Iron in PDB 8dpn: Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction

All present enzymatic activity of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction:
1.18.6.1;

The structure of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction also contains other interesting chemical elements:

Molybdenum

(Mo)

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 Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction (pdb code 8dpn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction, PDB code: 8dpn:
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 Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE1 A:ICS502 0.0 50.5 1.0 S2A A:ICS502 2.3 50.5 1.0 S4A A:ICS502 2.3 50.5 1.0 SG A:CYS275 2.3 1.5 1.0 S1A A:ICS502 2.3 50.5 1.0 FE4 A:ICS502 2.7 50.5 1.0 FE3 A:ICS502 2.7 50.5 1.0 FE2 A:ICS502 2.7 50.5 1.0 CB A:CYS275 3.4 17.7 1.0 CX A:ICS502 3.5 50.5 1.0 OG A:SER278 4.2 36.6 1.0 CB A:SER278 4.2 23.4 1.0 CB A:LEU358 4.4 39.0 1.0 CA A:CYS275 4.7 21.4 1.0 CE2 A:TYR229 4.7 23.9 1.0 S2B A:ICS502 4.8 50.5 1.0 S5A A:ICS502 4.8 50.5 1.0 S3A A:ICS502 4.8 50.5 1.0 N A:LEU358 4.9 35.6 1.0 N A:SER278 4.9 30.6 1.0 FE6 A:ICS502 5.0 50.5 1.0 FE7 A:ICS502 5.0 50.5 1.0

Iron binding site 2 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE2 A:ICS502 0.0 50.5 1.0 CX A:ICS502 2.0 50.5 1.0 S2B A:ICS502 2.2 50.5 1.0 S2A A:ICS502 2.2 50.5 1.0 S1A A:ICS502 2.3 50.5 1.0 FE6 A:ICS502 2.6 50.5 1.0 FE4 A:ICS502 2.7 50.5 1.0 FE1 A:ICS502 2.7 50.5 1.0 FE3 A:ICS502 2.7 50.5 1.0 FE5 A:ICS502 3.7 50.5 1.0 FE7 A:ICS502 3.7 50.5 1.0 S4A A:ICS502 3.9 50.5 1.0 CE1 A:HIS195 3.9 23.7 1.0 CZ A:PHE381 4.0 44.3 1.0 NE2 A:HIS195 4.2 26.8 1.0 S3B A:ICS502 4.2 50.5 1.0 S1B A:ICS502 4.2 50.5 1.0 CE1 A:PHE381 4.4 45.1 1.0 CG1 A:VAL70 4.5 29.0 1.0 S3A A:ICS502 4.5 50.5 1.0 S5A A:ICS502 4.5 50.5 1.0 SG A:CYS275 4.7 1.5 1.0 CG2 A:VAL70 4.9 25.6 1.0 ND1 A:HIS195 5.0 17.9 1.0 N A:GLY357 5.0 38.5 1.0

Iron binding site 3 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE3 A:ICS502 0.0 50.5 1.0 CX A:ICS502 2.0 50.5 1.0 S5A A:ICS502 2.2 50.5 1.0 S4A A:ICS502 2.2 50.5 1.0 S2A A:ICS502 2.3 50.5 1.0 FE7 A:ICS502 2.6 50.5 1.0 FE4 A:ICS502 2.6 50.5 1.0 FE1 A:ICS502 2.7 50.5 1.0 FE2 A:ICS502 2.7 50.5 1.0 FE6 A:ICS502 3.7 50.5 1.0 FE5 A:ICS502 3.7 50.5 1.0 S1A A:ICS502 3.9 50.5 1.0 NH2 A:ARG96 3.9 36.2 1.0 S3B A:ICS502 4.2 50.5 1.0 S4B A:ICS502 4.2 50.5 1.0 CD2 A:TYR229 4.3 28.1 1.0 S2B A:ICS502 4.5 50.5 1.0 S3A A:ICS502 4.5 50.5 1.0 CE2 A:TYR229 4.6 23.9 1.0 SG A:CYS275 4.8 1.5 1.0 CZ A:ARG96 5.0 29.5 1.0 NE A:ARG359 5.0 46.5 1.0

