502 3.0 47.5 1.0 C4D A:HEM502 3.0 48.4 1.0 C1A A:HEM502 3.0 49.1 1.0 C4A A:HEM502 3.0 49.0 1.0 CHD A:HEM502 3.4 47.1 1.0 CHC A:HEM502 3.4 48.3 1.0 CHA A:HEM502 3.4 49.6 1.0 CHB A:HEM502 3.4 48.4 1.0 ND1 A:HIS198 4.1 45.2 1.0 ND1 A:HIS97 4.1 50.5 1.0 CG A:HIS198 4.1 46.5 1.0 CG A:HIS97 4.1 51.4 1.0 C2C A:HEM502 4.2 48.3 1.0 C3C A:HEM502 4.2 46.8 1.0 C2D A:HEM502 4.3 47.9 1.0 C3D A:HEM502 4.3 48.6 1.0 C2A A:HEM502 4.3 50.3 1.0 C2B A:HEM502 4.3 47.5 1.0 C3B A:HEM502 4.3 47.9 1.0 C3A A:HEM502 4.3 50.2 1.0 NE2 A:GLN58 4.6 51.6 1.0 CA A:GLY146 4.7 48.1 1.0

Iron binding site 3 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:61.8 occ:1.00 FE B:HEM301 0.0 61.8 1.0 NA B:HEM301 2.0 66.3 1.0 NC B:HEM301 2.0 66.7 1.0 NB B:HEM301 2.0 67.8 1.0 ND B:HEM301 2.0 66.6 1.0 NE2 B:HIS40 2.0 67.9 1.0 SD B:MET185 2.2 73.3 1.0 CD2 B:HIS40 3.0 67.7 1.0 CE1 B:HIS40 3.0 67.5 1.0 C4A B:HEM301 3.0 66.2 1.0 C1A B:HEM301 3.0 65.4 1.0 C4C B:HEM301 3.0 66.9 1.0 C1B B:HEM301 3.0 67.6 1.0 C1C B:HEM301 3.0 66.0 1.0 C1D B:HEM301 3.0 66.8 1.0 C4B B:HEM301 3.0 67.3 1.0 C4D B:HEM301 3.0 65.9 1.0 CHB B:HEM301 3.4 67.2 1.0 CHD B:HEM301 3.4 66.7 1.0 CHA B:HEM301 3.4 64.3 1.0 CHC B:HEM301 3.4 65.8 1.0 CG B:MET185 3.5 75.4 1.0 CE B:MET185 3.5 71.2 1.0 ND1 B:HIS40 4.1 67.4 1.0 CG B:HIS40 4.1 68.0 1.0 CB B:MET185 4.1 79.0 1.0 C2A B:HEM301 4.2 64.5 1.0 C3A B:HEM301 4.2 65.3 1.0 C3C B:HEM301 4.2 66.2 1.0 C2C B:HEM301 4.3 65.5 1.0 C2B B:HEM301 4.3 67.8 1.0 C2D B:HEM301 4.3 66.4 1.0 C3D B:HEM301 4.3 66.0 1.0 C3B B:HEM301 4.3 67.8 1.0

Iron binding site 4 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:54.9 occ:1.00 FE1 C:FES200 0.0 54.9 1.0 SG C:CYS129 2.2 54.5 1.0 S1 C:FES200 2.2 54.1 1.0 S2 C:FES200 2.2 54.3 1.0 SG C:CYS149 2.3 56.5 1.0 FE2 C:FES200 2.7 54.2 1.0 CB C:CYS129 3.0 54.5 1.0 CB C:CYS149 3.1 57.9 1.0 CB C:HIS131 3.9 52.9 1.0 CB C:CYS151 4.2 55.0 1.0 ND1 C:HIS131 4.4 55.5 1.0 CB C:CYS134 4.5 54.1 1.0 CA C:CYS149 4.5 58.7 1.0 CA C:CYS129 4.5 55.3 1.0 OG C:SER154 4.6 61.5 1.0 N C:HIS152 4.6 56.8 1.0 CB C:SER154 4.6 58.3 1.0 N C:LEU132 4.6 47.6 1.0 ND1 C:HIS152 4.6 53.8 1.0 CG C:HIS131 4.6 54.2 1.0 N C:CYS134 4.8 53.9 1.0 N C:HIS131 4.9 50.8 1.0 C C:CYS149 4.9 58.0 1.0 CA C:HIS131 4.9 50.2 1.0 N C:CYS151 4.9 56.4 1.0 O C:CYS149 4.9 58.4 1.0 CA C:CYS151 5.0 56.1 1.0

