Iron in PDB 2qjy: Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2

All present enzymatic activity of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2:
1.10.2.2;

The structure of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2, PDB code: 2qjy 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 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	351.891, 147.042, 161.312, 90.00, 104.25, 90.00
R / Rfree (%)	22.6 / 25.1

The structure of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 also contains other interesting chemical elements:

Strontium	(Sr)	9 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

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 of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 (pdb code 2qjy). 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 of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2, PDB code: 2qjy:
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 of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:46.4 occ:1.00 FE A:HEM501 0.0 46.4 1.0 NB A:HEM501 1.9 46.1 1.0 ND A:HEM501 1.9 49.2 1.0 NA A:HEM501 2.0 49.2 1.0 NC A:HEM501 2.0 45.4 1.0 NE2 A:HIS111 2.0 42.4 1.0 NE2 A:HIS212 2.0 46.1 1.0 CE1 A:HIS111 3.0 41.0 1.0 C1B A:HEM501 3.0 46.2 1.0 C1D A:HEM501 3.0 49.0 1.0 CE1 A:HIS212 3.0 45.1 1.0 CD2 A:HIS212 3.0 46.6 1.0 CD2 A:HIS111 3.0 42.9 1.0 C4A A:HEM501 3.0 49.1 1.0 C4B A:HEM501 3.0 45.3 1.0 C4D A:HEM501 3.0 50.8 1.0 C4C A:HEM501 3.0 44.9 1.0 C1A A:HEM501 3.0 50.3 1.0 C1C A:HEM501 3.0 44.7 1.0 CHB A:HEM501 3.4 47.0 1.0 CHD A:HEM501 3.4 46.3 1.0 CHA A:HEM501 3.4 51.8 1.0 CHC A:HEM501 3.4 45.6 1.0 ND1 A:HIS111 4.1 42.0 1.0 ND1 A:HIS212 4.1 46.6 1.0 CG A:HIS212 4.1 46.9 1.0 CG A:HIS111 4.2 43.1 1.0 C2D A:HEM501 4.2 51.1 1.0 C2B A:HEM501 4.2 45.6 1.0 C3D A:HEM501 4.2 51.5 1.0 C3B A:HEM501 4.3 45.0 1.0 C3A A:HEM501 4.3 50.4 1.0 C3C A:HEM501 4.3 44.6 1.0 C2A A:HEM501 4.3 50.5 1.0 C2C A:HEM501 4.3 44.1 1.0

Iron binding site 2 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:37.2 occ:1.00 FE A:HEM502 0.0 37.2 1.0 ND A:HEM502 1.9 35.5 1.0 NB A:HEM502 2.0 37.5 1.0 NC A:HEM502 2.0 37.5 1.0 NE2 A:HIS198 2.0 40.4 1.0 NA A:HEM502 2.0 35.1 1.0 NE2 A:HIS97 2.0 39.6 1.0 CE1 A:HIS198 3.0 39.3 1.0 CE1 A:HIS97 3.0 39.1 1.0 CD2 A:HIS198 3.0 38.9 1.0 C1D A:HEM502 3.0 34.7 1.0 C4C A:HEM502 3.0 37.3 1.0 C4D A:HEM502 3.0 36.0 1.0 C1A A:HEM502 3.0 36.1 1.0 C4B A:HEM502 3.0 39.5 1.0 C1C A:HEM502 3.0 38.9 1.0 C4A A:HEM502 3.0 34.1 1.0 C1B A:HEM502 3.0 37.1 1.0 CD2 A:HIS97 3.0 39.1 1.0 CHD A:HEM502 3.4 35.1 1.0 CHA A:HEM502 3.4 37.1 1.0 CHC A:HEM502 3.4 40.2 1.0 CHB A:HEM502 3.4 34.9 1.0 ND1 A:HIS198 4.1 37.7 1.0 ND1 A:HIS97 4.1 39.2 1.0 CG A:HIS198 4.1 38.2 1.0 CG A:HIS97 4.2 40.0 1.0 C2D A:HEM502 4.2 34.4 1.0 C3D A:HEM502 4.2 35.6 1.0 C2A A:HEM502 4.3 35.8 1.0 C3B A:HEM502 4.3 40.7 1.0 C2C A:HEM502 4.3 38.7 1.0 C3A A:HEM502 4.3 33.9 1.0 C3C A:HEM502 4.3 38.3 1.0 C2B A:HEM502 4.3 38.7 1.0 CA A:GLY146 4.7 40.5 1.0 NE2 A:GLN58 4.9 38.1 1.0

