Iron in PDB 8eno: Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft

All present enzymatic activity of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft:
1.18.6.1;

The structure of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft 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 Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft (pdb code 8eno). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft, PDB code: 8eno:
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 Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:137.7 occ:1.00 FE1 A:ICS600 0.0 137.7 1.0 SG A:CYS275 2.2 103.8 1.0 S2A A:ICS600 2.3 129.9 1.0 S4A A:ICS600 2.3 126.1 1.0 S1A A:ICS600 2.3 125.7 1.0 FE4 A:ICS600 2.6 139.0 1.0 FE3 A:ICS600 2.7 135.5 1.0 FE2 A:ICS600 2.7 136.9 1.0 CX A:ICS600 3.5 128.6 1.0 CB A:CYS275 3.5 90.5 1.0 OG A:SER278 3.7 82.8 1.0 CB A:LEU358 4.2 104.8 1.0 CB A:SER278 4.3 84.1 1.0 CE2 A:TYR229 4.4 72.9 1.0 CA A:CYS275 4.7 90.6 1.0 N A:LEU358 4.8 106.2 1.0 S3A A:ICS600 4.8 122.2 1.0 N A:SER278 4.8 92.4 1.0 CE1 A:HIS195 4.8 79.4 1.0 S2B A:ICS600 4.8 122.0 1.0 S5A A:ICS600 4.8 127.5 1.0 CD2 A:TYR229 4.9 70.4 1.0

Iron binding site 2 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:136.9 occ:1.00 FE2 A:ICS600 0.0 136.9 1.0 CX A:ICS600 2.0 128.6 1.0 S2B A:ICS600 2.2 122.0 1.0 S2A A:ICS600 2.2 129.9 1.0 S1A A:ICS600 2.3 125.7 1.0 FE6 A:ICS600 2.6 132.7 1.0 FE4 A:ICS600 2.7 139.0 1.0 FE1 A:ICS600 2.7 137.7 1.0 FE3 A:ICS600 2.7 135.5 1.0 CE1 A:HIS195 3.6 79.4 1.0 FE5 A:ICS600 3.7 131.6 1.0 FE7 A:ICS600 3.7 134.0 1.0 NE2 A:HIS195 3.8 78.4 1.0 CZ A:PHE381 3.9 115.0 1.0 S4A A:ICS600 3.9 126.1 1.0 S1B A:ICS600 4.2 132.1 1.0 S3B A:ICS600 4.2 129.1 1.0 CE1 A:PHE381 4.4 115.5 1.0 S3A A:ICS600 4.5 122.2 1.0 S5A A:ICS600 4.5 127.5 1.0 CG1 A:VAL70 4.5 61.4 1.0 SG A:CYS275 4.7 103.8 1.0 ND1 A:HIS195 4.8 78.8 1.0 CG2 A:VAL70 4.8 71.8 1.0 N A:GLY357 4.9 112.6 1.0 CE2 A:PHE381 5.0 113.4 1.0

Iron binding site 3 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:135.5 occ:1.00 FE3 A:ICS600 0.0 135.5 1.0 CX A:ICS600 2.0 128.6 1.0 S5A A:ICS600 2.2 127.5 1.0 S4A A:ICS600 2.3 126.1 1.0 S2A A:ICS600 2.3 129.9 1.0 FE7 A:ICS600 2.6 134.0 1.0 FE4 A:ICS600 2.6 139.0 1.0 FE1 A:ICS600 2.7 137.7 1.0 FE2 A:ICS600 2.7 136.9 1.0 FE6 A:ICS600 3.7 132.7 1.0 FE5 A:ICS600 3.7 131.6 1.0 S1A A:ICS600 3.9 125.7 1.0 NH1 A:ARG96 4.0 80.7 1.0 CD2 A:TYR229 4.1 70.4 1.0 S4B A:ICS600 4.2 129.0 1.0 S3B A:ICS600 4.2 129.1 1.0 CE2 A:TYR229 4.4 72.9 1.0 S2B A:ICS600 4.5 122.0 1.0 S3A A:ICS600 4.5 122.2 1.0 SG A:CYS275 4.6 103.8 1.0 NE A:ARG359 4.9 104.6 1.0