Iron binding site 5 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:54.2 occ:1.00 FE2 C:FES200 0.0 54.2 1.0 ND1 C:HIS131 2.1 55.5 1.0 ND1 C:HIS152 2.2 53.8 1.0 S1 C:FES200 2.2 54.1 1.0 S2 C:FES200 2.3 54.3 1.0 FE1 C:FES200 2.7 54.9 1.0 CG C:HIS152 3.0 52.9 1.0 CG C:HIS131 3.1 54.2 1.0 CE1 C:HIS131 3.2 55.8 1.0 CE1 C:HIS152 3.2 51.5 1.0 CB C:HIS152 3.2 54.8 1.0 CB C:HIS131 3.3 52.9 1.0 N C:HIS152 3.7 56.8 1.0 CB C:CYS151 4.0 55.0 1.0 CA C:HIS152 4.0 56.0 1.0 N C:LEU132 4.1 47.6 1.0 C C:CYS151 4.2 56.8 1.0 CD2 C:HIS152 4.2 52.8 1.0 CD2 C:HIS131 4.2 54.6 1.0 NE2 C:HIS131 4.3 55.2 1.0 NE2 C:HIS152 4.3 51.8 1.0 SG C:CYS129 4.3 54.5 1.0 CB C:LEU132 4.4 48.8 1.0 SG C:CYS149 4.6 56.5 1.0 CA C:HIS131 4.6 50.2 1.0 CA C:CYS151 4.7 56.1 1.0 CG C:LEU132 4.7 48.6 1.0 C C:HIS131 4.7 49.1 1.0 CA C:LEU132 4.8 48.4 1.0 C C:HIS152 4.9 55.9 1.0 CD1 C:LEU132 4.9 48.5 1.0 O C:CYS151 4.9 57.0 1.0

Iron binding site 6 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:60.7 occ:1.00 FE D:HEM501 0.0 60.7 1.0 ND D:HEM501 2.0 60.4 1.0 NC D:HEM501 2.0 61.8 1.0 NA D:HEM501 2.0 61.4 1.0 NB D:HEM501 2.0 61.3 1.0 NE2 D:HIS212 2.0 60.9 1.0 NE2 D:HIS111 2.0 59.6 1.0 CE1 D:HIS212 3.0 60.9 1.0 CE1 D:HIS111 3.0 59.1 1.0 CD2 D:HIS212 3.0 61.3 1.0 C1D D:HEM501 3.0 60.6 1.0 CD2 D:HIS111 3.0 58.6 1.0 C4D D:HEM501 3.0 61.1 1.0 C4C D:HEM501 3.0 61.4 1.0 C1A D:HEM501 3.0 60.7 1.0 C1C D:HEM501 3.0 61.2 1.0 C4B D:HEM501 3.0 61.9 1.0 C4A D:HEM501 3.0 60.7 1.0 C1B D:HEM501 3.0 61.5 1.0 CHD D:HEM501 3.4 61.0 1.0 CHA D:HEM501 3.4 61.4 1.0 CHC D:HEM501 3.4 61.6 1.0 CHB D:HEM501 3.4 61.2 1.0 ND1 D:HIS212 4.1 62.0 1.0 ND1 D:HIS111 4.1 58.9 1.0 CG D:HIS212 4.1 61.7 1.0 CG D:HIS111 4.2 58.0 1.0 C2D D:HEM501 4.3 60.3 1.0 C3D D:HEM501 4.3 61.1 1.0 C3A D:HEM501 4.3 61.0 1.0 C2A D:HEM501 4.3 60.8 1.0 C2C D:HEM501 4.3 62.2 1.0 C3C D:HEM501 4.3 61.2 1.0 C2B D:HEM501 4.3 61.1 1.0 C3B D:HEM501 4.3 62.1 1.0

