Iron in PDB 6rk0: Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii

The structure of Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii, PDB code: 6rk0 was solved by J.W.Murray, F.Varghese, B.Kabasakal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.24 / 0.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.970, 89.870, 59.030, 90.00, 109.06, 90.00
R / Rfree (%)	12.4 / 13.8

The binding sites of Iron atom in the Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii (pdb code 6rk0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii, PDB code: 6rk0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:8.9 occ:0.78 FE A:HEM301 0.0 8.9 0.8 FE A:HEM301 0.2 8.8 0.2 NA A:HEM301 1.9 8.7 0.2 ND A:HEM301 2.0 9.3 0.8 NC A:HEM301 2.0 9.2 0.8 NA A:HEM301 2.0 8.6 0.8 NE2 A:HIS70 2.0 9.2 1.0 NB A:HEM301 2.0 8.9 0.8 NB A:HEM301 2.0 8.9 0.2 ND A:HEM301 2.1 9.2 0.2 O B:HOH550 2.1 9.7 1.0 NC A:HEM301 2.1 9.2 0.2 C4A A:HEM301 2.9 9.0 0.2 C1A A:HEM301 3.0 8.8 0.2 CE1 A:HIS70 3.0 9.4 1.0 CD2 A:HIS70 3.0 9.0 1.0 C1D A:HEM301 3.0 9.3 0.8 C1C A:HEM301 3.0 9.3 0.8 C1B A:HEM301 3.0 9.1 0.2 C4C A:HEM301 3.0 9.3 0.8 C4D A:HEM301 3.0 9.3 0.8 C4B A:HEM301 3.0 9.6 0.8 C1A A:HEM301 3.0 8.8 0.8 C4D A:HEM301 3.1 9.3 0.2 C4A A:HEM301 3.1 9.0 0.8 C1B A:HEM301 3.1 9.2 0.8 C4B A:HEM301 3.1 9.6 0.2 C1D A:HEM301 3.1 9.3 0.2 C1C A:HEM301 3.1 9.3 0.2 C4C A:HEM301 3.1 9.3 0.2 CHB A:HEM301 3.3 9.1 0.2 CHD A:HEM301 3.4 9.5 0.8 CHC A:HEM301 3.4 9.7 0.8 CHA A:HEM301 3.4 9.2 0.2 CHA A:HEM301 3.4 9.2 0.8 CHB A:HEM301 3.4 9.1 0.8 CHD A:HEM301 3.5 9.5 0.2 CHC A:HEM301 3.5 9.7 0.2 ND1 A:HIS70 4.1 9.8 1.0 CG A:HIS70 4.1 9.3 1.0 C3A A:HEM301 4.2 9.2 0.2 C2A A:HEM301 4.2 9.2 0.2 O B:HOH718 4.2 19.1 1.0 C2C A:HEM301 4.2 10.0 0.8 C2D A:HEM301 4.2 9.9 0.8 C3C A:HEM301 4.2 10.1 0.8 O B:PHE105 4.2 9.3 1.0 C3D A:HEM301 4.2 9.9 0.8 C2B A:HEM301 4.2 9.9 0.2 C3B A:HEM301 4.3 10.3 0.8 C2A A:HEM301 4.3 9.2 0.8 C3B A:HEM301 4.3 10.4 0.2 C2B A:HEM301 4.3 9.9 0.8 C3D A:HEM301 4.3 9.9 0.2 C3A A:HEM301 4.3 9.2 0.8 C2C A:HEM301 4.3 10.0 0.2 C2D A:HEM301 4.3 9.9 0.2 C3C A:HEM301 4.3 10.1 0.2 O B:TYR103 4.5 10.4 1.0 O B:HOH681 4.7 14.9 1.0