Iron binding site 4 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:139.0 occ:1.00 FE4 A:ICS600 0.0 139.0 1.0 CX A:ICS600 2.0 128.6 1.0 S3A A:ICS600 2.2 122.2 1.0 S4A A:ICS600 2.3 126.1 1.0 S1A A:ICS600 2.3 125.7 1.0 FE5 A:ICS600 2.6 131.6 1.0 FE3 A:ICS600 2.6 135.5 1.0 FE1 A:ICS600 2.6 137.7 1.0 FE2 A:ICS600 2.7 136.9 1.0 FE7 A:ICS600 3.7 134.0 1.0 FE6 A:ICS600 3.7 132.7 1.0 S2A A:ICS600 3.8 129.9 1.0 N A:LEU358 3.8 106.2 1.0 N A:GLY357 3.9 112.6 1.0 CB A:LEU358 4.2 104.8 1.0 S4B A:ICS600 4.3 129.0 1.0 S1B A:ICS600 4.3 132.1 1.0 S5A A:ICS600 4.5 127.5 1.0 CA A:GLY357 4.5 114.2 1.0 S2B A:ICS600 4.5 122.0 1.0 SG A:CYS275 4.5 103.8 1.0 CA A:LEU358 4.6 104.2 1.0 CD A:ARG359 4.6 105.0 1.0 N A:ARG359 4.7 106.3 1.0 C A:GLY357 4.7 115.3 1.0 C A:GLY356 4.7 114.0 1.0 CZ A:PHE381 4.8 115.0 1.0 CA A:GLY356 4.9 113.8 1.0 NE A:ARG359 4.9 104.6 1.0

Iron binding site 5 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:131.6 occ:1.00 FE5 A:ICS600 0.0 131.6 1.0 CX A:ICS600 2.0 128.6 1.0 S4B A:ICS600 2.3 129.0 1.0 S3A A:ICS600 2.3 122.2 1.0 S1B A:ICS600 2.3 132.1 1.0 FE4 A:ICS600 2.6 139.0 1.0 FE7 A:ICS600 2.6 134.0 1.0 FE6 A:ICS600 2.6 132.7 1.0 MO1 A:ICS600 2.7 157.4 1.0 ND1 A:HIS442 3.7 104.9 1.0 FE2 A:ICS600 3.7 136.9 1.0 FE3 A:ICS600 3.7 135.5 1.0 CE1 A:HIS442 3.7 104.0 1.0 S3B A:ICS600 3.9 129.1 1.0 N A:GLY356 4.1 115.6 1.0 CA A:GLY356 4.1 113.8 1.0 S1A A:ICS600 4.3 125.7 1.0 S4A A:ICS600 4.3 126.1 1.0 CG2 A:ILE355 4.4 117.1 1.0 S5A A:ICS600 4.5 127.5 1.0 S2B A:ICS600 4.5 122.0 1.0 CD A:ARG359 4.5 105.0 1.0 N A:GLY357 4.5 112.6 1.0 O7 A:CIT601 4.6 123.2 1.0 O6 A:CIT601 4.7 119.6 1.0 CG A:HIS442 4.7 102.3 1.0 NE2 A:HIS442 4.8 103.3 1.0 C A:GLY356 4.8 114.0 1.0 NE A:ARG359 4.9 104.6 1.0 CZ A:PHE381 5.0 115.0 1.0 NH1 A:ARG359 5.0 104.3 1.0

