Iron in PDB 9i0g: Cryoem Structure of Holo-Gmnifen

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Cryoem Structure of Holo-Gmnifen (pdb code 9i0g). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Cryoem Structure of Holo-Gmnifen, PDB code: 9i0g:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:141.3 occ:1.00 FE1 A:SF41001 0.0 141.3 1.0 SG A:CYS124 2.3 84.1 1.0 S2 A:SF41001 2.3 137.4 1.0 S4 A:SF41001 2.3 135.6 1.0 S3 A:SF41001 2.3 146.5 1.0 FE4 A:SF41001 2.7 182.5 1.0 FE3 A:SF41001 2.7 144.6 1.0 FE2 A:SF41001 2.7 160.0 1.0 CB A:CYS124 3.0 67.9 1.0 N A:CYS124 3.7 72.7 1.0 S1 A:SF41001 3.9 135.7 1.0 CA A:CYS124 3.9 70.4 1.0 CA A:GLY155 4.0 85.5 1.0 N A:GLY155 4.4 76.3 1.0 CB B:ALA522 4.4 76.6 1.0 CB A:CYS36 4.5 83.8 1.0 C A:GLY155 4.7 88.1 1.0 SG A:CYS61 4.7 85.9 1.0 SG A:CYS36 4.7 83.8 1.0 SG B:CYS525 4.7 70.2 1.0 N A:PHE156 4.8 80.2 1.0 C A:THR123 4.9 75.3 1.0

Iron binding site 2 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:160.0 occ:1.00 FE2 A:SF41001 0.0 160.0 1.0 SG A:CYS61 2.3 85.9 1.0 S1 A:SF41001 2.3 135.7 1.0 S3 A:SF41001 2.3 146.5 1.0 S4 A:SF41001 2.3 135.6 1.0 FE4 A:SF41001 2.7 182.5 1.0 FE1 A:SF41001 2.7 141.3 1.0 FE3 A:SF41001 2.7 144.6 1.0 CB A:CYS61 3.6 70.7 1.0 S2 A:SF41001 3.9 137.4 1.0 CA A:CYS61 4.0 71.1 1.0 CB A:THR123 4.4 67.9 1.0 N A:CYS61 4.4 71.2 1.0 N A:CYS124 4.6 72.7 1.0 SG B:CYS525 4.7 70.2 1.0 CG2 A:THR123 4.8 66.6 1.0 SG A:CYS36 4.8 83.8 1.0 SG A:CYS124 4.9 84.1 1.0 CB A:CYS124 4.9 67.9 1.0

Iron binding site 3 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:144.6 occ:1.00 FE3 A:SF41001 0.0 144.6 1.0 SG A:CYS36 2.3 83.8 1.0 S2 A:SF41001 2.3 137.4 1.0 S4 A:SF41001 2.3 135.6 1.0 S1 A:SF41001 2.3 135.7 1.0 FE1 A:SF41001 2.7 141.3 1.0 FE4 A:SF41001 2.7 182.5 1.0 FE2 A:SF41001 2.7 160.0 1.0 CB A:CYS36 2.9 83.8 1.0 S3 A:SF41001 3.9 146.5 1.0 CA B:GLY524 4.0 67.2 1.0 C B:GLY524 4.0 68.6 1.0 N B:CYS525 4.2 69.5 1.0 CA A:CYS36 4.4 74.8 1.0 O B:GLY524 4.4 69.1 1.0 CB A:TYR38 4.5 65.5 1.0 CA A:GLY155 4.6 85.5 1.0 SG A:CYS124 4.7 84.1 1.0 CD2 A:TYR38 4.8 65.8 1.0 SG B:CYS525 4.8 70.2 1.0 SG A:CYS61 4.8 85.9 1.0 N B:GLY524 4.8 70.7 1.0 N A:CYS36 4.9 73.5 1.0

Iron binding site 4 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:182.5 occ:1.00 FE4 A:SF41001 0.0 182.5 1.0 SG B:CYS525 2.3 70.2 1.0 S3 A:SF41001 2.3 146.5 1.0 S1 A:SF41001 2.3 135.7 1.0 S2 A:SF41001 2.3 137.4 1.0 FE2 A:SF41001 2.7 160.0 1.0 FE1 A:SF41001 2.7 141.3 1.0 FE3 A:SF41001 2.7 144.6 1.0 N B:CYS525 3.3 69.5 1.0 CB B:CYS525 3.6 62.3 1.0 CA B:CYS525 3.7 62.5 1.0 S4 A:SF41001 3.9 135.6 1.0 C B:GLY524 4.0 68.6 1.0 CA B:GLY524 4.4 67.2 1.0 CB B:ALA522 4.4 76.6 1.0 SG A:CYS124 4.7 84.1 1.0 N B:GLY524 4.7 70.7 1.0 O B:GLY524 4.7 69.1 1.0 SG A:CYS36 4.8 83.8 1.0 SG A:CYS61 4.8 85.9 1.0

