Iron in PDB 8boq: A. Vinelandii Fe-Nitrogenase Fefe Protein

All present enzymatic activity of A. Vinelandii Fe-Nitrogenase Fefe Protein:
1.18.6.1;

The structure of A. Vinelandii Fe-Nitrogenase Fefe Protein, PDB code: 8boq was solved by C.Trncik, F.Detemple, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.969, 151.048, 158.863, 90, 90, 90
R / Rfree (%)	16.9 / 21.6

The structure of A. Vinelandii Fe-Nitrogenase Fefe Protein also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the A. Vinelandii Fe-Nitrogenase Fefe Protein (pdb code 8boq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the A. Vinelandii Fe-Nitrogenase Fefe Protein, PDB code: 8boq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:13.4 occ:1.00 FE8 A:S5Q601 0.0 13.4 1.0 O6 A:HCA602 2.1 14.1 1.0 O7 A:HCA602 2.1 13.4 1.0 ND1 A:HIS423 2.2 12.2 1.0 S1B A:S5Q601 2.3 14.8 1.0 S4B A:S5Q601 2.3 13.8 1.0 S3B A:S5Q601 2.4 16.1 1.0 FE7 A:S5Q601 2.8 14.8 1.0 FE5 A:S5Q601 2.9 15.2 1.0 FE6 A:S5Q601 2.9 17.0 1.0 C7 A:HCA602 3.0 14.0 1.0 C3 A:HCA602 3.1 13.7 1.0 CE1 A:HIS423 3.2 13.2 1.0 CG A:HIS423 3.3 13.2 1.0 CB A:HIS423 3.6 13.7 1.0 CX A:S5Q601 3.8 16.0 1.0 C2 A:HCA602 4.0 14.6 1.0 O A:HOH887 4.2 8.8 1.0 O5 A:HCA602 4.2 12.2 1.0 C4 A:HCA602 4.2 13.9 1.0 C5 A:HCA602 4.3 14.4 1.0 NE2 A:HIS423 4.3 12.2 1.0 CD2 A:HIS423 4.4 13.1 1.0 CA A:HIS423 4.4 13.9 1.0 NZ A:LYS83 4.5 17.4 1.0 O2 A:HCA602 4.6 16.4 1.0 O A:O604 4.9 16.1 0.5 C1 A:HCA602 4.9 15.8 1.0

Iron binding site 2 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:15.2 occ:1.00 FE5 A:S5Q601 0.0 15.2 1.0 CX A:S5Q601 2.0 16.0 1.0 S4B A:S5Q601 2.2 13.8 1.0 S1B A:S5Q601 2.2 14.8 1.0 S3A A:S5Q601 2.3 13.8 1.0 FE4 A:S5Q601 2.6 16.1 1.0 FE7 A:S5Q601 2.6 14.8 1.0 FE6 A:S5Q601 2.6 17.0 1.0 FE8 A:S5Q601 2.9 13.4 1.0 FE2 A:S5Q601 3.7 15.6 1.0 FE3 A:S5Q601 3.7 15.9 1.0 S3B A:S5Q601 3.8 16.1 1.0 ND1 A:HIS423 3.8 12.2 1.0 O A:O604 4.2 16.1 0.5 N A:GLY336 4.2 19.7 1.0 CE1 A:HIS423 4.2 13.2 1.0 S4A A:S5Q601 4.3 17.1 1.0 N A:GLY337 4.3 16.5 1.0 S1A A:S5Q601 4.3 16.4 1.0 S2B A:S5Q601 4.5 15.3 0.5 S5A A:S5Q601 4.5 15.8 1.0 CD A:LYS339 4.6 19.8 1.0 CA A:GLY336 4.6 18.2 1.0 CE A:LYS339 4.6 20.3 1.0 NZ A:LYS339 4.6 21.6 1.0 CG A:HIS423 4.7 13.2 1.0 O7 A:HCA602 4.7 13.4 1.0 O6 A:HCA602 4.7 14.1 1.0 CZ A:PHE362 4.8 23.8 1.0 C A:GLY336 4.9 17.5 1.0 FE1 A:S5Q601 5.0 16.1 1.0 CB A:PRO335 5.0 19.3 1.0

