Iron in PDB 9hb9: A. Vinelandii Nitrogenase Mofe Protein ANC1A

All present enzymatic activity of A. Vinelandii Nitrogenase Mofe Protein ANC1A:
1.18.6.1;

The structure of A. Vinelandii Nitrogenase Mofe Protein ANC1A, PDB code: 9hb9 was solved by F.Detemple, B.Kacar, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.29, 138.615, 208.581, 90, 90, 90
R / Rfree (%)	16.9 / 22

The structure of A. Vinelandii Nitrogenase Mofe Protein ANC1A also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Magnesium	(Mg)	2 atoms

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 A. Vinelandii Nitrogenase Mofe Protein ANC1A (pdb code 9hb9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the A. Vinelandii Nitrogenase Mofe Protein ANC1A, PDB code: 9hb9:
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 A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:45.5 occ:1.00 FE1 A:ICS501 0.0 45.5 1.0 S2A A:ICS501 2.3 48.5 1.0 S4A A:ICS501 2.3 46.5 1.0 S1A A:ICS501 2.3 48.6 1.0 SG A:CYS275 2.4 49.5 1.0 FE4 A:ICS501 2.7 47.5 1.0 FE2 A:ICS501 2.7 46.9 1.0 FE3 A:ICS501 2.7 50.8 1.0 CB A:CYS275 3.4 44.9 1.0 CX A:ICS501 3.5 49.0 1.0 OG A:SER278 4.0 48.8 1.0 CB A:LEU358 4.1 47.8 1.0 CB A:SER278 4.3 44.3 1.0 CD2 A:LEU358 4.5 47.8 1.0 CE2 A:TYR229 4.6 37.0 1.0 CA A:CYS275 4.6 45.3 1.0 S3A A:ICS501 4.8 46.2 1.0 S2B A:ICS501 4.8 47.5 1.0 S5A A:ICS501 4.9 47.9 1.0 N A:LEU358 4.9 48.2 1.0 CG A:LEU358 5.0 47.9 1.0 N A:SER278 5.0 43.3 1.0 FE7 A:ICS501 5.0 47.3 1.0

Iron binding site 2 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:46.9 occ:1.00 FE2 A:ICS501 0.0 46.9 1.0 CX A:ICS501 2.0 49.0 1.0 S2B A:ICS501 2.2 47.5 1.0 S2A A:ICS501 2.2 48.5 1.0 S1A A:ICS501 2.3 48.6 1.0 FE6 A:ICS501 2.6 50.5 1.0 FE1 A:ICS501 2.7 45.5 1.0 FE3 A:ICS501 2.7 50.8 1.0 FE4 A:ICS501 2.7 47.5 1.0 FE7 A:ICS501 3.7 47.3 1.0 FE5 A:ICS501 3.8 47.4 1.0 CZ A:PHE381 3.8 56.7 1.0 S4A A:ICS501 3.9 46.5 1.0 NE2 A:HIS195 4.1 31.6 1.0 S3B A:ICS501 4.2 48.1 1.0 S1B A:ICS501 4.2 46.7 1.0 CE1 A:HIS195 4.2 33.9 1.0 CE1 A:PHE381 4.3 56.0 1.0 CG1 A:VAL70 4.4 33.5 1.0 S5A A:ICS501 4.5 47.9 1.0 S3A A:ICS501 4.6 46.2 1.0 SG A:CYS275 4.7 49.5 1.0 CG2 A:VAL70 4.8 33.2 1.0 CE2 A:PHE381 4.9 59.2 1.0 N A:GLY357 4.9 47.3 1.0