Iron binding site 3 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:58.5 occ:1.00 FE B:HEM301 0.0 58.5 1.0 NA B:HEM301 1.9 55.6 1.0 ND B:HEM301 2.0 55.1 1.0 NB B:HEM301 2.0 56.6 1.0 NC B:HEM301 2.0 57.3 1.0 NE2 B:HIS40 2.0 65.0 1.0 SD B:MET185 2.2 66.0 1.0 CD2 B:HIS40 3.0 65.2 1.0 CE1 B:HIS40 3.0 64.7 1.0 C4A B:HEM301 3.0 56.7 1.0 C1B B:HEM301 3.0 56.8 1.0 C4D B:HEM301 3.0 55.2 1.0 C1A B:HEM301 3.0 55.1 1.0 C1D B:HEM301 3.0 55.3 1.0 C4C B:HEM301 3.0 58.9 1.0 C1C B:HEM301 3.0 57.6 1.0 C4B B:HEM301 3.0 57.2 1.0 CHB B:HEM301 3.4 56.8 1.0 CHA B:HEM301 3.4 53.6 1.0 CHD B:HEM301 3.4 57.0 1.0 CHC B:HEM301 3.4 56.6 1.0 CG B:MET185 3.5 66.0 1.0 CE B:MET185 3.5 63.4 1.0 ND1 B:HIS40 4.1 65.4 1.0 CB B:MET185 4.1 66.5 1.0 CG B:HIS40 4.1 64.6 1.0 C3D B:HEM301 4.2 56.3 1.0 C3A B:HEM301 4.2 56.6 1.0 C2B B:HEM301 4.2 57.0 1.0 C2A B:HEM301 4.2 55.3 1.0 C2D B:HEM301 4.2 55.0 1.0 C3C B:HEM301 4.2 62.1 1.0 C2C B:HEM301 4.3 59.1 1.0 C3B B:HEM301 4.3 58.1 1.0

Iron binding site 4 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:43.5 occ:1.00 FE1 C:FES200 0.0 43.5 1.0 S1 C:FES200 2.2 42.1 1.0 S2 C:FES200 2.2 43.0 1.0 SG C:CYS149 2.2 44.2 1.0 SG C:CYS129 2.3 43.0 1.0 FE2 C:FES200 2.7 41.2 1.0 CB C:CYS129 3.1 41.7 1.0 CB C:CYS149 3.1 45.9 1.0 CB C:HIS131 4.0 35.7 1.0 CB C:CYS151 4.2 47.6 1.0 ND1 C:HIS131 4.4 37.4 1.0 CB C:CYS134 4.5 41.3 1.0 N C:HIS152 4.5 44.9 1.0 CB C:SER154 4.5 41.7 1.0 OG C:SER154 4.5 39.1 1.0 ND1 C:HIS152 4.5 42.0 1.0 CA C:CYS149 4.5 45.8 1.0 CA C:CYS129 4.6 41.7 1.0 N C:LEU132 4.6 41.6 1.0 CG C:HIS131 4.7 34.3 1.0 N C:CYS134 4.8 39.9 1.0 C C:CYS149 4.9 45.8 1.0 O C:CYS149 4.9 44.3 1.0 N C:CYS151 4.9 46.1 1.0 N C:HIS131 5.0 36.7 1.0 CA C:CYS151 5.0 46.5 1.0

Iron binding site 5 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:41.2 occ:1.00 FE2 C:FES200 0.0 41.2 1.0 ND1 C:HIS131 2.1 37.4 1.0 S1 C:FES200 2.2 42.1 1.0 ND1 C:HIS152 2.2 42.0 1.0 S2 C:FES200 2.2 43.0 1.0 FE1 C:FES200 2.7 43.5 1.0 CG C:HIS131 3.1 34.3 1.0 CG C:HIS152 3.1 42.4 1.0 CE1 C:HIS131 3.2 35.1 1.0 CE1 C:HIS152 3.2 43.1 1.0 CB C:HIS152 3.3 42.9 1.0 CB C:HIS131 3.3 35.7 1.0 N C:HIS152 3.7 44.9 1.0 N C:LEU132 4.0 41.6 1.0 CA C:HIS152 4.0 44.6 1.0 CB C:CYS151 4.0 47.6 1.0 CD2 C:HIS131 4.2 36.0 1.0 CD2 C:HIS152 4.2 42.6 1.0 NE2 C:HIS131 4.3 34.6 1.0 SG C:CYS129 4.3 43.0 1.0 NE2 C:HIS152 4.3 42.4 1.0 C C:CYS151 4.3 45.9 1.0 CB C:LEU132 4.4 38.6 1.0 SG C:CYS149 4.5 44.2 1.0 CA C:HIS131 4.6 38.2 1.0 CG C:PRO166 4.6 45.3 1.0 CA C:CYS151 4.7 46.5 1.0 C C:HIS131 4.7 40.2 1.0 CG C:LEU132 4.8 36.3 1.0 CA C:LEU132 4.8 41.7 1.0 C C:HIS152 4.8 45.2 1.0 CD1 C:LEU132 4.9 34.3 1.0