Iron binding site 3 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:14.8 occ:1.00 FE7 A:S5Q601 0.0 14.8 1.0 CX A:S5Q601 2.0 16.0 1.0 S4B A:S5Q601 2.2 13.8 1.0 S3B A:S5Q601 2.3 16.1 1.0 S5A A:S5Q601 2.3 15.8 1.0 FE6 A:S5Q601 2.6 17.0 1.0 FE3 A:S5Q601 2.6 15.9 1.0 FE5 A:S5Q601 2.6 15.2 1.0 FE8 A:S5Q601 2.8 13.4 1.0 NZ A:LYS83 3.5 17.4 1.0 S1B A:S5Q601 3.7 14.8 1.0 FE2 A:S5Q601 3.7 15.6 1.0 FE4 A:S5Q601 3.7 16.1 1.0 O6 A:HCA602 3.8 14.1 1.0 O A:HOH887 3.9 8.8 1.0 O A:O604 4.2 16.1 0.5 S2A A:S5Q601 4.3 16.5 1.0 S4A A:S5Q601 4.4 17.1 1.0 S2B A:S5Q601 4.4 15.3 0.5 S3A A:S5Q601 4.5 13.8 1.0 O A:HOH877 4.5 13.2 1.0 O A:HOH878 4.6 22.1 1.0 NZ A:LYS339 4.6 21.6 1.0 O7 A:HCA602 4.6 13.4 1.0 CG1 A:VAL57 4.7 15.4 1.0 ND1 A:HIS423 4.7 12.2 1.0 C7 A:HCA602 4.8 14.0 1.0 CE A:LYS83 4.8 16.0 1.0

Iron binding site 4 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:17.0 occ:1.00 FE6 A:S5Q601 0.0 17.0 1.0 O A:O604 2.0 16.1 0.5 CX A:S5Q601 2.0 16.0 1.0 S2B A:S5Q601 2.2 15.3 0.5 S3B A:S5Q601 2.2 16.1 1.0 S1B A:S5Q601 2.2 14.8 1.0 FE2 A:S5Q601 2.6 15.6 1.0 FE7 A:S5Q601 2.6 14.8 1.0 FE5 A:S5Q601 2.6 15.2 1.0 FE8 A:S5Q601 2.9 13.4 1.0 FE4 A:S5Q601 3.7 16.1 1.0 FE3 A:S5Q601 3.7 15.9 1.0 NE2 A:GLN176 3.8 15.7 0.5 S4B A:S5Q601 3.8 13.8 1.0 CZ A:PHE362 3.8 23.8 1.0 OE1 A:GLN176 3.9 15.7 0.5 O7 A:HCA602 4.0 13.4 1.0 CE2 A:PHE362 4.1 23.3 1.0 CD A:GLN176 4.3 16.8 0.5 S2A A:S5Q601 4.3 16.5 1.0 S1A A:S5Q601 4.4 16.4 1.0 CG1 A:VAL57 4.4 15.4 1.0 CG2 A:VAL57 4.4 15.6 1.0 S5A A:S5Q601 4.5 15.8 1.0 S3A A:S5Q601 4.5 13.8 1.0 O6 A:HCA602 4.6 14.1 1.0 ND1 A:HIS423 4.8 12.2 1.0 CE1 A:PHE362 5.0 22.5 1.0

Iron binding site 5 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:16.1 occ:1.00 FE4 A:S5Q601 0.0 16.1 1.0 CX A:S5Q601 2.0 16.0 1.0 S3A A:S5Q601 2.2 13.8 1.0 S1A A:S5Q601 2.3 16.4 1.0 S4A A:S5Q601 2.3 17.1 1.0 FE5 A:S5Q601 2.6 15.2 1.0 FE2 A:S5Q601 2.6 15.6 1.0 FE1 A:S5Q601 2.6 16.1 1.0 FE3 A:S5Q601 2.6 15.9 1.0 FE6 A:S5Q601 3.7 17.0 1.0 FE7 A:S5Q601 3.7 14.8 1.0 S2A A:S5Q601 3.8 16.5 1.0 N A:SER338 3.9 18.7 1.0 O A:O604 4.2 16.1 0.5 S4B A:S5Q601 4.2 13.8 1.0 CA A:GLY337 4.3 17.1 1.0 S1B A:S5Q601 4.3 14.8 1.0 CB A:SER338 4.4 21.6 1.0 N A:GLY337 4.4 16.5 1.0 C A:GLY337 4.4 17.5 1.0 S2B A:S5Q601 4.5 15.3 0.5 SG A:CYS257 4.5 15.4 1.0 S5A A:S5Q601 4.6 15.8 1.0 N A:LYS339 4.6 18.0 1.0 CA A:SER338 4.7 19.4 1.0 OG A:SER338 4.7 25.1 1.0 CZ A:PHE362 4.8 23.8 1.0 CE A:LYS339 4.8 20.3 1.0 CG A:LYS339 4.8 19.8 1.0 O A:HOH939 4.8 26.9 1.0 CD A:LYS339 4.9 19.8 1.0

