Iron in PDB 3tor: Crystal Structure of Escherichia Coli Nrfa with Europium Bound

All present enzymatic activity of Crystal Structure of Escherichia Coli Nrfa with Europium Bound:
1.7.2.2;

The structure of Crystal Structure of Escherichia Coli Nrfa with Europium Bound, PDB code: 3tor was solved by C.W.J.Lockwood, T.A.Clarke, J.N.Butt, A.M.Hemmings, D.J.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	146.10 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.884, 90.489, 292.196, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 22.2

The structure of Crystal Structure of Escherichia Coli Nrfa with Europium Bound also contains other interesting chemical elements:

Europium	(Eu)	9 atoms
Calcium	(Ca)	4 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound (pdb code 3tor). 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 Escherichia Coli Nrfa with Europium Bound, PDB code: 3tor:
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 Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3 b:10.5 occ:1.00 FE A:HEC3 0.0 10.5 1.0 ND A:HEC3 2.0 9.8 1.0 NZ A:LYS126 2.0 14.1 1.0 NB A:HEC3 2.0 10.6 1.0 NA A:HEC3 2.1 7.9 1.0 NC A:HEC3 2.1 7.3 1.0 O A:HOH1316 2.4 23.1 1.0 C1D A:HEC3 3.0 6.8 1.0 C4C A:HEC3 3.0 7.5 1.0 C1B A:HEC3 3.0 12.3 1.0 C1A A:HEC3 3.1 7.6 1.0 C4A A:HEC3 3.1 11.5 1.0 C4B A:HEC3 3.1 12.5 1.0 C1C A:HEC3 3.1 8.8 1.0 C4D A:HEC3 3.1 8.6 1.0 CE A:LYS126 3.1 9.7 1.0 CHD A:HEC3 3.4 7.0 1.0 CHB A:HEC3 3.4 10.9 1.0 CHC A:HEC3 3.4 10.9 1.0 CHA A:HEC3 3.5 5.0 1.0 O A:HOH10 4.1 9.0 1.0 O A:HOH551 4.3 26.7 1.0 C3C A:HEC3 4.3 8.4 1.0 C2B A:HEC3 4.3 12.5 1.0 C2D A:HEC3 4.3 7.0 1.0 C3A A:HEC3 4.3 8.4 1.0 C3B A:HEC3 4.3 11.7 1.0 C2A A:HEC3 4.3 6.0 1.0 C2C A:HEC3 4.3 10.1 1.0 C3D A:HEC3 4.3 5.3 1.0 NE2 A:HIS264 4.4 13.3 1.0 CD A:LYS126 4.5 12.6 1.0 CMD A:HEC5 4.7 6.0 1.0 O A:HOH537 4.8 16.4 1.0 O A:HOH577 5.0 28.0 1.0

Iron binding site 2 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe4 b:14.2 occ:1.00 FE A:HEC4 0.0 14.2 1.0 NE2 A:HIS164 2.0 9.3 1.0 NE2 A:HIS301 2.0 8.9 1.0 NA A:HEC4 2.0 13.3 1.0 NC A:HEC4 2.1 15.1 1.0 NB A:HEC4 2.1 16.4 1.0 ND A:HEC4 2.1 16.1 1.0 CE1 A:HIS301 2.9 14.5 1.0 CE1 A:HIS164 2.9 12.1 1.0 CD2 A:HIS164 3.0 11.8 1.0 CD2 A:HIS301 3.0 9.9 1.0 C1D A:HEC4 3.0 17.0 1.0 C4A A:HEC4 3.0 14.8 1.0 C1C A:HEC4 3.1 11.6 1.0 C4B A:HEC4 3.1 13.7 1.0 C1A A:HEC4 3.1 15.2 1.0 C4D A:HEC4 3.1 16.5 1.0 C4C A:HEC4 3.1 14.5 1.0 C1B A:HEC4 3.1 13.3 1.0 CHC A:HEC4 3.4 13.2 1.0 CHD A:HEC4 3.4 14.1 1.0 CHA A:HEC4 3.4 15.9 1.0 CHB A:HEC4 3.4 13.0 1.0 ND1 A:HIS164 4.1 13.7 1.0 ND1 A:HIS301 4.1 10.2 1.0 CG A:HIS164 4.1 14.1 1.0 CG A:HIS301 4.1 12.1 1.0 C3A A:HEC4 4.3 11.6 1.0 C2C A:HEC4 4.3 13.8 1.0 C2A A:HEC4 4.3 14.5 1.0 C3B A:HEC4 4.3 12.4 1.0 C2D A:HEC4 4.3 13.4 1.0 C2B A:HEC4 4.3 13.2 1.0 C3D A:HEC4 4.3 16.6 1.0 C3C A:HEC4 4.3 12.5 1.0 CE A:MET287 4.8 9.5 1.0