Iron binding site 4 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE4 A:ICS502 0.0 50.5 1.0 CX A:ICS502 2.0 50.5 1.0 S3A A:ICS502 2.2 50.5 1.0 S1A A:ICS502 2.3 50.5 1.0 S4A A:ICS502 2.3 50.5 1.0 FE5 A:ICS502 2.6 50.5 1.0 FE3 A:ICS502 2.6 50.5 1.0 FE2 A:ICS502 2.7 50.5 1.0 FE1 A:ICS502 2.7 50.5 1.0 FE7 A:ICS502 3.7 50.5 1.0 FE6 A:ICS502 3.7 50.5 1.0 S2A A:ICS502 3.8 50.5 1.0 N A:LEU358 4.0 35.6 1.0 N A:GLY357 4.0 38.5 1.0 S4B A:ICS502 4.3 50.5 1.0 S1B A:ICS502 4.3 50.5 1.0 CB A:LEU358 4.3 39.0 1.0 S5A A:ICS502 4.5 50.5 1.0 S2B A:ICS502 4.5 50.5 1.0 N A:ARG359 4.6 36.8 1.0 SG A:CYS275 4.7 1.5 1.0 CG A:ARG359 4.7 45.5 1.0 CA A:LEU358 4.7 38.1 1.0 CA A:GLY357 4.7 38.9 1.0 C A:GLY357 4.8 38.4 1.0 C A:GLY356 4.8 44.5 1.0 CA A:GLY356 4.9 41.0 1.0 CZ A:PHE381 4.9 44.3 1.0 NE A:ARG359 4.9 46.5 1.0 CD A:ARG359 5.0 46.1 1.0

Iron binding site 5 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE5 A:ICS502 0.0 50.5 1.0 CX A:ICS502 2.0 50.5 1.0 S4B A:ICS502 2.2 50.5 1.0 S3A A:ICS502 2.3 50.5 1.0 S1B A:ICS502 2.3 50.5 1.0 FE4 A:ICS502 2.6 50.5 1.0 FE7 A:ICS502 2.6 50.5 1.0 FE6 A:ICS502 2.6 50.5 1.0 MO1 A:ICS502 2.7 50.5 1.0 FE2 A:ICS502 3.7 50.5 1.0 FE3 A:ICS502 3.7 50.5 1.0 ND1 A:HIS442 3.8 24.6 1.0 S3B A:ICS502 3.9 50.5 1.0 N A:GLY356 4.1 40.3 1.0 CE1 A:HIS442 4.1 36.8 1.0 CA A:GLY356 4.2 41.0 1.0 CG2 A:ILE355 4.2 47.0 1.0 S1A A:ICS502 4.3 50.5 1.0 S4A A:ICS502 4.3 50.5 1.0 S2B A:ICS502 4.5 50.5 1.0 S5A A:ICS502 4.5 50.5 1.0 CD A:ARG359 4.7 46.1 1.0 N A:GLY357 4.7 38.5 1.0 NE A:ARG359 4.8 46.5 1.0 CG A:HIS442 4.8 29.6 1.0 CZ A:PHE381 4.9 44.3 1.0 C A:GLY356 4.9 44.5 1.0 CG A:ARG359 5.0 45.5 1.0

Iron binding site 6 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE6 A:ICS502 0.0 50.5 1.0 CX A:ICS502 2.0 50.5 1.0 S2B A:ICS502 2.2 50.5 1.0 S3B A:ICS502 2.2 50.5 1.0 S1B A:ICS502 2.2 50.5 1.0 FE2 A:ICS502 2.6 50.5 1.0 FE7 A:ICS502 2.6 50.5 1.0 FE5 A:ICS502 2.6 50.5 1.0 MO1 A:ICS502 2.7 50.5 1.0 FE3 A:ICS502 3.7 50.5 1.0 FE4 A:ICS502 3.7 50.5 1.0 S4B A:ICS502 3.8 50.5 1.0 O7 A:HCA501 4.1 49.1 1.0 CZ A:PHE381 4.1 44.3 1.0 O1 A:HCA501 4.2 49.1 1.0 S2A A:ICS502 4.2 50.5 1.0 S1A A:ICS502 4.3 50.5 1.0 CG2 A:VAL70 4.4 25.6 1.0 S5A A:ICS502 4.5 50.5 1.0 S3A A:ICS502 4.5 50.5 1.0 CE2 A:PHE381 4.6 42.5 1.0 ND1 A:HIS442 4.8 24.6 1.0 O5 A:HCA501 4.9 49.1 1.0 FE1 A:ICS502 5.0 50.5 1.0

Iron binding site 7 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:50.5 occ:1.00 FE7 A:ICS502 0.0 50.5 1.0 CX A:ICS502 2.0 50.5 1.0 S5A A:ICS502 2.2 50.5 1.0 S4B A:ICS502 2.2 50.5 1.0 S3B A:ICS502 2.2 50.5 1.0 FE3 A:ICS502 2.6 50.5 1.0 FE6 A:ICS502 2.6 50.5 1.0 FE5 A:ICS502 2.6 50.5 1.0 MO1 A:ICS502 2.7 50.5 1.0 FE2 A:ICS502 3.7 50.5 1.0 FE4 A:ICS502 3.7 50.5 1.0 S1B A:ICS502 3.8 50.5 1.0 NH2 A:ARG96 4.0 36.2 1.0 NE A:ARG96 4.1 30.8 1.0 O5 A:HCA501 4.2 49.1 1.0 S2A A:ICS502 4.3 50.5 1.0 S4A A:ICS502 4.3 50.5 1.0 S2B A:ICS502 4.4 50.5 1.0 S3A A:ICS502 4.5 50.5 1.0 CZ A:ARG96 4.6 29.5 1.0 NH2 A:ARG359 4.6 42.8 1.0 CZ A:ARG359 4.7 42.6 1.0 ND1 A:HIS442 4.7 24.6 1.0 NE A:ARG359 4.8 46.5 1.0 O7 A:HCA501 4.9 49.1 1.0 FE1 A:ICS502 5.0 50.5 1.0