Iron binding site 2 out of 4 in the Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:8.8 occ:0.22 FE A:HEM301 0.0 8.8 0.2 FE A:HEM301 0.2 8.9 0.8 NB A:HEM301 1.9 8.9 0.8 NA A:HEM301 1.9 8.6 0.8 ND A:HEM301 2.0 9.2 0.2 NC A:HEM301 2.0 9.2 0.2 NA A:HEM301 2.0 8.7 0.2 O B:HOH550 2.1 9.7 1.0 NE2 A:HIS70 2.1 9.2 1.0 NC A:HEM301 2.1 9.2 0.8 ND A:HEM301 2.1 9.3 0.8 NB A:HEM301 2.1 8.9 0.2 C1B A:HEM301 2.9 9.2 0.8 C4B A:HEM301 2.9 9.6 0.8 C4A A:HEM301 2.9 9.0 0.8 C4C A:HEM301 3.0 9.3 0.2 C1D A:HEM301 3.0 9.3 0.2 CE1 A:HIS70 3.0 9.4 1.0 C1A A:HEM301 3.0 8.8 0.8 C4D A:HEM301 3.0 9.3 0.2 C1C A:HEM301 3.0 9.3 0.2 C1C A:HEM301 3.0 9.3 0.8 C1A A:HEM301 3.1 8.8 0.2 C4A A:HEM301 3.1 9.0 0.2 C4D A:HEM301 3.1 9.3 0.8 CD2 A:HIS70 3.1 9.0 1.0 C4B A:HEM301 3.1 9.6 0.2 C1B A:HEM301 3.1 9.1 0.2 C4C A:HEM301 3.2 9.3 0.8 C1D A:HEM301 3.2 9.3 0.8 CHB A:HEM301 3.3 9.1 0.8 CHD A:HEM301 3.3 9.5 0.2 CHC A:HEM301 3.4 9.7 0.8 CHA A:HEM301 3.4 9.2 0.2 CHA A:HEM301 3.4 9.2 0.8 CHC A:HEM301 3.5 9.7 0.2 CHB A:HEM301 3.5 9.1 0.2 CHD A:HEM301 3.5 9.5 0.8 O B:PHE105 4.1 9.3 1.0 ND1 A:HIS70 4.1 9.8 1.0 C3B A:HEM301 4.1 10.3 0.8 C2B A:HEM301 4.1 9.9 0.8 O B:HOH718 4.2 19.1 1.0 C3C A:HEM301 4.2 10.1 0.2 C3A A:HEM301 4.2 9.2 0.8 C2D A:HEM301 4.2 9.9 0.2 C2C A:HEM301 4.2 10.0 0.2 C2A A:HEM301 4.2 9.2 0.8 C3D A:HEM301 4.2 9.9 0.2 CG A:HIS70 4.2 9.3 1.0 C2A A:HEM301 4.3 9.2 0.2 C2C A:HEM301 4.3 10.0 0.8 C3A A:HEM301 4.3 9.2 0.2 C3C A:HEM301 4.3 10.1 0.8 C3B A:HEM301 4.4 10.4 0.2 C2B A:HEM301 4.4 9.9 0.2 C3D A:HEM301 4.4 9.9 0.8 C2D A:HEM301 4.4 9.9 0.8 O B:TYR103 4.5 10.4 1.0 O B:HOH681 4.7 14.9 1.0

Iron binding site 3 out of 4 in the Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe405 b:8.6 occ:0.18 FE B:HEM405 0.0 8.6 0.2 FE B:HEM405 0.1 8.7 0.8 NC B:HEM405 1.9 9.0 0.8 ND B:HEM405 1.9 8.8 0.8 NB B:HEM405 2.0 8.8 0.2 NE2 B:HIS70 2.0 8.9 1.0 NA B:HEM405 2.0 8.7 0.2 NB B:HEM405 2.0 8.8 0.8 NC B:HEM405 2.0 9.0 0.2 O A:HOH456 2.1 9.8 1.0 ND B:HEM405 2.1 8.8 0.2 NA B:HEM405 2.1 8.7 0.8 C4C B:HEM405 2.9 9.1 0.8 C1C B:HEM405 2.9 9.1 0.8 C1D B:HEM405 3.0 9.2 0.8 CD2 B:HIS70 3.0 8.8 1.0 CE1 B:HIS70 3.0 9.7 1.0 C1B B:HEM405 3.0 9.1 0.2 C4D B:HEM405 3.0 9.4 0.8 C4B B:HEM405 3.0 9.2 0.2 C4B B:HEM405 3.0 9.2 0.8 C4A B:HEM405 3.0 8.9 0.2 C1C B:HEM405 3.1 9.1 0.2 C4C B:HEM405 3.1 9.1 0.2 C1A B:HEM405 3.1 8.9 0.2 C1A B:HEM405 3.1 8.9 0.8 C1D B:HEM405 3.1 9.2 0.2 C4D B:HEM405 3.1 9.4 0.2 C1B B:HEM405 3.1 9.1 0.8 C4A B:HEM405 3.1 8.9 0.8 CHD B:HEM405 3.3 9.4 0.8 CHC B:HEM405 3.3 9.4 0.8 CHB B:HEM405 3.4 9.3 0.2 CHC B:HEM405 3.4 9.4 0.2 CHA B:HEM405 3.4 9.3 0.8 CHD B:HEM405 3.5 9.4 0.2 CHA B:HEM405 3.5 9.3 0.2 CHB B:HEM405 3.5 9.3 0.8 ND1 B:HIS70 4.1 10.0 1.0 CG B:HIS70 4.1 9.3 1.0 C2C B:HEM405 4.1 9.6 0.8 C3C B:HEM405 4.2 9.6 0.8 C2D B:HEM405 4.2 10.0 0.8 C2B B:HEM405 4.2 9.8 0.2 C3D B:HEM405 4.2 10.1 0.8 O A:PHE105 4.2 9.3 1.0 C3B B:HEM405 4.2 10.1 0.2 O A:HOH591 4.2 18.5 1.0 C3A B:HEM405 4.3 9.3 0.2 C2C B:HEM405 4.3 9.6 0.2 C3C B:HEM405 4.3 9.6 0.2 C2A B:HEM405 4.3 9.2 0.2 C3B B:HEM405 4.3 10.1 0.8 C2D B:HEM405 4.3 10.0 0.2 C3D B:HEM405 4.3 10.1 0.2 C2B B:HEM405 4.3 9.8 0.8 C2A B:HEM405 4.4 9.2 0.8 C3A B:HEM405 4.4 9.3 0.8 O A:TYR103 4.4 10.2 1.0 O A:HOH533 4.7 14.1 1.0