Iron binding site 3 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe5 b:10.7 occ:1.00 FE A:HEC5 0.0 10.7 1.0 NE2 A:HIS213 1.9 9.0 1.0 NA A:HEC5 2.0 11.1 1.0 NB A:HEC5 2.0 11.6 1.0 NE2 A:HIS94 2.0 15.1 1.0 NC A:HEC5 2.1 10.7 1.0 ND A:HEC5 2.1 9.7 1.0 CD2 A:HIS213 2.9 9.2 1.0 CE1 A:HIS213 2.9 11.6 1.0 CE1 A:HIS94 3.0 12.3 1.0 C4A A:HEC5 3.0 10.2 1.0 C1B A:HEC5 3.0 12.3 1.0 C4B A:HEC5 3.0 12.3 1.0 C1A A:HEC5 3.0 11.8 1.0 C1C A:HEC5 3.1 10.6 1.0 C4C A:HEC5 3.1 12.6 1.0 CD2 A:HIS94 3.1 12.6 1.0 C1D A:HEC5 3.1 12.4 1.0 C4D A:HEC5 3.1 13.1 1.0 CHD A:HEC5 3.4 9.2 1.0 CHB A:HEC5 3.4 11.2 1.0 CHC A:HEC5 3.4 9.8 1.0 CHA A:HEC5 3.5 11.8 1.0 ND1 A:HIS213 4.0 11.5 1.0 CG A:HIS213 4.0 8.6 1.0 ND1 A:HIS94 4.1 14.9 1.0 CG A:HIS94 4.2 11.3 1.0 C3A A:HEC5 4.2 9.4 1.0 C2B A:HEC5 4.2 12.8 1.0 C3B A:HEC5 4.2 12.5 1.0 C2A A:HEC5 4.2 9.3 1.0 C2C A:HEC5 4.3 9.8 1.0 C3C A:HEC5 4.3 7.9 1.0 C2D A:HEC5 4.3 9.5 1.0 C3D A:HEC5 4.3 8.9 1.0

Iron binding site 4 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe6 b:11.7 occ:1.00 FE A:HEC6 0.0 11.7 1.0 NB A:HEC6 2.0 11.5 1.0 NA A:HEC6 2.0 10.1 1.0 ND A:HEC6 2.0 10.5 1.0 NC A:HEC6 2.1 9.7 1.0 NE2 A:HIS286 2.1 12.8 1.0 NE2 A:HIS393 2.1 11.2 1.0 CE1 A:HIS393 3.0 12.2 1.0 C4A A:HEC6 3.0 9.9 1.0 C1B A:HEC6 3.0 9.7 1.0 CD2 A:HIS286 3.0 8.6 1.0 C4B A:HEC6 3.0 11.6 1.0 C1D A:HEC6 3.0 11.8 1.0 C4D A:HEC6 3.1 12.8 1.0 C1C A:HEC6 3.1 12.7 1.0 C4C A:HEC6 3.1 9.4 1.0 C1A A:HEC6 3.1 12.1 1.0 CE1 A:HIS286 3.1 4.5 1.0 CD2 A:HIS393 3.2 11.8 1.0 CHB A:HEC6 3.3 9.7 1.0 CHC A:HEC6 3.4 12.7 1.0 CHD A:HEC6 3.4 11.4 1.0 CHA A:HEC6 3.5 10.2 1.0 ND1 A:HIS393 4.1 9.8 1.0 CG A:HIS286 4.2 10.6 1.0 ND1 A:HIS286 4.2 7.2 1.0 C2B A:HEC6 4.2 11.5 1.0 C3A A:HEC6 4.2 9.4 1.0 CG A:HIS393 4.2 13.0 1.0 C3B A:HEC6 4.2 9.3 1.0 C2A A:HEC6 4.3 10.9 1.0 C3C A:HEC6 4.3 10.1 1.0 C2C A:HEC6 4.3 12.4 1.0 C2D A:HEC6 4.3 9.9 1.0 C3D A:HEC6 4.3 11.0 1.0

