Iron in PDB 8bcx: Crystal Structure of Nrfa-1 From Geobacter Metallireducens

All present enzymatic activity of Crystal Structure of Nrfa-1 From Geobacter Metallireducens:
1.7.2.2;

The structure of Crystal Structure of Nrfa-1 From Geobacter Metallireducens, PDB code: 8bcx was solved by L.Denkhaus, F.Siffert, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	122.39 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.085, 91.965, 123.939, 90, 99.06, 90
R / Rfree (%)	19.3 / 22.7

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens (pdb code 8bcx). 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 Nrfa-1 From Geobacter Metallireducens, PDB code: 8bcx:
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 Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:36.8 occ:1.00 FE A:HEC501 0.0 36.8 1.0 NE2 A:HIS294 2.0 28.3 1.0 NB A:HEC501 2.0 35.4 1.0 ND A:HEC501 2.1 36.5 1.0 NA A:HEC501 2.1 36.2 1.0 NC A:HEC501 2.1 36.6 1.0 NE2 A:HIS336 2.1 30.9 1.0 CE1 A:HIS294 3.0 28.2 1.0 CD2 A:HIS294 3.0 27.7 1.0 CE1 A:HIS336 3.0 31.1 1.0 C1B A:HEC501 3.0 34.8 1.0 C1C A:HEC501 3.1 36.3 1.0 C4D A:HEC501 3.1 36.6 1.0 C4A A:HEC501 3.1 35.7 1.0 C1D A:HEC501 3.1 36.4 1.0 C1A A:HEC501 3.1 36.2 1.0 C4B A:HEC501 3.1 35.1 1.0 C4C A:HEC501 3.1 36.7 1.0 CD2 A:HIS336 3.2 30.4 1.0 CHB A:HEC501 3.4 35.1 1.0 CHA A:HEC501 3.4 36.1 1.0 CHC A:HEC501 3.4 35.4 1.0 CHD A:HEC501 3.5 36.2 1.0 ND1 A:HIS294 4.1 28.6 1.0 CG A:HIS294 4.1 27.9 1.0 ND1 A:HIS336 4.2 31.4 1.0 CG A:HIS336 4.3 30.6 1.0 C3B A:HEC501 4.3 34.8 1.0 C2B A:HEC501 4.3 34.7 1.0 C3D A:HEC501 4.3 37.6 1.0 C3C A:HEC501 4.3 37.8 1.0 C2D A:HEC501 4.3 36.6 1.0 C2A A:HEC501 4.3 36.8 1.0 C3A A:HEC501 4.3 35.8 1.0 C2C A:HEC501 4.3 36.8 1.0 CBC A:HEC503 4.9 29.6 1.0

Iron binding site 2 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:27.3 occ:1.00 FE A:HEC502 0.0 27.3 1.0 NB A:HEC502 2.1 24.8 1.0 NA A:HEC502 2.1 26.4 1.0 ND A:HEC502 2.1 26.5 1.0 NC A:HEC502 2.1 25.6 1.0 O A:HOH619 2.2 17.2 1.0 NZ A:LYS137 2.2 31.8 1.0 C1A A:HEC502 3.1 26.6 1.0 C1C A:HEC502 3.1 24.7 1.0 C4D A:HEC502 3.1 26.9 1.0 C4B A:HEC502 3.1 24.4 1.0 C1B A:HEC502 3.1 24.1 1.0 C1D A:HEC502 3.1 26.3 1.0 C4A A:HEC502 3.1 25.4 1.0 C4C A:HEC502 3.1 25.5 1.0 CE A:LYS137 3.2 30.3 1.0 CHA A:HEC502 3.4 26.6 1.0 CHC A:HEC502 3.4 24.0 1.0 CHB A:HEC502 3.5 24.1 1.0 CHD A:HEC502 3.5 25.7 1.0 OD2 A:ASP80 4.1 27.8 1.0 NE2 A:HIS282 4.1 21.4 1.0 O A:HOH756 4.3 15.5 1.0 C3B A:HEC502 4.3 24.9 1.0 C2A A:HEC502 4.3 27.4 1.0 C2B A:HEC502 4.3 24.0 1.0 C3C A:HEC502 4.3 25.6 1.0 C3D A:HEC502 4.3 28.2 1.0 C2C A:HEC502 4.3 25.2 1.0 C3A A:HEC502 4.3 25.8 1.0 C2D A:HEC502 4.3 27.0 1.0 CD A:LYS137 4.6 29.0 1.0 CB A:ASP80 4.7 23.4 1.0 CD2 A:HIS282 4.8 20.3 1.0 CG A:ASP80 4.9 27.8 1.0 O A:HOH606 4.9 27.9 1.0