Iron binding site 5 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:152.1 occ:1.00 FE8 A:S5Q1002 0.0 152.1 1.0 S1B A:S5Q1002 2.3 147.0 1.0 S3B A:S5Q1002 2.3 155.2 1.0 SG A:CYS241 2.3 78.5 1.0 S4B A:S5Q1002 2.3 153.4 1.0 FE6 A:S5Q1002 2.7 186.7 1.0 FE7 A:S5Q1002 2.7 181.9 1.0 FE5 A:S5Q1002 2.7 174.1 1.0 CB A:CYS241 3.3 66.6 1.0 OG A:SER244 3.4 77.7 1.0 CX A:S5Q1002 3.5 173.0 1.0 CA A:CYS241 4.6 64.8 1.0 CE2 A:TYR195 4.6 61.8 1.0 CB A:SER244 4.7 70.8 1.0 CB A:LYS243 4.8 90.7 1.0 CA A:GLY331 4.8 87.5 1.0 S3A A:S5Q1002 4.8 97.6 1.0 S2B A:S5Q1002 4.8 135.9 1.0 S5A A:S5Q1002 4.8 134.1 1.0 CG A:LYS243 4.9 95.6 1.0 FE2 A:S5Q1002 5.0 175.5 1.0 FE4 A:S5Q1002 5.0 167.3 1.0

Iron binding site 6 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:174.1 occ:1.00 FE5 A:S5Q1002 0.0 174.1 1.0 CX A:S5Q1002 2.0 173.0 1.0 S3A A:S5Q1002 2.2 97.6 1.0 S1B A:S5Q1002 2.2 147.0 1.0 S4B A:S5Q1002 2.3 153.4 1.0 FE4 A:S5Q1002 2.6 167.3 1.0 FE7 A:S5Q1002 2.7 181.9 1.0 FE8 A:S5Q1002 2.7 152.1 1.0 FE6 A:S5Q1002 2.7 186.7 1.0 FE2 A:S5Q1002 3.7 175.5 1.0 FE3 A:S5Q1002 3.7 179.4 1.0 S3B A:S5Q1002 3.9 155.2 1.0 CE2 A:TYR195 4.0 61.8 1.0 CD2 A:TYR195 4.1 61.0 1.0 S4A A:S5Q1002 4.3 159.5 1.0 S1A A:S5Q1002 4.3 136.0 1.0 S5A A:S5Q1002 4.5 134.1 1.0 S2B A:S5Q1002 4.5 135.9 1.0 NZ A:LYS333 4.6 76.6 1.0 SG A:CYS241 4.6 78.5 1.0 CG2 A:VAL43 4.9 63.6 1.0 CZ A:TYR195 5.0 62.1 1.0 OG A:SER244 5.0 77.7 1.0

Iron binding site 7 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:181.9 occ:1.00 FE7 A:S5Q1002 0.0 181.9 1.0 CX A:S5Q1002 2.0 173.0 1.0 S5A A:S5Q1002 2.2 134.1 1.0 S3B A:S5Q1002 2.3 155.2 1.0 S4B A:S5Q1002 2.3 153.4 1.0 FE3 A:S5Q1002 2.6 179.4 1.0 FE6 A:S5Q1002 2.6 186.7 1.0 FE5 A:S5Q1002 2.7 174.1 1.0 FE8 A:S5Q1002 2.7 152.1 1.0 FE2 A:S5Q1002 3.7 175.5 1.0 FE4 A:S5Q1002 3.7 167.3 1.0 S1B A:S5Q1002 3.8 147.0 1.0 S2A A:S5Q1002 4.3 153.5 1.0 S4A A:S5Q1002 4.3 159.5 1.0 OG A:SER244 4.4 77.7 1.0 S2B A:S5Q1002 4.5 135.9 1.0 S3A A:S5Q1002 4.5 97.6 1.0 CG2 A:VAL43 4.7 63.6 1.0 SG A:CYS241 4.7 78.5 1.0