Iron binding site 5 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe7 b:14.6 occ:1.00 FE A:HEC7 0.0 14.6 1.0 NC A:HEC7 2.0 14.2 1.0 ND A:HEC7 2.0 16.0 1.0 NA A:HEC7 2.1 18.0 1.0 NE2 A:HIS275 2.1 11.5 1.0 NE2 A:HIS318 2.1 13.9 1.0 NB A:HEC7 2.1 15.4 1.0 CE1 A:HIS318 3.0 15.0 1.0 C1A A:HEC7 3.0 13.0 1.0 CE1 A:HIS275 3.0 14.9 1.0 C4C A:HEC7 3.0 18.2 1.0 C4D A:HEC7 3.1 16.5 1.0 C1C A:HEC7 3.1 15.0 1.0 C1D A:HEC7 3.1 16.4 1.0 CD2 A:HIS275 3.1 10.6 1.0 C4A A:HEC7 3.1 15.7 1.0 C4B A:HEC7 3.1 13.0 1.0 CD2 A:HIS318 3.2 15.3 1.0 C1B A:HEC7 3.2 15.3 1.0 CHA A:HEC7 3.4 16.6 1.0 CHD A:HEC7 3.4 16.2 1.0 CHC A:HEC7 3.5 13.6 1.0 CHB A:HEC7 3.5 13.5 1.0 ND1 A:HIS318 4.1 17.1 1.0 ND1 A:HIS275 4.2 14.4 1.0 CG A:HIS275 4.2 11.0 1.0 C2A A:HEC7 4.2 19.4 1.0 CG A:HIS318 4.3 17.7 1.0 C3C A:HEC7 4.3 19.1 1.0 C2C A:HEC7 4.3 18.3 1.0 C3A A:HEC7 4.3 20.1 1.0 C2D A:HEC7 4.3 15.4 1.0 C3D A:HEC7 4.3 15.2 1.0 C3B A:HEC7 4.4 12.1 1.0 C2B A:HEC7 4.4 15.1 1.0 CBC A:HEC6 4.7 12.7 1.0

Iron binding site 6 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3 b:13.5 occ:1.00 FE B:HEC3 0.0 13.5 1.0 NC B:HEC3 2.0 9.9 1.0 ND B:HEC3 2.0 10.1 1.0 NA B:HEC3 2.1 9.0 1.0 NZ B:LYS126 2.1 12.3 1.0 NB B:HEC3 2.1 11.2 1.0 O B:HOH829 2.2 25.1 1.0 C4C B:HEC3 3.0 11.8 1.0 C1D B:HEC3 3.0 10.3 1.0 C1C B:HEC3 3.0 12.0 1.0 C1A B:HEC3 3.1 12.2 1.0 C1B B:HEC3 3.1 11.0 1.0 CE B:LYS126 3.1 11.8 1.0 C4A B:HEC3 3.1 12.1 1.0 C4D B:HEC3 3.1 11.2 1.0 C4B B:HEC3 3.2 14.2 1.0 CHD B:HEC3 3.4 8.3 1.0 CHA B:HEC3 3.4 6.9 1.0 CHB B:HEC3 3.5 10.3 1.0 CHC B:HEC3 3.5 10.7 1.0 O B:HOH22 4.2 13.3 1.0 C3C B:HEC3 4.2 10.2 1.0 C2C B:HEC3 4.3 10.4 1.0 C2D B:HEC3 4.3 6.2 1.0 C3A B:HEC3 4.3 10.8 1.0 C2A B:HEC3 4.3 4.7 1.0 C2B B:HEC3 4.3 12.9 1.0 NE2 B:HIS264 4.4 12.9 1.0 C3D B:HEC3 4.4 7.2 1.0 C3B B:HEC3 4.4 12.5 1.0 CD B:LYS126 4.5 13.0 1.0 O B:HOH677 4.5 32.3 1.0 CMD B:HEC5 4.7 4.5 1.0 O B:HOH533 4.8 12.1 1.0