Iron binding site 6 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:47.4 occ:1.00 FE D:HEM501 0.0 47.4 1.0 NB D:HEM501 1.9 47.9 1.0 NA D:HEM501 2.0 49.0 1.0 NC D:HEM501 2.0 47.9 1.0 ND D:HEM501 2.0 49.6 1.0 NE2 D:HIS212 2.0 46.6 1.0 NE2 D:HIS111 2.0 43.5 1.0 CE1 D:HIS212 3.0 47.2 1.0 C1B D:HEM501 3.0 47.4 1.0 CE1 D:HIS111 3.0 41.6 1.0 C4A D:HEM501 3.0 48.4 1.0 CD2 D:HIS111 3.0 44.1 1.0 C4B D:HEM501 3.0 47.9 1.0 CD2 D:HIS212 3.0 48.1 1.0 C4C D:HEM501 3.0 47.1 1.0 C1D D:HEM501 3.0 49.4 1.0 C1C D:HEM501 3.0 47.1 1.0 C1A D:HEM501 3.0 49.6 1.0 C4D D:HEM501 3.1 50.0 1.0 CHB D:HEM501 3.4 47.7 1.0 CHD D:HEM501 3.4 48.4 1.0 CHC D:HEM501 3.4 48.6 1.0 CHA D:HEM501 3.4 50.1 1.0 ND1 D:HIS212 4.1 46.5 1.0 ND1 D:HIS111 4.1 42.9 1.0 CG D:HIS212 4.1 48.2 1.0 CG D:HIS111 4.1 43.7 1.0 C2B D:HEM501 4.2 47.3 1.0 C3A D:HEM501 4.2 49.5 1.0 C3B D:HEM501 4.2 46.7 1.0 C2A D:HEM501 4.3 50.0 1.0 C2D D:HEM501 4.3 50.2 1.0 C3C D:HEM501 4.3 46.2 1.0 C2C D:HEM501 4.3 46.0 1.0 C3D D:HEM501 4.3 50.1 1.0

Iron binding site 7 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:37.5 occ:1.00 FE D:HEM502 0.0 37.5 1.0 NA D:HEM502 1.9 35.4 1.0 NB D:HEM502 2.0 36.9 1.0 ND D:HEM502 2.0 37.5 1.0 NC D:HEM502 2.0 35.4 1.0 NE2 D:HIS198 2.0 43.5 1.0 NE2 D:HIS97 2.0 38.9 1.0 CE1 D:HIS198 3.0 43.7 1.0 CE1 D:HIS97 3.0 37.4 1.0 C4A D:HEM502 3.0 34.1 1.0 C1B D:HEM502 3.0 36.8 1.0 C1A D:HEM502 3.0 36.2 1.0 C1D D:HEM502 3.0 36.8 1.0 C4C D:HEM502 3.0 34.3 1.0 CD2 D:HIS198 3.0 41.3 1.0 C4D D:HEM502 3.0 39.7 1.0 CD2 D:HIS97 3.0 37.1 1.0 C4B D:HEM502 3.0 39.2 1.0 C1C D:HEM502 3.0 36.8 1.0 CHB D:HEM502 3.4 33.6 1.0 CHD D:HEM502 3.4 33.6 1.0 CHA D:HEM502 3.4 38.9 1.0 CHC D:HEM502 3.4 38.1 1.0 ND1 D:HIS198 4.1 43.5 1.0 ND1 D:HIS97 4.1 37.6 1.0 CG D:HIS198 4.1 40.9 1.0 CG D:HIS97 4.2 37.6 1.0 C2A D:HEM502 4.2 34.0 1.0 C2D D:HEM502 4.2 38.2 1.0 C3A D:HEM502 4.2 32.7 1.0 C3C D:HEM502 4.2 34.7 1.0 C3D D:HEM502 4.3 40.6 1.0 C2B D:HEM502 4.3 38.6 1.0 C2C D:HEM502 4.3 35.2 1.0 C3B D:HEM502 4.3 40.7 1.0 CA D:GLY146 4.7 41.7 1.0 NE2 D:GLN58 4.8 39.8 1.0