Iron binding site 3 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:50.8 occ:1.00 FE3 A:ICS501 0.0 50.8 1.0 CX A:ICS501 2.0 49.0 1.0 S4A A:ICS501 2.2 46.5 1.0 S5A A:ICS501 2.2 47.9 1.0 S2A A:ICS501 2.3 48.5 1.0 FE7 A:ICS501 2.6 47.3 1.0 FE1 A:ICS501 2.7 45.5 1.0 FE2 A:ICS501 2.7 46.9 1.0 FE4 A:ICS501 2.7 47.5 1.0 FE5 A:ICS501 3.7 47.4 1.0 FE6 A:ICS501 3.7 50.5 1.0 S1A A:ICS501 3.9 48.6 1.0 NH2 A:ARG96 4.1 50.8 1.0 CD2 A:TYR229 4.2 36.1 1.0 S4B A:ICS501 4.2 43.6 1.0 S3B A:ICS501 4.2 48.1 1.0 CE2 A:TYR229 4.5 37.0 1.0 S2B A:ICS501 4.5 47.5 1.0 S3A A:ICS501 4.6 46.2 1.0 SG A:CYS275 4.9 49.5 1.0

Iron binding site 4 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:47.5 occ:1.00 FE4 A:ICS501 0.0 47.5 1.0 CX A:ICS501 2.0 49.0 1.0 S3A A:ICS501 2.2 46.2 1.0 S1A A:ICS501 2.3 48.6 1.0 S4A A:ICS501 2.3 46.5 1.0 FE5 A:ICS501 2.6 47.4 1.0 FE1 A:ICS501 2.7 45.5 1.0 FE3 A:ICS501 2.7 50.8 1.0 FE2 A:ICS501 2.7 46.9 1.0 FE7 A:ICS501 3.7 47.3 1.0 FE6 A:ICS501 3.8 50.5 1.0 S2A A:ICS501 3.9 48.5 1.0 N A:LEU358 3.9 48.2 1.0 N A:GLY357 3.9 47.3 1.0 CB A:LEU358 3.9 47.8 1.0 S1B A:ICS501 4.2 46.7 1.0 S4B A:ICS501 4.3 43.6 1.0 CA A:LEU358 4.5 46.9 1.0 C A:GLY357 4.5 48.7 1.0 CA A:GLY357 4.6 49.1 1.0 N A:ARG359 4.6 45.6 1.0 S5A A:ICS501 4.6 47.9 1.0 S2B A:ICS501 4.6 47.5 1.0 CG A:ARG359 4.6 43.6 1.0 SG A:CYS275 4.7 49.5 1.0 CA A:GLY356 4.8 46.6 1.0 CZ A:PHE381 4.8 56.7 1.0 CD A:ARG359 4.9 42.1 1.0 C A:GLY356 4.9 46.4 1.0 NE A:ARG359 5.0 40.0 1.0 N A:GLY356 5.0 46.0 1.0

Iron binding site 5 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:47.4 occ:1.00 FE5 A:ICS501 0.0 47.4 1.0 CX A:ICS501 2.0 49.0 1.0 S4B A:ICS501 2.3 43.6 1.0 S1B A:ICS501 2.3 46.7 1.0 S3A A:ICS501 2.3 46.2 1.0 FE4 A:ICS501 2.6 47.5 1.0 FE7 A:ICS501 2.6 47.3 1.0 MO1 A:ICS501 2.7 47.8 1.0 FE6 A:ICS501 2.7 50.5 1.0 ND1 A:HIS442 3.5 51.1 1.0 FE3 A:ICS501 3.7 50.8 1.0 FE2 A:ICS501 3.8 46.9 1.0 CE1 A:HIS442 3.8 48.0 1.0 S3B A:ICS501 3.9 48.1 1.0 N A:GLY356 3.9 46.0 1.0 CG1 A:VAL355 4.0 41.2 1.0 CA A:GLY356 4.1 46.6 1.0 O7 A:HCA502 4.2 53.6 1.0 S1A A:ICS501 4.3 48.6 1.0 S4A A:ICS501 4.3 46.5 1.0 O5 A:HCA502 4.3 51.6 1.0 S5A A:ICS501 4.5 47.9 1.0 S2B A:ICS501 4.6 47.5 1.0 CG A:HIS442 4.6 47.9 1.0 CD A:ARG359 4.6 42.1 1.0 N A:GLY357 4.6 47.3 1.0 NE2 A:HIS442 4.8 45.4 1.0 CB A:VAL355 4.9 43.7 1.0 CZ A:PHE381 4.9 56.7 1.0 NE A:ARG359 4.9 40.0 1.0 C A:GLY356 5.0 46.4 1.0