Iron binding site 7 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe4 b:11.8 occ:1.00 FE B:HEC4 0.0 11.8 1.0 NA B:HEC4 2.0 13.3 1.0 NE2 B:HIS164 2.0 5.3 1.0 NE2 B:HIS301 2.0 8.3 1.0 ND B:HEC4 2.0 9.7 1.0 NC B:HEC4 2.0 12.3 1.0 NB B:HEC4 2.0 13.1 1.0 CD2 B:HIS301 2.9 11.5 1.0 CD2 B:HIS164 3.0 9.9 1.0 CE1 B:HIS164 3.0 10.8 1.0 C1A B:HEC4 3.0 13.1 1.0 C4A B:HEC4 3.0 12.9 1.0 C4D B:HEC4 3.0 13.1 1.0 C4C B:HEC4 3.0 14.2 1.0 C1D B:HEC4 3.0 10.6 1.0 C4B B:HEC4 3.1 11.2 1.0 C1B B:HEC4 3.1 12.9 1.0 CE1 B:HIS301 3.1 9.2 1.0 C1C B:HEC4 3.1 11.1 1.0 CHA B:HEC4 3.4 11.0 1.0 CHD B:HEC4 3.4 9.7 1.0 CHC B:HEC4 3.4 11.0 1.0 CHB B:HEC4 3.4 11.1 1.0 ND1 B:HIS164 4.1 10.8 1.0 CG B:HIS301 4.1 9.8 1.0 CG B:HIS164 4.1 12.1 1.0 ND1 B:HIS301 4.1 8.1 1.0 C2A B:HEC4 4.2 12.9 1.0 C3A B:HEC4 4.2 12.3 1.0 C3C B:HEC4 4.3 11.8 1.0 C3D B:HEC4 4.3 15.3 1.0 C3B B:HEC4 4.3 14.6 1.0 C2D B:HEC4 4.3 11.0 1.0 C2B B:HEC4 4.3 14.8 1.0 C2C B:HEC4 4.3 13.0 1.0 CE B:MET287 4.7 8.0 1.0

Iron binding site 8 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5 b:11.0 occ:1.00 FE B:HEC5 0.0 11.0 1.0 NE2 B:HIS213 2.0 13.9 1.0 NB B:HEC5 2.0 9.0 1.0 NA B:HEC5 2.0 12.5 1.0 NE2 B:HIS94 2.1 12.5 1.0 NC B:HEC5 2.1 10.2 1.0 ND B:HEC5 2.1 11.6 1.0 CE1 B:HIS213 2.9 12.2 1.0 C1B B:HEC5 3.0 9.9 1.0 CD2 B:HIS213 3.0 11.2 1.0 CE1 B:HIS94 3.0 13.3 1.0 C4B B:HEC5 3.0 12.1 1.0 C4A B:HEC5 3.1 11.4 1.0 C1A B:HEC5 3.1 9.1 1.0 CD2 B:HIS94 3.1 13.2 1.0 C1C B:HEC5 3.1 8.6 1.0 C1D B:HEC5 3.1 12.3 1.0 C4C B:HEC5 3.1 9.3 1.0 C4D B:HEC5 3.1 10.8 1.0 CHB B:HEC5 3.4 13.1 1.0 CHC B:HEC5 3.4 9.4 1.0 CHD B:HEC5 3.4 9.2 1.0 CHA B:HEC5 3.5 8.3 1.0 ND1 B:HIS213 4.0 10.6 1.0 CG B:HIS213 4.1 11.1 1.0 ND1 B:HIS94 4.1 12.8 1.0 CG B:HIS94 4.2 9.4 1.0 C2B B:HEC5 4.2 11.1 1.0 C2A B:HEC5 4.2 10.4 1.0 C3B B:HEC5 4.2 10.1 1.0 C3A B:HEC5 4.3 11.4 1.0 C3C B:HEC5 4.3 11.5 1.0 C2C B:HEC5 4.3 12.3 1.0 C3D B:HEC5 4.3 8.0 1.0 C2D B:HEC5 4.3 8.7 1.0