Iron binding site 8 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:186.7 occ:1.00 FE6 A:S5Q1002 0.0 186.7 1.0 CX A:S5Q1002 2.0 173.0 1.0 S2B A:S5Q1002 2.2 135.9 1.0 S3B A:S5Q1002 2.3 155.2 1.0 S1B A:S5Q1002 2.3 147.0 1.0 FE2 A:S5Q1002 2.6 175.5 1.0 FE7 A:S5Q1002 2.6 181.9 1.0 FE8 A:S5Q1002 2.7 152.1 1.0 FE5 A:S5Q1002 2.7 174.1 1.0 NZ A:LYS333 3.6 76.6 1.0 FE4 A:S5Q1002 3.7 167.3 1.0 FE3 A:S5Q1002 3.7 179.4 1.0 CA A:GLY331 3.8 87.5 1.0 N A:GLY331 3.9 98.0 1.0 S4B A:S5Q1002 3.9 153.4 1.0 S1A A:S5Q1002 4.3 136.0 1.0 S2A A:S5Q1002 4.3 153.5 1.0 CE A:LYS333 4.5 58.7 1.0 S3A A:S5Q1002 4.5 97.6 1.0 S5A A:S5Q1002 4.5 134.1 1.0 SG A:CYS241 4.8 78.5 1.0 C A:GLY331 4.9 83.3 1.0

Iron binding site 9 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:167.3 occ:1.00 FE4 A:S5Q1002 0.0 167.3 1.0 CX A:S5Q1002 2.0 173.0 1.0 S3A A:S5Q1002 2.2 97.6 1.0 S4A A:S5Q1002 2.2 159.5 1.0 S1A A:S5Q1002 2.3 136.0 1.0 FE5 A:S5Q1002 2.6 174.1 1.0 FE2 A:S5Q1002 2.6 175.5 1.0 FE3 A:S5Q1002 2.6 179.4 1.0 FE1 A:S5Q1002 2.7 167.2 1.0 FE6 A:S5Q1002 3.7 186.7 1.0 FE7 A:S5Q1002 3.7 181.9 1.0 S2A A:S5Q1002 3.8 153.5 1.0 CD1 A:ILE197 4.1 57.2 1.0 NH1 A:ARG69 4.1 82.0 1.0 S1B A:S5Q1002 4.2 147.0 1.0 ND1 A:HIS417 4.3 69.2 1.0 S4B A:S5Q1002 4.3 153.4 1.0 S2B A:S5Q1002 4.5 135.9 1.0 S5A A:S5Q1002 4.5 134.1 1.0 CG2 A:VAL43 4.6 63.6 1.0 NZ A:LYS333 4.9 76.6 1.0 CZ A:ARG69 4.9 72.5 1.0 N A:HIS417 5.0 71.1 1.0 FE8 A:S5Q1002 5.0 152.1 1.0

Iron binding site 10 out of 24 in the Cryoem Structure of Holo-Gmnifen


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 Holo-Gmnifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:167.2 occ:1.00 FE1 A:S5Q1002 0.0 167.2 1.0 ND1 A:HIS417 2.2 69.2 1.0 S4A A:S5Q1002 2.3 159.5 1.0 S2A A:S5Q1002 2.3 153.5 1.0 S1A A:S5Q1002 2.3 136.0 1.0 FE2 A:S5Q1002 2.6 175.5 1.0 FE3 A:S5Q1002 2.7 179.4 1.0 FE4 A:S5Q1002 2.7 167.3 1.0 CE1 A:HIS417 2.7 74.0 1.0 CG A:HIS417 3.5 70.2 1.0 CX A:S5Q1002 3.5 173.0 1.0 OD1 A:ASN416 3.8 73.4 1.0 N A:HIS417 3.9 71.1 1.0 CG A:ASN416 3.9 77.4 1.0 NE2 A:HIS417 4.0 71.5 1.0 CB A:HIS417 4.2 70.1 1.0 ND2 A:ASN416 4.3 81.3 1.0 CD2 A:HIS417 4.4 73.0 1.0 CB A:ASN416 4.4 69.7 1.0 CA A:ASN416 4.6 65.9 1.0 CA A:HIS417 4.6 73.9 1.0 C A:ASN416 4.7 74.0 1.0 S2B A:S5Q1002 4.8 135.9 1.0 S3A A:S5Q1002 4.8 97.6 1.0 S5A A:S5Q1002 4.9 134.1 1.0

L.Paya Tormo, T.Q.Nguyen, C.Fyfe, H.Basbous, K.Dobrzynska, C.Echavarri-Erasun, L.Martin, G.Caserta, P.Legrand, A.Thorn, P.Amara, G.Schoehn, M.V.Cherrier, L.M.Rubio, Y.Nicolet. Dynamics Driving the Precursor in Nifen Scaffold During Nitrogenase Femo-Cofactor Assembly Nature Chemical Biology 2025.