Iron binding site 6 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:50.5 occ:1.00 FE6 A:ICS501 0.0 50.5 1.0 CX A:ICS501 2.0 49.0 1.0 S2B A:ICS501 2.2 47.5 1.0 S3B A:ICS501 2.2 48.1 1.0 S1B A:ICS501 2.2 46.7 1.0 FE2 A:ICS501 2.6 46.9 1.0 FE7 A:ICS501 2.6 47.3 1.0 FE5 A:ICS501 2.7 47.4 1.0 MO1 A:ICS501 2.7 47.8 1.0 O7 A:HCA502 3.1 53.6 1.0 FE3 A:ICS501 3.7 50.8 1.0 FE4 A:ICS501 3.8 47.5 1.0 S4B A:ICS501 3.9 43.6 1.0 CZ A:PHE381 3.9 56.7 1.0 O5 A:HCA502 4.1 51.6 1.0 S1A A:ICS501 4.3 48.6 1.0 S2A A:ICS501 4.3 48.5 1.0 CE2 A:PHE381 4.3 59.2 1.0 C3 A:HCA502 4.4 53.4 1.0 CG2 A:VAL70 4.4 33.2 1.0 ND1 A:HIS442 4.5 51.1 1.0 S5A A:ICS501 4.5 47.9 1.0 S3A A:ICS501 4.6 46.2 1.0 O2 A:HCA502 4.6 44.5 1.0 C7 A:HCA502 4.8 51.5 1.0 CE1 A:HIS442 4.8 48.0 1.0 CA A:GLY356 5.0 46.6 1.0 C2 A:HCA502 5.0 51.9 1.0

Iron binding site 7 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:47.3 occ:1.00 FE7 A:ICS501 0.0 47.3 1.0 CX A:ICS501 2.0 49.0 1.0 S5A A:ICS501 2.2 47.9 1.0 S4B A:ICS501 2.2 43.6 1.0 S3B A:ICS501 2.3 48.1 1.0 FE3 A:ICS501 2.6 50.8 1.0 FE6 A:ICS501 2.6 50.5 1.0 FE5 A:ICS501 2.6 47.4 1.0 MO1 A:ICS501 2.7 47.8 1.0 O5 A:HCA502 3.3 51.6 1.0 FE2 A:ICS501 3.7 46.9 1.0 FE4 A:ICS501 3.7 47.5 1.0 S1B A:ICS501 3.8 46.7 1.0 O7 A:HCA502 4.0 53.6 1.0 NH2 A:ARG96 4.2 50.8 1.0 S4A A:ICS501 4.3 46.5 1.0 S2A A:ICS501 4.3 48.5 1.0 ND1 A:HIS442 4.3 51.1 1.0 C7 A:HCA502 4.3 51.5 1.0 NE A:ARG96 4.4 45.6 1.0 S2B A:ICS501 4.4 47.5 1.0 S3A A:ICS501 4.6 46.2 1.0 CZ A:ARG96 4.8 49.3 1.0 CZ A:ARG359 4.8 40.4 1.0 NH1 A:ARG359 4.8 41.2 1.0 C3 A:HCA502 4.9 53.4 1.0 FE1 A:ICS501 5.0 45.5 1.0