Iron binding site 9 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe6 b:11.7 occ:1.00 FE B:HEC6 0.0 11.7 1.0 NB B:HEC6 2.0 11.2 1.0 NE2 B:HIS286 2.0 10.9 1.0 NC B:HEC6 2.0 11.2 1.0 NA B:HEC6 2.0 10.0 1.0 ND B:HEC6 2.1 12.8 1.0 NE2 B:HIS393 2.1 10.8 1.0 CE1 B:HIS286 2.9 11.8 1.0 CE1 B:HIS393 3.0 8.7 1.0 C4C B:HEC6 3.0 9.2 1.0 C4B B:HEC6 3.0 9.4 1.0 C1B B:HEC6 3.0 10.1 1.0 C4A B:HEC6 3.0 8.2 1.0 C1D B:HEC6 3.0 11.2 1.0 C1C B:HEC6 3.1 9.9 1.0 C1A B:HEC6 3.1 12.3 1.0 C4D B:HEC6 3.1 13.5 1.0 CD2 B:HIS286 3.1 9.8 1.0 CD2 B:HIS393 3.2 7.6 1.0 CHD B:HEC6 3.4 10.3 1.0 CHB B:HEC6 3.4 9.7 1.0 CHC B:HEC6 3.4 10.1 1.0 CHA B:HEC6 3.4 12.0 1.0 ND1 B:HIS286 4.1 9.4 1.0 ND1 B:HIS393 4.1 9.9 1.0 CG B:HIS286 4.2 10.2 1.0 C3C B:HEC6 4.2 10.0 1.0 C3B B:HEC6 4.2 7.7 1.0 C2B B:HEC6 4.2 10.2 1.0 C2C B:HEC6 4.3 10.7 1.0 C3A B:HEC6 4.3 10.4 1.0 CG B:HIS393 4.3 11.5 1.0 C2A B:HEC6 4.3 10.9 1.0 C2D B:HEC6 4.3 12.1 1.0 C3D B:HEC6 4.3 13.4 1.0

Iron binding site 10 out of 20 in the Crystal Structure of Escherichia Coli Nrfa with Europium Bound


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 Escherichia Coli Nrfa with Europium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe7 b:13.6 occ:1.00 FE B:HEC7 0.0 13.6 1.0 NA B:HEC7 2.0 15.3 1.0 ND B:HEC7 2.0 14.4 1.0 NE2 B:HIS275 2.1 12.4 1.0 NB B:HEC7 2.1 14.0 1.0 NE2 B:HIS318 2.1 15.4 1.0 NC B:HEC7 2.1 15.5 1.0 C1A B:HEC7 3.0 13.4 1.0 CE1 B:HIS318 3.0 14.4 1.0 C4D B:HEC7 3.0 16.9 1.0 CD2 B:HIS275 3.0 9.6 1.0 C4A B:HEC7 3.0 14.6 1.0 CE1 B:HIS275 3.1 13.7 1.0 C1D B:HEC7 3.1 15.4 1.0 C1B B:HEC7 3.1 15.0 1.0 C4B B:HEC7 3.1 10.9 1.0 C1C B:HEC7 3.1 13.6 1.0 C4C B:HEC7 3.1 14.0 1.0 CD2 B:HIS318 3.2 17.2 1.0 CHA B:HEC7 3.3 16.3 1.0 CHB B:HEC7 3.4 14.8 1.0 CHC B:HEC7 3.5 10.1 1.0 CHD B:HEC7 3.5 14.0 1.0 ND1 B:HIS318 4.1 17.6 1.0 CG B:HIS275 4.2 13.7 1.0 ND1 B:HIS275 4.2 13.2 1.0 C2A B:HEC7 4.2 15.7 1.0 C3A B:HEC7 4.2 17.8 1.0 C3D B:HEC7 4.3 16.9 1.0 CG B:HIS318 4.3 16.3 1.0 C2B B:HEC7 4.3 13.6 1.0 C3B B:HEC7 4.3 13.3 1.0 C2D B:HEC7 4.3 15.6 1.0 C2C B:HEC7 4.4 14.4 1.0 C3C B:HEC7 4.4 15.6 1.0 CBC B:HEC6 4.7 10.8 1.0

C.W.Lockwood, T.A.Clarke, J.N.Butt, A.M.Hemmings, D.J.Richardson. Characterization of the Active Site and Calcium Binding in Cytochrome C Nitrite Reductases. Biochem.Soc.Trans. V. 39 1871 2011.
ISSN: ISSN 0300-5127
PubMed: 22103542
DOI: 10.1042/BST20110731