Iron binding site 6 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:132.7 occ:1.00 FE6 A:ICS600 0.0 132.7 1.0 CX A:ICS600 2.0 128.6 1.0 S2B A:ICS600 2.2 122.0 1.0 S3B A:ICS600 2.2 129.1 1.0 S1B A:ICS600 2.2 132.1 1.0 FE2 A:ICS600 2.6 136.9 1.0 FE7 A:ICS600 2.6 134.0 1.0 FE5 A:ICS600 2.6 131.6 1.0 MO1 A:ICS600 2.7 157.4 1.0 O7 A:CIT601 3.1 123.2 1.0 FE3 A:ICS600 3.7 135.5 1.0 FE4 A:ICS600 3.7 139.0 1.0 S4B A:ICS600 3.8 129.0 1.0 CZ A:PHE381 4.2 115.0 1.0 S2A A:ICS600 4.2 129.9 1.0 S1A A:ICS600 4.3 125.7 1.0 OE1 A:GLN191 4.3 83.3 1.0 S5A A:ICS600 4.4 127.5 1.0 NH1 A:ARG96 4.5 80.7 1.0 CG2 A:VAL70 4.5 71.8 1.0 C3 A:CIT601 4.5 121.3 1.0 S3A A:ICS600 4.5 122.2 1.0 O6 A:CIT601 4.6 119.6 1.0 O4 A:CIT601 4.6 118.0 1.0 CE2 A:PHE381 4.6 113.4 1.0 ND1 A:HIS442 4.7 104.9 1.0 CE1 A:HIS442 4.9 104.0 1.0 C6 A:CIT601 4.9 120.5 1.0 NE2 A:GLN191 4.9 90.5 1.0 CD A:GLN191 5.0 89.0 1.0

Iron binding site 7 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe600 b:134.0 occ:1.00 FE7 A:ICS600 0.0 134.0 1.0 CX A:ICS600 2.0 128.6 1.0 S5A A:ICS600 2.2 127.5 1.0 S4B A:ICS600 2.2 129.0 1.0 S3B A:ICS600 2.3 129.1 1.0 FE6 A:ICS600 2.6 132.7 1.0 FE3 A:ICS600 2.6 135.5 1.0 FE5 A:ICS600 2.6 131.6 1.0 MO1 A:ICS600 2.7 157.4 1.0 NH1 A:ARG96 3.3 80.7 1.0 FE2 A:ICS600 3.7 136.9 1.0 FE4 A:ICS600 3.7 139.0 1.0 O6 A:CIT601 3.8 119.6 1.0 S1B A:ICS600 3.8 132.1 1.0 O7 A:CIT601 4.1 123.2 1.0 S2A A:ICS600 4.3 129.9 1.0 S4A A:ICS600 4.3 126.1 1.0 S2B A:ICS600 4.4 122.0 1.0 S3A A:ICS600 4.5 122.2 1.0 NH1 A:ARG359 4.6 104.3 1.0 ND1 A:HIS442 4.6 104.9 1.0 CZ A:ARG96 4.6 82.7 1.0 C6 A:CIT601 4.6 120.5 1.0 CZ A:ARG359 4.7 103.6 1.0 NE A:ARG359 5.0 104.6 1.0 NH2 A:ARG359 5.0 102.7 1.0

Iron binding site 8 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:82.7 occ:1.00 FE1 B:CLF601 0.0 82.7 1.0 SG A:CYS154 2.3 53.8 1.0 S2A B:CLF601 2.3 65.6 1.0 S3A B:CLF601 2.3 78.4 1.0 S1 B:CLF601 2.4 70.1 1.0 FE2 B:CLF601 2.5 79.3 1.0 FE4 B:CLF601 2.6 78.7 1.0 FE3 B:CLF601 2.8 87.4 1.0 CB A:CYS154 3.3 42.8 1.0 N A:CYS154 3.8 53.9 1.0 S4A B:CLF601 3.8 69.0 1.0 CA A:GLY185 3.9 50.2 1.0 SG B:CYS95 4.0 53.3 1.0 CA A:CYS154 4.1 50.0 1.0 N A:GLY185 4.1 51.5 1.0 SG A:CYS88 4.4 68.6 1.0 FE8 B:CLF601 4.4 74.6 1.0 SG B:CYS153 4.5 65.5 1.0 FE5 B:CLF601 4.7 84.4 1.0 C A:GLY185 4.8 55.5 1.0 CB B:SER92 4.8 53.5 1.0 OG B:SER92 4.8 62.2 1.0 FE6 B:CLF601 4.9 83.8 1.0 C A:GLU153 4.9 62.6 1.0 N A:PHE186 5.0 53.6 1.0 SG A:CYS62 5.0 68.4 1.0