Iron binding site 3 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:30.1 occ:1.00 FE A:HEC503 0.0 30.1 1.0 NE2 A:HIS305 2.0 29.5 1.0 NE2 A:HIS416 2.0 19.7 1.0 NA A:HEC503 2.0 29.9 1.0 NB A:HEC503 2.0 28.4 1.0 ND A:HEC503 2.1 29.8 1.0 NC A:HEC503 2.1 29.0 1.0 CE1 A:HIS305 2.9 29.3 1.0 CE1 A:HIS416 2.9 20.8 1.0 C1D A:HEC503 3.0 30.1 1.0 CD2 A:HIS305 3.0 29.2 1.0 C1B A:HEC503 3.0 28.1 1.0 C4A A:HEC503 3.0 28.8 1.0 C1A A:HEC503 3.1 30.2 1.0 C4C A:HEC503 3.1 28.8 1.0 C1C A:HEC503 3.1 28.3 1.0 C4B A:HEC503 3.1 27.8 1.0 C4D A:HEC503 3.1 30.2 1.0 CD2 A:HIS416 3.1 19.7 1.0 CHB A:HEC503 3.4 28.1 1.0 CHD A:HEC503 3.4 29.0 1.0 CHC A:HEC503 3.4 27.6 1.0 CHA A:HEC503 3.4 29.7 1.0 ND1 A:HIS305 4.0 29.8 1.0 CG A:HIS305 4.1 29.1 1.0 ND1 A:HIS416 4.1 21.2 1.0 CG A:HIS416 4.2 20.0 1.0 C3B A:HEC503 4.3 27.8 1.0 C3A A:HEC503 4.3 29.1 1.0 C2B A:HEC503 4.3 28.3 1.0 C2A A:HEC503 4.3 31.2 1.0 C2D A:HEC503 4.3 31.0 1.0 C3C A:HEC503 4.3 29.4 1.0 C2C A:HEC503 4.3 29.0 1.0 C3D A:HEC503 4.3 31.8 1.0

Iron binding site 4 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:31.5 occ:1.00 FE A:HEC504 0.0 31.5 1.0 NE2 A:HIS222 2.0 22.3 1.0 ND A:HEC504 2.0 30.7 1.0 NC A:HEC504 2.0 29.5 1.0 NA A:HEC504 2.1 31.7 1.0 NB A:HEC504 2.1 30.2 1.0 NE2 A:HIS112 2.1 37.3 1.0 CE1 A:HIS112 3.0 38.0 1.0 CE1 A:HIS222 3.0 22.4 1.0 CD2 A:HIS222 3.0 21.8 1.0 C1D A:HEC504 3.1 30.2 1.0 C1A A:HEC504 3.1 32.3 1.0 C1C A:HEC504 3.1 28.6 1.0 C4D A:HEC504 3.1 31.1 1.0 C1B A:HEC504 3.1 29.9 1.0 C4C A:HEC504 3.1 28.9 1.0 C4A A:HEC504 3.1 31.5 1.0 C4B A:HEC504 3.1 29.4 1.0 CD2 A:HIS112 3.2 36.4 1.0 CHA A:HEC504 3.4 31.4 1.0 CHD A:HEC504 3.4 29.2 1.0 CHB A:HEC504 3.4 30.7 1.0 CHC A:HEC504 3.4 28.9 1.0 ND1 A:HIS222 4.1 22.4 1.0 ND1 A:HIS112 4.1 37.2 1.0 CG A:HIS222 4.1 21.2 1.0 CG A:HIS112 4.2 36.0 1.0 C3C A:HEC504 4.3 28.2 1.0 C2D A:HEC504 4.3 30.9 1.0 C3D A:HEC504 4.3 31.8 1.0 C2C A:HEC504 4.3 28.1 1.0 C3B A:HEC504 4.3 29.2 1.0 C2A A:HEC504 4.3 33.8 1.0 C2B A:HEC504 4.3 29.2 1.0 C3A A:HEC504 4.3 32.4 1.0 CMD A:HEC502 5.0 26.8 1.0