Iron binding site 8 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:28.4 occ:1.00 FE1 B:CLF601 0.0 28.4 1.0 S3A B:CLF601 2.2 27.4 1.0 S2A B:CLF601 2.3 27.9 1.0 SG A:CYS154 2.3 36.1 1.0 S1 B:CLF601 2.4 29.5 1.0 FE2 B:CLF601 2.5 26.8 1.0 FE4 B:CLF601 2.6 30.9 1.0 FE3 B:CLF601 2.8 26.0 1.0 CB A:CYS154 3.5 38.0 1.0 CA A:GLY185 3.6 40.0 1.0 S4A B:CLF601 3.8 27.2 1.0 N A:CYS154 3.9 37.5 1.0 N A:GLY185 4.0 40.1 1.0 SG B:CYS95 4.2 34.8 1.0 CA A:CYS154 4.2 38.2 1.0 OG B:SER92 4.3 34.0 0.6 FE8 B:CLF601 4.3 30.8 1.0 CB B:SER92 4.5 35.5 1.0 FE5 B:CLF601 4.5 34.0 1.0 C A:GLY185 4.6 38.0 1.0 SG A:CYS88 4.7 34.0 1.0 FE6 B:CLF601 4.9 31.3 1.0 SG A:CYS62 4.9 32.8 1.0 SG B:CYS153 4.9 33.4 1.0 C A:GLU153 5.0 37.4 1.0

Iron binding site 9 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:26.8 occ:1.00 FE2 B:CLF601 0.0 26.8 1.0 S4A B:CLF601 2.2 27.2 1.0 S2A B:CLF601 2.3 27.9 1.0 SG B:CYS95 2.3 34.8 1.0 FE1 B:CLF601 2.5 28.4 1.0 S1 B:CLF601 2.5 29.5 1.0 FE4 B:CLF601 2.6 30.9 1.0 FE3 B:CLF601 2.7 26.0 1.0 FE8 B:CLF601 2.8 30.8 1.0 N B:CYS95 3.5 32.4 1.0 FE5 B:CLF601 3.6 34.0 1.0 CB B:CYS95 3.6 35.0 1.0 CA B:CYS95 3.7 34.6 1.0 S3A B:CLF601 3.7 27.4 1.0 S4B B:CLF601 3.8 33.6 1.0 C B:GLY94 4.1 33.4 1.0 SG A:CYS154 4.5 36.1 1.0 SG A:CYS88 4.5 34.0 1.0 CA B:GLY94 4.6 34.9 1.0 CB B:SER92 4.6 35.5 1.0 FE6 B:CLF601 4.6 31.3 1.0 O B:GLY94 4.7 34.5 1.0 SG A:CYS62 4.8 32.8 1.0 OG B:SER92 4.8 34.0 0.6

Iron binding site 10 out of 30 in the A. Vinelandii Nitrogenase Mofe Protein ANC1A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of A. Vinelandii Nitrogenase Mofe Protein ANC1A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:26.0 occ:1.00 FE3 B:CLF601 0.0 26.0 1.0 S2A B:CLF601 2.3 27.9 1.0 S4A B:CLF601 2.3 27.2 1.0 SG A:CYS62 2.4 32.8 1.0 S3A B:CLF601 2.4 27.4 1.0 FE2 B:CLF601 2.7 26.8 1.0 FE4 B:CLF601 2.7 30.9 1.0 FE1 B:CLF601 2.8 28.4 1.0 CB A:CYS62 3.4 33.4 1.0 CA A:GLY185 3.8 40.0 1.0 CB A:TYR64 4.1 28.8 1.0 S1 B:CLF601 4.2 29.5 1.0 CA B:GLY94 4.3 34.9 1.0 C B:GLY94 4.5 33.4 1.0 N A:GLY185 4.6 40.1 1.0 CG A:TYR64 4.6 28.3 1.0 N B:CYS95 4.7 32.4 1.0 CD1 A:TYR64 4.7 27.8 1.0 CA A:CYS62 4.8 32.9 1.0 SG A:CYS154 4.8 36.1 1.0 SG B:CYS95 4.9 34.8 1.0 SG A:CYS88 4.9 34.0 1.0 CE2 B:TYR98 4.9 32.3 1.0 O B:GLY94 5.0 34.5 1.0 N A:TYR64 5.0 29.9 1.0

B.Cuevas-Zuviria, F.Detemple, K.Amritkar, A.K.Garcia, L.C.Seefeldt, O.Einsle, B.Kacar. Structural Evolution of Nitrogenase Enzymes Over Geologic Time Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.105613.3