Iron binding site 7 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:46.5 occ:1.00 FE D:HEM502 0.0 46.5 1.0 ND D:HEM502 2.0 45.0 1.0 NA D:HEM502 2.0 45.3 1.0 NC D:HEM502 2.0 43.0 1.0 NB D:HEM502 2.0 42.9 1.0 NE2 D:HIS97 2.0 45.4 1.0 NE2 D:HIS198 2.0 43.8 1.0 CE1 D:HIS198 2.9 43.9 1.0 CE1 D:HIS97 3.0 45.5 1.0 C1A D:HEM502 3.0 43.8 1.0 C4D D:HEM502 3.0 44.9 1.0 CD2 D:HIS97 3.0 46.6 1.0 C1D D:HEM502 3.0 44.0 1.0 C1C D:HEM502 3.0 41.1 1.0 CD2 D:HIS198 3.0 45.1 1.0 C4B D:HEM502 3.0 42.0 1.0 C4C D:HEM502 3.0 41.3 1.0 C4A D:HEM502 3.0 43.2 1.0 C1B D:HEM502 3.1 41.5 1.0 CHA D:HEM502 3.4 45.5 1.0 CHC D:HEM502 3.4 41.4 1.0 CHD D:HEM502 3.4 42.7 1.0 CHB D:HEM502 3.4 43.4 1.0 ND1 D:HIS198 4.1 44.6 1.0 ND1 D:HIS97 4.1 46.1 1.0 CG D:HIS97 4.1 47.5 1.0 CG D:HIS198 4.1 45.9 1.0 C2A D:HEM502 4.2 44.1 1.0 C3D D:HEM502 4.2 45.5 1.0 C2D D:HEM502 4.2 45.0 1.0 C2C D:HEM502 4.3 40.9 1.0 C3A D:HEM502 4.3 44.3 1.0 C3B D:HEM502 4.3 41.6 1.0 C2B D:HEM502 4.3 41.4 1.0 C3C D:HEM502 4.3 41.3 1.0 NE2 D:GLN58 4.6 49.8 1.0 CA D:GLY146 4.7 51.3 1.0

Iron binding site 8 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:74.5 occ:1.00 FE E:HEM301 0.0 74.5 1.0 NA E:HEM301 2.0 79.7 1.0 NC E:HEM301 2.0 81.0 1.0 NE2 E:HIS40 2.0 80.7 1.0 ND E:HEM301 2.0 81.4 1.0 NB E:HEM301 2.0 80.9 1.0 SD E:MET185 2.1 82.4 1.0 CD2 E:HIS40 2.9 79.9 1.0 CE1 E:HIS40 3.0 80.5 1.0 C1A E:HEM301 3.0 79.1 1.0 C4A E:HEM301 3.0 79.0 1.0 C4C E:HEM301 3.0 80.7 1.0 C1C E:HEM301 3.0 81.2 1.0 C1B E:HEM301 3.0 80.1 1.0 C1D E:HEM301 3.0 81.0 1.0 C4D E:HEM301 3.0 80.6 1.0 C4B E:HEM301 3.0 80.7 1.0 CHA E:HEM301 3.4 79.1 1.0 CHB E:HEM301 3.4 79.0 1.0 CHD E:HEM301 3.4 80.2 1.0 CHC E:HEM301 3.4 80.7 1.0 CE E:MET185 3.5 80.4 1.0 CG E:MET185 3.5 83.3 1.0 ND1 E:HIS40 4.0 80.0 1.0 CG E:HIS40 4.1 79.7 1.0 CB E:MET185 4.2 86.2 1.0 C2A E:HEM301 4.2 77.8 1.0 C3A E:HEM301 4.2 77.8 1.0 C2B E:HEM301 4.3 80.1 1.0 C2C E:HEM301 4.3 80.6 1.0 C3C E:HEM301 4.3 79.7 1.0 C3B E:HEM301 4.3 80.2 1.0 C3D E:HEM301 4.3 80.2 1.0 C2D E:HEM301 4.3 80.3 1.0