Iron binding site 9 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:79.3 occ:1.00 FE2 B:CLF601 0.0 79.3 1.0 SG B:CYS95 2.2 53.3 1.0 S4A B:CLF601 2.3 69.0 1.0 S2A B:CLF601 2.3 65.6 1.0 S1 B:CLF601 2.5 70.1 1.0 FE1 B:CLF601 2.5 82.7 1.0 FE4 B:CLF601 2.6 78.7 1.0 FE3 B:CLF601 2.8 87.4 1.0 FE8 B:CLF601 3.0 74.6 1.0 N B:CYS95 3.3 48.3 1.0 CB B:CYS95 3.4 38.4 1.0 CA B:CYS95 3.5 31.4 1.0 S3A B:CLF601 3.8 78.4 1.0 FE5 B:CLF601 3.8 84.4 1.0 C B:GLY94 3.9 43.0 1.0 S4B B:CLF601 4.0 70.2 1.0 SG A:CYS88 4.2 68.6 1.0 SG A:CYS154 4.5 53.8 1.0 CA B:GLY94 4.5 28.2 1.0 O B:GLY94 4.6 48.8 1.0 FE6 B:CLF601 4.6 83.8 1.0 SG A:CYS62 4.6 68.4 1.0 CB B:SER92 4.9 53.5 1.0 N B:GLY94 5.0 39.0 1.0

Iron binding site 10 out of 32 in the Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Homocitrate-Deficient Nitrogenase Mofe-Protein From A. Vinelandii Nifv Knockout in Complex with Naft within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:87.4 occ:1.00 FE3 B:CLF601 0.0 87.4 1.0 S4A B:CLF601 2.3 69.0 1.0 S2A B:CLF601 2.3 65.6 1.0 SG A:CYS62 2.3 68.4 1.0 S3A B:CLF601 2.3 78.4 1.0 FE4 B:CLF601 2.7 78.7 1.0 FE2 B:CLF601 2.8 79.3 1.0 FE1 B:CLF601 2.8 82.7 1.0 CB A:CYS62 3.1 60.4 1.0 CA A:GLY185 3.8 50.2 1.0 CB A:TYR64 3.9 52.2 1.0 S1 B:CLF601 4.2 70.1 1.0 CD2 A:TYR64 4.4 54.3 1.0 N A:GLY185 4.5 51.5 1.0 CG A:TYR64 4.5 52.0 1.0 CA A:CYS62 4.6 59.8 1.0 CA B:GLY94 4.6 28.2 1.0 SG A:CYS154 4.6 53.8 1.0 C B:GLY94 4.7 43.0 1.0 SG A:CYS88 4.7 68.6 1.0 N A:TYR64 4.8 59.2 1.0 N B:CYS95 4.8 48.3 1.0 CA A:TYR64 4.9 57.3 1.0 C A:GLY185 4.9 55.5 1.0 SG B:CYS95 4.9 53.3 1.0 CE2 B:TYR98 5.0 32.3 1.0

R.A.Warmack, A.O.Maggiolo, A.Orta, B.B.Wenke, J.B.Howard, D.C.Rees. Structural Consequences of Turnover-Induced Homocitrate Loss in Nitrogenase. Nat Commun V. 14 1091 2023.
ISSN: ESSN 2041-1723
PubMed: 36841829
DOI: 10.1038/S41467-023-36636-4