Iron binding site 8 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:58.9 occ:1.00 FE1 B:CLF601 0.0 58.9 1.0 S3A B:CLF601 2.3 58.9 1.0 S2A B:CLF601 2.3 58.9 1.0 S1 B:CLF601 2.4 58.9 1.0 SG A:CYS154 2.4 21.8 1.0 FE2 B:CLF601 2.5 58.9 1.0 FE4 B:CLF601 2.7 58.9 1.0 FE3 B:CLF601 2.8 58.9 1.0 CB A:CYS154 3.6 16.5 1.0 S4A B:CLF601 3.8 58.9 1.0 CA A:GLY185 4.0 24.4 1.0 SG B:CYS95 4.1 21.6 1.0 N A:CYS154 4.1 24.3 1.0 N A:GLY185 4.2 25.2 1.0 FE8 B:CLF601 4.3 58.9 1.0 CA A:CYS154 4.4 19.8 1.0 FE5 B:CLF601 4.7 58.9 1.0 OG B:SER92 4.8 41.5 1.0 C A:GLY185 4.8 25.9 1.0 CB B:SER92 4.8 36.4 1.0 FE6 B:CLF601 4.8 58.9 1.0 SG A:CYS88 4.9 23.0 1.0

Iron binding site 9 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:58.9 occ:1.00 FE2 B:CLF601 0.0 58.9 1.0 S4A B:CLF601 2.3 58.9 1.0 S2A B:CLF601 2.3 58.9 1.0 SG B:CYS95 2.3 21.6 1.0 S1 B:CLF601 2.5 58.9 1.0 FE1 B:CLF601 2.5 58.9 1.0 FE4 B:CLF601 2.6 58.9 1.0 FE3 B:CLF601 2.7 58.9 1.0 FE8 B:CLF601 2.9 58.9 1.0 N B:CYS95 3.3 21.5 1.0 CB B:CYS95 3.5 23.2 1.0 CA B:CYS95 3.6 13.1 1.0 S3A B:CLF601 3.7 58.9 1.0 FE5 B:CLF601 3.9 58.9 1.0 S4B B:CLF601 4.0 58.9 1.0 C B:GLY94 4.0 18.8 1.0 CA B:GLY94 4.5 13.2 1.0 FE6 B:CLF601 4.6 58.9 1.0 O B:GLY94 4.7 28.5 1.0 SG A:CYS154 4.7 21.8 1.0 SG A:CYS88 4.8 23.0 1.0 SG A:CYS62 4.9 28.9 1.0 CB B:SER92 4.9 36.4 1.0 N B:GLY94 4.9 16.8 1.0

Iron binding site 10 out of 32 in the Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryoem Structure of Azotobacter Vinelandii Nitrogenase Mofep During Catalytic N2 Reduction within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:58.9 occ:1.00 FE3 B:CLF601 0.0 58.9 1.0 S4A B:CLF601 2.3 58.9 1.0 S2A B:CLF601 2.3 58.9 1.0 S3A B:CLF601 2.3 58.9 1.0 SG A:CYS62 2.4 28.9 1.0 FE2 B:CLF601 2.7 58.9 1.0 FE4 B:CLF601 2.7 58.9 1.0 FE1 B:CLF601 2.8 58.9 1.0 CB A:CYS62 3.2 25.6 1.0 CA A:GLY185 3.9 24.4 1.0 CB A:TYR64 4.0 23.4 1.0 S1 B:CLF601 4.2 58.9 1.0 CA B:GLY94 4.4 13.2 1.0 CD1 A:TYR64 4.6 24.3 1.0 C B:GLY94 4.6 18.8 1.0 N A:GLY185 4.6 25.2 1.0 CG A:TYR64 4.6 26.6 1.0 N B:CYS95 4.7 21.5 1.0 CA A:CYS62 4.7 22.8 1.0 SG A:CYS154 4.8 21.8 1.0 CE2 B:TYR98 4.8 20.3 1.0 N A:TYR64 4.9 19.0 1.0 SG B:CYS95 4.9 21.6 1.0 C A:GLY185 5.0 25.9 1.0

H.L.Rutledge, B.D.Cook, H.P.M.Nguyen, M.A.Herzik Jr., F.A.Tezcan. Structures of the Nitrogenase Complex Prepared Under Catalytic Turnover Conditions. Science V. 377 865 2022.
ISSN: ESSN 1095-9203
PubMed: 35901182
DOI: 10.1126/SCIENCE.ABQ7641