Iron binding site 9 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe200 b:55.1 occ:1.00 FE1 F:FES200 0.0 55.1 1.0 S1 F:FES200 2.2 55.0 1.0 S2 F:FES200 2.2 55.7 1.0 SG F:CYS149 2.2 55.6 1.0 SG F:CYS129 2.3 54.5 1.0 FE2 F:FES200 2.7 55.0 1.0 CB F:CYS129 3.0 55.6 1.0 CB F:CYS149 3.1 56.8 1.0 CB F:HIS131 3.9 52.3 1.0 CB F:CYS151 4.2 59.6 1.0 CB F:CYS134 4.4 57.5 1.0 ND1 F:HIS131 4.4 55.5 1.0 CA F:CYS149 4.5 59.4 1.0 CA F:CYS129 4.5 56.4 1.0 N F:HIS152 4.5 56.6 1.0 ND1 F:HIS152 4.6 55.8 1.0 N F:LEU132 4.6 50.4 1.0 OG F:SER154 4.6 61.9 1.0 CB F:SER154 4.7 58.9 1.0 CG F:HIS131 4.7 54.7 1.0 N F:CYS134 4.7 55.8 1.0 C F:CYS149 4.9 58.5 1.0 N F:CYS151 4.9 58.2 1.0 N F:HIS131 4.9 53.5 1.0 CA F:CYS151 4.9 58.3 1.0 CA F:HIS131 4.9 53.6 1.0 O F:CYS149 4.9 58.9 1.0 SG F:CYS134 4.9 58.6 1.0

Iron binding site 10 out of 20 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe200 b:55.0 occ:1.00 FE2 F:FES200 0.0 55.0 1.0 ND1 F:HIS131 2.2 55.5 1.0 ND1 F:HIS152 2.2 55.8 1.0 S1 F:FES200 2.2 55.0 1.0 S2 F:FES200 2.2 55.7 1.0 FE1 F:FES200 2.7 55.1 1.0 CG F:HIS152 3.1 56.3 1.0 CG F:HIS131 3.1 54.7 1.0 CE1 F:HIS131 3.2 57.6 1.0 CE1 F:HIS152 3.2 56.5 1.0 CB F:HIS152 3.3 56.0 1.0 CB F:HIS131 3.3 52.3 1.0 N F:HIS152 3.7 56.6 1.0 CB F:CYS151 3.9 59.6 1.0 CA F:HIS152 4.0 56.0 1.0 N F:LEU132 4.1 50.4 1.0 C F:CYS151 4.2 57.3 1.0 CD2 F:HIS152 4.2 55.5 1.0 CD2 F:HIS131 4.2 55.4 1.0 NE2 F:HIS131 4.3 57.2 1.0 NE2 F:HIS152 4.3 56.3 1.0 SG F:CYS129 4.3 54.5 1.0 CB F:LEU132 4.4 49.1 1.0 SG F:CYS149 4.6 55.6 1.0 CA F:HIS131 4.6 53.6 1.0 CA F:CYS151 4.6 58.3 1.0 CG F:LEU132 4.7 49.3 1.0 C F:HIS131 4.7 52.1 1.0 CA F:LEU132 4.8 49.6 1.0 CD1 F:LEU132 4.8 48.5 1.0 C F:HIS152 4.9 55.6 1.0 O F:CYS151 4.9 57.7 1.0

L.Esser, M.Elberry, F.Zhou, C.A.Yu, L.Yu, D.Xia. Inhibitor-Complexed Structures of the Cytochrome BC1 From the Photosynthetic Bacterium Rhodobacter Sphaeroides. J.Biol.Chem. V. 283 2846 2008.
ISSN: ISSN 0021-9258
PubMed: 18039651
DOI: 10.1074/JBC.M708608200