Iron binding site 5 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe505 b:45.6 occ:1.00 FE A:HEC505 0.0 45.6 1.0 NE2 A:HIS319 2.0 42.4 1.0 ND A:HEC505 2.1 45.4 1.0 NB A:HEC505 2.1 44.7 1.0 NC A:HEC505 2.1 44.3 1.0 NA A:HEC505 2.1 45.9 1.0 NE2 A:HIS179 2.1 44.1 1.0 CD2 A:HIS319 3.0 41.9 1.0 C1A A:HEC505 3.1 46.4 1.0 C1C A:HEC505 3.1 43.1 1.0 C1D A:HEC505 3.1 45.2 1.0 C4B A:HEC505 3.1 44.1 1.0 CE1 A:HIS179 3.1 44.3 1.0 C4D A:HEC505 3.1 46.1 1.0 C1B A:HEC505 3.1 44.8 1.0 CD2 A:HIS179 3.1 43.0 1.0 CE1 A:HIS319 3.1 42.3 1.0 C4C A:HEC505 3.1 43.7 1.0 C4A A:HEC505 3.1 45.5 1.0 CHC A:HEC505 3.4 43.5 1.0 CHA A:HEC505 3.4 46.1 1.0 CHD A:HEC505 3.4 44.4 1.0 CHB A:HEC505 3.5 45.0 1.0 CG A:HIS319 4.1 42.2 1.0 ND1 A:HIS319 4.2 42.4 1.0 CG A:HIS179 4.2 42.8 1.0 ND1 A:HIS179 4.2 44.3 1.0 C3B A:HEC505 4.3 44.3 1.0 C3C A:HEC505 4.3 42.1 1.0 C2A A:HEC505 4.3 47.1 1.0 C2C A:HEC505 4.3 41.9 1.0 C2D A:HEC505 4.3 45.5 1.0 C3D A:HEC505 4.3 46.6 1.0 C2B A:HEC505 4.3 44.5 1.0 C3A A:HEC505 4.3 46.1 1.0 CE A:MET306 4.7 31.6 1.0

Iron binding site 6 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:29.7 occ:1.00 FE B:HEC501 0.0 29.7 1.0 NB B:HEC501 2.1 28.4 1.0 NA B:HEC501 2.1 29.9 1.0 NC B:HEC501 2.1 27.1 1.0 ND B:HEC501 2.1 27.9 1.0 O B:HOH614 2.3 14.1 1.0 NZ B:LYS137 2.3 33.2 1.0 C1A B:HEC501 3.1 30.4 1.0 C1C B:HEC501 3.1 25.8 1.0 C1B B:HEC501 3.1 28.5 1.0 C4B B:HEC501 3.1 27.7 1.0 C4D B:HEC501 3.1 28.0 1.0 C4A B:HEC501 3.1 30.3 1.0 C1D B:HEC501 3.1 26.7 1.0 C4C B:HEC501 3.1 25.9 1.0 CE B:LYS137 3.3 31.7 1.0 CHA B:HEC501 3.4 29.0 1.0 CHC B:HEC501 3.4 26.3 1.0 CHB B:HEC501 3.4 29.2 1.0 CHD B:HEC501 3.5 26.1 1.0 NE2 B:HIS282 4.0 19.3 1.0 OD2 B:ASP80 4.0 32.9 1.0 C3B B:HEC501 4.3 28.6 1.0 C2A B:HEC501 4.3 32.6 1.0 C2B B:HEC501 4.3 28.7 1.0 C3C B:HEC501 4.3 24.9 1.0 C2C B:HEC501 4.3 24.6 1.0 C3A B:HEC501 4.3 31.4 1.0 C3D B:HEC501 4.3 27.9 1.0 C2D B:HEC501 4.4 26.7 1.0 O B:HOH740 4.4 18.1 1.0 CD B:LYS137 4.7 30.6 1.0 CD2 B:HIS282 4.8 18.4 1.0 CB B:ASP80 4.9 30.6 1.0 CG B:ASP80 4.9 32.3 1.0 CE1 B:HIS282 5.0 20.2 1.0