Iron binding site 4 out of 4 in the Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Flavocytochrome ANF3 From Azotobacter Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe405 b:8.7 occ:0.82 FE B:HEM405 0.0 8.7 0.8 FE B:HEM405 0.1 8.6 0.2 ND B:HEM405 2.0 8.8 0.2 NA B:HEM405 2.0 8.7 0.8 ND B:HEM405 2.0 8.8 0.8 NB B:HEM405 2.0 8.8 0.8 NC B:HEM405 2.0 9.0 0.8 NE2 B:HIS70 2.0 8.9 1.0 NC B:HEM405 2.0 9.0 0.2 NA B:HEM405 2.1 8.7 0.2 O A:HOH456 2.1 9.8 1.0 NB B:HEM405 2.1 8.8 0.2 CE1 B:HIS70 2.9 9.7 1.0 C1D B:HEM405 3.0 9.2 0.2 C4C B:HEM405 3.0 9.1 0.2 C4D B:HEM405 3.0 9.4 0.8 C1A B:HEM405 3.0 8.9 0.8 CD2 B:HIS70 3.0 8.8 1.0 C4B B:HEM405 3.0 9.2 0.8 C4D B:HEM405 3.0 9.4 0.2 C4A B:HEM405 3.0 8.9 0.8 C1C B:HEM405 3.0 9.1 0.8 C1B B:HEM405 3.0 9.1 0.8 C1D B:HEM405 3.0 9.2 0.8 C4C B:HEM405 3.0 9.1 0.8 C1C B:HEM405 3.0 9.1 0.2 C1A B:HEM405 3.1 8.9 0.2 C4B B:HEM405 3.1 9.2 0.2 C1B B:HEM405 3.1 9.1 0.2 C4A B:HEM405 3.1 8.9 0.2 CHD B:HEM405 3.3 9.4 0.2 CHC B:HEM405 3.4 9.4 0.8 CHA B:HEM405 3.4 9.3 0.8 CHB B:HEM405 3.4 9.3 0.8 CHD B:HEM405 3.4 9.4 0.8 CHA B:HEM405 3.4 9.3 0.2 CHC B:HEM405 3.4 9.4 0.2 CHB B:HEM405 3.5 9.3 0.2 ND1 B:HIS70 4.1 10.0 1.0 CG B:HIS70 4.1 9.3 1.0 O A:PHE105 4.2 9.3 1.0 C3C B:HEM405 4.2 9.6 0.2 C2D B:HEM405 4.2 10.0 0.2 O A:HOH591 4.2 18.5 1.0 C3D B:HEM405 4.2 10.1 0.2 C2C B:HEM405 4.2 9.6 0.2 C2C B:HEM405 4.2 9.6 0.8 C3D B:HEM405 4.2 10.1 0.8 C3B B:HEM405 4.3 10.1 0.8 C2A B:HEM405 4.3 9.2 0.8 C2D B:HEM405 4.3 10.0 0.8 C2B B:HEM405 4.3 9.8 0.8 C3A B:HEM405 4.3 9.3 0.8 C3C B:HEM405 4.3 9.6 0.8 C2A B:HEM405 4.3 9.2 0.2 C3B B:HEM405 4.3 10.1 0.2 C2B B:HEM405 4.3 9.8 0.2 C3A B:HEM405 4.3 9.3 0.2 O A:TYR103 4.5 10.2 1.0 O A:HOH533 4.7 14.1 1.0

F.Varghese, B.V.Kabasakal, C.A.R.Cotton, J.Schumacher, A.W.Rutherford, A.Fantuzzi, J.W.Murray. A Low-Potential Terminal Oxidase Associated with the Iron-Only Nitrogenase From the Nitrogen-Fixing Bacteriumazotobacter Vinelandii. J.Biol.Chem. V. 294 9367 2019.
ISSN: ESSN 1083-351X
PubMed: 31043481
DOI: 10.1074/JBC.RA118.007285