Iron binding site 6 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:16.1 occ:1.00 FE1 A:S5Q601 0.0 16.1 1.0 S2A A:S5Q601 2.2 16.5 1.0 SG A:CYS257 2.3 15.4 1.0 S4A A:S5Q601 2.3 17.1 1.0 S1A A:S5Q601 2.3 16.4 1.0 FE4 A:S5Q601 2.6 16.1 1.0 FE3 A:S5Q601 2.6 15.9 1.0 FE2 A:S5Q601 2.7 15.6 1.0 CB A:CYS257 3.3 16.0 1.0 CX A:S5Q601 3.4 16.0 1.0 OG A:SER338 3.9 25.1 1.0 OG A:SER260 3.9 17.2 1.0 CB A:SER260 4.1 16.5 1.0 CB A:SER338 4.1 21.6 1.0 CE2 A:TYR211 4.4 15.2 1.0 O A:HOH939 4.6 26.9 1.0 CA A:CYS257 4.6 17.1 1.0 O A:O604 4.6 16.1 0.5 S3A A:S5Q601 4.7 13.8 1.0 CD2 A:TYR211 4.8 15.8 1.0 N A:SER338 4.8 18.7 1.0 N A:SER260 4.8 17.0 1.0 S5A A:S5Q601 4.8 15.8 1.0 S2B A:S5Q601 4.9 15.3 0.5 FE5 A:S5Q601 5.0 15.2 1.0

Iron binding site 7 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:15.9 occ:1.00 FE3 A:S5Q601 0.0 15.9 1.0 CX A:S5Q601 2.0 16.0 1.0 S5A A:S5Q601 2.2 15.8 1.0 S4A A:S5Q601 2.3 17.1 1.0 S2A A:S5Q601 2.3 16.5 1.0 FE1 A:S5Q601 2.6 16.1 1.0 FE4 A:S5Q601 2.6 16.1 1.0 FE7 A:S5Q601 2.6 14.8 1.0 FE2 A:S5Q601 2.7 15.6 1.0 FE5 A:S5Q601 3.7 15.2 1.0 FE6 A:S5Q601 3.7 17.0 1.0 S1A A:S5Q601 3.9 16.4 1.0 CD2 A:TYR211 4.1 15.8 1.0 S4B A:S5Q601 4.2 13.8 1.0 O A:O604 4.2 16.1 0.5 O A:HOH878 4.2 22.1 1.0 S3B A:S5Q601 4.4 16.1 1.0 O A:HOH952 4.4 15.0 1.0 S3A A:S5Q601 4.4 13.8 1.0 S2B A:S5Q601 4.5 15.3 0.5 CE2 A:TYR211 4.5 15.2 1.0 CG1 A:VAL57 4.5 15.4 1.0 SG A:CYS257 4.8 15.4 1.0 O A:HOH877 4.9 13.2 1.0