Iron binding site 8 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:65.5 occ:1.00 FE E:HEM301 0.0 65.5 1.0 NA E:HEM301 2.0 61.6 1.0 NC E:HEM301 2.0 62.8 1.0 ND E:HEM301 2.0 62.4 1.0 NB E:HEM301 2.0 62.5 1.0 NE2 E:HIS40 2.0 77.1 1.0 SD E:MET185 2.1 69.2 1.0 CD2 E:HIS40 3.0 79.5 1.0 CE1 E:HIS40 3.0 78.1 1.0 C4A E:HEM301 3.0 61.5 1.0 C4C E:HEM301 3.0 63.9 1.0 C1A E:HEM301 3.0 60.4 1.0 C1D E:HEM301 3.0 63.0 1.0 C1B E:HEM301 3.0 62.4 1.0 C4D E:HEM301 3.0 62.6 1.0 C1C E:HEM301 3.0 62.6 1.0 C4B E:HEM301 3.0 63.0 1.0 CHB E:HEM301 3.4 62.9 1.0 CHD E:HEM301 3.4 63.6 1.0 CHA E:HEM301 3.4 60.1 1.0 CHC E:HEM301 3.4 62.0 1.0 CG E:MET185 3.5 68.3 1.0 CE E:MET185 3.5 67.2 1.0 CB E:MET185 4.1 68.7 1.0 ND1 E:HIS40 4.1 79.1 1.0 CG E:HIS40 4.1 77.6 1.0 C3A E:HEM301 4.2 59.8 1.0 C2A E:HEM301 4.2 59.0 1.0 C3C E:HEM301 4.2 65.7 1.0 C2B E:HEM301 4.2 62.2 1.0 C2D E:HEM301 4.3 63.7 1.0 C2C E:HEM301 4.3 63.7 1.0 C3D E:HEM301 4.3 64.5 1.0 C3B E:HEM301 4.3 64.3 1.0

Iron binding site 9 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe200 b:45.1 occ:1.00 FE1 F:FES200 0.0 45.1 1.0 S1 F:FES200 2.2 44.7 1.0 S2 F:FES200 2.2 43.3 1.0 SG F:CYS149 2.3 46.4 1.0 SG F:CYS129 2.3 44.4 1.0 FE2 F:FES200 2.7 43.4 1.0 CB F:CYS129 3.1 44.6 1.0 CB F:CYS149 3.2 45.9 1.0 CB F:HIS131 3.9 37.6 1.0 CB F:CYS151 4.2 45.8 1.0 ND1 F:HIS131 4.4 39.7 1.0 CB F:CYS134 4.5 41.7 1.0 ND1 F:HIS152 4.5 44.8 1.0 CB F:SER154 4.5 44.8 1.0 N F:HIS152 4.5 47.8 1.0 OG F:SER154 4.5 45.6 1.0 CA F:CYS149 4.6 45.3 1.0 CA F:CYS129 4.6 45.0 1.0 N F:LEU132 4.6 41.1 1.0 CG F:HIS131 4.7 37.1 1.0 N F:CYS134 4.8 38.1 1.0 N F:HIS131 4.9 39.5 1.0 C F:CYS149 4.9 44.5 1.0 O F:CYS149 4.9 43.8 1.0 N F:CYS151 5.0 44.3 1.0 CA F:HIS131 5.0 39.8 1.0 CA F:CYS151 5.0 45.8 1.0

Iron binding site 10 out of 30 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


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 Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe200 b:43.4 occ:1.00 FE2 F:FES200 0.0 43.4 1.0 ND1 F:HIS152 2.1 44.8 1.0 ND1 F:HIS131 2.2 39.7 1.0 S2 F:FES200 2.2 43.3 1.0 S1 F:FES200 2.2 44.7 1.0 FE1 F:FES200 2.7 45.1 1.0 CG F:HIS152 3.1 46.8 1.0 CG F:HIS131 3.1 37.1 1.0 CE1 F:HIS152 3.1 45.5 1.0 CE1 F:HIS131 3.2 36.9 1.0 CB F:HIS131 3.3 37.6 1.0 CB F:HIS152 3.3 48.1 1.0 N F:HIS152 3.7 47.8 1.0 N F:LEU132 4.0 41.1 1.0 CB F:CYS151 4.0 45.8 1.0 CA F:HIS152 4.1 48.7 1.0 NE2 F:HIS152 4.2 44.6 1.0 CD2 F:HIS152 4.2 46.0 1.0 CD2 F:HIS131 4.2 38.5 1.0 NE2 F:HIS131 4.3 38.8 1.0 C F:CYS151 4.3 46.5 1.0 SG F:CYS129 4.3 44.4 1.0 CB F:LEU132 4.3 37.4 1.0 SG F:CYS149 4.5 46.4 1.0 CA F:HIS131 4.6 39.8 1.0 CG F:LEU132 4.7 35.3 1.0 CA F:LEU132 4.7 40.5 1.0 C F:HIS131 4.7 40.6 1.0 CG F:PRO166 4.7 48.8 1.0 CA F:CYS151 4.7 45.8 1.0 CD1 F:LEU132 4.8 32.7 1.0 C F:HIS152 4.9 49.2 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