Iron binding site 7 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:33.1 occ:1.00 FE B:HEC502 0.0 33.1 1.0 NE2 B:HIS416 2.0 22.9 1.0 NE2 B:HIS305 2.0 31.5 1.0 NC B:HEC502 2.0 30.8 1.0 NA B:HEC502 2.1 32.5 1.0 NB B:HEC502 2.1 30.2 1.0 ND B:HEC502 2.1 33.3 1.0 CE1 B:HIS416 2.9 23.7 1.0 CE1 B:HIS305 2.9 31.3 1.0 C1A B:HEC502 3.1 32.9 1.0 C1C B:HEC502 3.1 29.6 1.0 C1B B:HEC502 3.1 29.6 1.0 C1D B:HEC502 3.1 33.2 1.0 C4B B:HEC502 3.1 28.7 1.0 C4C B:HEC502 3.1 31.4 1.0 C4D B:HEC502 3.1 33.9 1.0 C4A B:HEC502 3.1 31.7 1.0 CD2 B:HIS305 3.1 31.2 1.0 CD2 B:HIS416 3.1 22.6 1.0 CHA B:HEC502 3.4 33.4 1.0 CHC B:HEC502 3.4 28.8 1.0 CHB B:HEC502 3.4 30.2 1.0 CHD B:HEC502 3.4 32.3 1.0 ND1 B:HIS416 4.1 24.1 1.0 ND1 B:HIS305 4.1 31.3 1.0 CG B:HIS305 4.2 30.9 1.0 CG B:HIS416 4.2 22.6 1.0 C3B B:HEC502 4.3 28.0 1.0 C3C B:HEC502 4.3 31.7 1.0 C2B B:HEC502 4.3 28.9 1.0 C2A B:HEC502 4.3 33.5 1.0 C2C B:HEC502 4.3 30.2 1.0 C3D B:HEC502 4.3 35.0 1.0 C2D B:HEC502 4.3 34.2 1.0 C3A B:HEC502 4.3 32.2 1.0

Iron binding site 8 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe503 b:47.5 occ:1.00 FE B:HEC503 0.0 47.5 1.0 NE2 B:HIS294 2.0 34.4 1.0 NE2 B:HIS336 2.0 53.7 1.0 NA B:HEC503 2.0 46.9 1.0 NB B:HEC503 2.1 46.3 1.0 ND B:HEC503 2.1 47.6 1.0 NC B:HEC503 2.1 47.4 1.0 CE1 B:HIS336 2.8 54.0 1.0 CD2 B:HIS294 3.0 33.3 1.0 CE1 B:HIS294 3.0 33.8 1.0 C1B B:HEC503 3.1 45.7 1.0 C4A B:HEC503 3.1 46.5 1.0 C1A B:HEC503 3.1 47.1 1.0 C1D B:HEC503 3.1 47.6 1.0 C1C B:HEC503 3.1 47.1 1.0 C4C B:HEC503 3.1 47.8 1.0 C4D B:HEC503 3.1 48.0 1.0 C4B B:HEC503 3.1 46.3 1.0 CD2 B:HIS336 3.2 53.1 1.0 CHB B:HEC503 3.4 45.9 1.0 CHD B:HEC503 3.4 47.4 1.0 CHA B:HEC503 3.4 47.2 1.0 CHC B:HEC503 3.5 46.5 1.0 ND1 B:HIS336 4.0 54.5 1.0 CG B:HIS294 4.1 32.6 1.0 ND1 B:HIS294 4.2 33.7 1.0 CG B:HIS336 4.2 53.1 1.0 C3C B:HEC503 4.3 49.0 1.0 C2B B:HEC503 4.3 45.6 1.0 C3A B:HEC503 4.3 46.6 1.0 C3B B:HEC503 4.3 46.6 1.0 C2A B:HEC503 4.3 47.9 1.0 C2D B:HEC503 4.3 48.3 1.0 C2C B:HEC503 4.3 47.6 1.0 C3D B:HEC503 4.3 49.2 1.0 CBC B:HEC502 4.9 33.6 1.0