Iron binding site 8 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:15.6 occ:1.00 FE2 A:S5Q601 0.0 15.6 1.0 O A:O604 2.0 16.1 0.5 CX A:S5Q601 2.0 16.0 1.0 S2B A:S5Q601 2.2 15.3 0.5 S1A A:S5Q601 2.3 16.4 1.0 S2A A:S5Q601 2.3 16.5 1.0 FE4 A:S5Q601 2.6 16.1 1.0 FE6 A:S5Q601 2.6 17.0 1.0 FE1 A:S5Q601 2.7 16.1 1.0 FE3 A:S5Q601 2.7 15.9 1.0 FE5 A:S5Q601 3.7 15.2 1.0 FE7 A:S5Q601 3.7 14.8 1.0 CZ A:PHE362 3.8 23.8 1.0 S4A A:S5Q601 3.9 17.1 1.0 CG1 A:VAL57 4.2 15.4 1.0 CE1 A:PHE362 4.3 22.5 1.0 S1B A:S5Q601 4.3 14.8 1.0 CE1 A:HIS180 4.3 17.1 1.0 OE1 A:GLN176 4.3 15.7 0.5 S3B A:S5Q601 4.3 16.1 1.0 NE2 A:HIS180 4.4 16.7 1.0 S3A A:S5Q601 4.5 13.8 1.0 S5A A:S5Q601 4.5 15.8 1.0 SG A:CYS257 4.6 15.4 1.0 CE2 A:PHE362 4.7 23.3 1.0 CB A:SER260 4.8 16.5 1.0

Iron binding site 9 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:17.6 occ:1.00 FE1 A:CLF603 0.0 17.6 1.0 SG A:CYS138 2.3 17.3 1.0 S2A A:CLF603 2.3 15.3 1.0 S3A A:CLF603 2.3 15.9 1.0 S1 A:CLF603 2.4 15.2 1.0 FE2 A:CLF603 2.5 16.6 1.0 FE4 A:CLF603 2.5 15.3 1.0 FE3 A:CLF603 2.9 13.8 1.0 CB A:CYS138 3.3 18.4 1.0 O B:HOH772 3.7 17.4 1.0 S4A A:CLF603 3.8 15.8 1.0 N A:CYS138 3.9 17.7 1.0 CA A:GLY170 4.0 17.4 1.0 SG B:CYS45 4.1 14.4 1.0 N A:GLY170 4.2 17.9 1.0 CA A:CYS138 4.2 17.5 1.0 SG A:CYS75 4.3 13.2 1.0 FE8 A:CLF603 4.4 16.5 1.0 FE5 A:CLF603 4.5 16.4 1.0 O A:HOH935 4.6 11.8 1.0 FE6 A:CLF603 4.9 19.5 1.0 SG A:CYS49 4.9 14.6 1.0 SG B:CYS104 5.0 16.4 1.0 C A:GLY170 5.0 17.2 1.0

Iron binding site 10 out of 32 in the A. Vinelandii Fe-Nitrogenase Fefe Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of A. Vinelandii Fe-Nitrogenase Fefe Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:16.6 occ:1.00 FE2 A:CLF603 0.0 16.6 1.0 S2A A:CLF603 2.3 15.3 1.0 S4A A:CLF603 2.3 15.8 1.0 SG B:CYS45 2.4 14.4 1.0 S1 A:CLF603 2.5 15.2 1.0 FE1 A:CLF603 2.5 17.6 1.0 FE4 A:CLF603 2.6 15.3 1.0 FE3 A:CLF603 2.8 13.8 1.0 FE8 A:CLF603 2.9 16.5 1.0 N B:CYS45 3.4 15.8 1.0 CB B:CYS45 3.7 14.3 1.0 CA B:CYS45 3.8 14.4 1.0 FE5 A:CLF603 3.8 16.4 1.0 S3A A:CLF603 3.8 15.9 1.0 S4B A:CLF603 3.9 14.1 1.0 C B:GLY44 4.0 14.9 1.0 O B:HOH772 4.0 17.4 1.0 CA B:GLY44 4.3 15.8 1.0 SG A:CYS138 4.5 17.3 1.0 N B:GLY44 4.5 14.6 1.0 SG A:CYS75 4.5 13.2 1.0 FE6 A:CLF603 4.6 19.5 1.0 O B:GLY44 4.6 14.2 1.0 O B:GLY42 4.7 17.3 1.0 SG A:CYS49 4.8 14.6 1.0 C B:GLY42 4.9 16.4 1.0 CA B:GLY42 4.9 16.6 1.0

C.Trncik, F.Detemple, O.Einsle. Iron-Only Fe-Nitrogenase Underscores Common Catalytic Principles in Biological Nitrogen Fixation Nat Catal 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-00952-1