Iron binding site 9 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe504 b:30.7 occ:1.00 FE B:HEC504 0.0 30.7 1.0 NE2 B:HIS222 2.0 21.5 1.0 NB B:HEC504 2.0 28.6 1.0 ND B:HEC504 2.0 30.8 1.0 NA B:HEC504 2.1 30.9 1.0 NC B:HEC504 2.1 28.6 1.0 NE2 B:HIS112 2.1 42.0 1.0 CE1 B:HIS112 3.0 42.3 1.0 CE1 B:HIS222 3.0 21.4 1.0 CD2 B:HIS222 3.0 20.5 1.0 C1B B:HEC504 3.1 28.5 1.0 C1A B:HEC504 3.1 31.7 1.0 C1C B:HEC504 3.1 27.5 1.0 C4D B:HEC504 3.1 31.4 1.0 C1D B:HEC504 3.1 30.1 1.0 C4B B:HEC504 3.1 27.5 1.0 C4A B:HEC504 3.1 30.6 1.0 C4C B:HEC504 3.1 28.1 1.0 CD2 B:HIS112 3.2 41.3 1.0 CHC B:HEC504 3.4 27.3 1.0 CHB B:HEC504 3.4 29.4 1.0 CHA B:HEC504 3.4 31.2 1.0 CHD B:HEC504 3.4 29.0 1.0 ND1 B:HIS112 4.1 41.7 1.0 ND1 B:HIS222 4.1 21.0 1.0 CG B:HIS222 4.2 19.1 1.0 CG B:HIS112 4.2 41.0 1.0 C3B B:HEC504 4.3 27.1 1.0 C2B B:HEC504 4.3 27.9 1.0 C3C B:HEC504 4.3 27.1 1.0 C2A B:HEC504 4.3 33.4 1.0 C2C B:HEC504 4.3 26.9 1.0 C3D B:HEC504 4.3 32.4 1.0 C2D B:HEC504 4.3 31.0 1.0 C3A B:HEC504 4.3 31.6 1.0 CMD B:HEC501 4.9 25.8 1.0

Iron binding site 10 out of 20 in the Crystal Structure of Nrfa-1 From Geobacter Metallireducens


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 Nrfa-1 From Geobacter Metallireducens within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe505 b:41.6 occ:1.00 FE B:HEC505 0.0 41.6 1.0 ND B:HEC505 2.1 41.4 1.0 NE2 B:HIS319 2.1 45.7 1.0 NB B:HEC505 2.1 40.9 1.0 NC B:HEC505 2.1 39.9 1.0 NA B:HEC505 2.1 41.7 1.0 NE2 B:HIS179 2.1 35.9 1.0 CD2 B:HIS319 3.0 45.8 1.0 C1A B:HEC505 3.1 42.0 1.0 C1C B:HEC505 3.1 39.1 1.0 C1D B:HEC505 3.1 40.9 1.0 C4D B:HEC505 3.1 42.1 1.0 C4B B:HEC505 3.1 40.3 1.0 C1B B:HEC505 3.1 41.0 1.0 CE1 B:HIS319 3.1 45.9 1.0 C4C B:HEC505 3.1 39.2 1.0 CE1 B:HIS179 3.1 35.4 1.0 CD2 B:HIS179 3.1 35.2 1.0 C4A B:HEC505 3.1 41.5 1.0 CHC B:HEC505 3.4 39.6 1.0 CHA B:HEC505 3.4 42.0 1.0 CHD B:HEC505 3.4 40.1 1.0 CHB B:HEC505 3.5 41.1 1.0 CG B:HIS319 4.2 46.5 1.0 ND1 B:HIS319 4.2 46.4 1.0 CG B:HIS179 4.2 34.8 1.0 ND1 B:HIS179 4.2 35.2 1.0 C3B B:HEC505 4.3 40.3 1.0 C3C B:HEC505 4.3 37.5 1.0 C2D B:HEC505 4.3 41.4 1.0 C2A B:HEC505 4.3 42.4 1.0 C3D B:HEC505 4.3 42.5 1.0 C2C B:HEC505 4.3 37.7 1.0 C2B B:HEC505 4.3 40.8 1.0 C3A B:HEC505 4.3 42.0 1.0 CE B:MET306 4.6 30.8 1.0

L.Denkhaus, F.Siffert, O.Einsle. An Unusual Active Site Architecture in Cytochrome C Nitrite Reductase Nrfa-1 From Geobacter Metallireducens. Fems Microbiol.Lett. V. 370 2023.
ISSN: ISSN 0378-1097
PubMed: 37460131
DOI: 10.1093/FEMSLE/FNAD068