Iron in PDB 9buo: Cryoem Structure of Dpor in the Presence of Adp-ALF3

All present enzymatic activity of Cryoem Structure of Dpor in the Presence of Adp-ALF3:
1.3.7.7;

The structure of Cryoem Structure of Dpor in the Presence of Adp-ALF3 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Copper	(Cu)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Cryoem Structure of Dpor in the Presence of Adp-ALF3 (pdb code 9buo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Cryoem Structure of Dpor in the Presence of Adp-ALF3, PDB code: 9buo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:227.2 occ:1.00 FE1 H:SF4301 0.0 227.2 1.0 S2 H:SF4301 2.3 227.2 1.0 S4 H:SF4301 2.3 227.2 1.0 S3 H:SF4301 2.3 227.2 1.0 FE3 H:SF4301 2.7 227.2 1.0 FE4 H:SF4301 2.7 227.2 1.0 FE2 H:SF4301 2.7 227.2 1.0 CB G:TYR129 3.6 191.0 1.0 S1 H:SF4301 3.9 227.2 1.0 SG H:CYS160 4.1 203.1 1.0 CB H:CYS160 4.2 203.1 1.0 CA G:TYR129 4.4 191.0 1.0 CG2 G:VAL131 4.5 188.7 1.0 N H:GLY161 4.5 197.3 1.0 CG G:TYR129 4.7 191.0 1.0 SG G:CYS160 4.7 190.4 1.0 CD2 G:TYR129 4.9 191.0 1.0

Iron binding site 2 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:227.2 occ:1.00 FE2 H:SF4301 0.0 227.2 1.0 S4 H:SF4301 2.3 227.2 1.0 S1 H:SF4301 2.3 227.2 1.0 S3 H:SF4301 2.3 227.2 1.0 FE3 H:SF4301 2.7 227.2 1.0 FE4 H:SF4301 2.7 227.2 1.0 FE1 H:SF4301 2.7 227.2 1.0 N H:GLY162 3.7 197.3 1.0 S2 H:SF4301 3.9 227.2 1.0 SG H:CYS160 4.0 203.1 1.0 CA H:GLY162 4.2 197.3 1.0 SG H:CYS126 4.6 207.7 1.0 C H:GLY161 4.7 197.3 1.0 N H:GLY161 4.8 197.3 1.0 SG G:CYS160 4.9 190.4 1.0 CA H:GLY161 4.9 197.3 1.0 O G:GLY161 5.0 183.8 1.0

Iron binding site 3 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:227.2 occ:1.00 FE3 H:SF4301 0.0 227.2 1.0 SG G:CYS160 2.2 190.4 1.0 S4 H:SF4301 2.3 227.2 1.0 S1 H:SF4301 2.3 227.2 1.0 SG H:CYS160 2.3 203.1 1.0 S2 H:SF4301 2.3 227.2 1.0 FE2 H:SF4301 2.7 227.2 1.0 FE1 H:SF4301 2.7 227.2 1.0 FE4 H:SF4301 2.7 227.2 1.0 CB H:CYS160 3.3 203.1 1.0 S3 H:SF4301 3.9 227.2 1.0 O G:GLY161 3.9 183.8 1.0 CB G:CYS160 4.0 190.4 1.0 N H:GLY162 4.6 197.3 1.0 CA H:CYS160 4.7 203.1 1.0 N G:GLY161 4.7 183.8 1.0 C G:CYS160 4.8 190.4 1.0 CD2 H:PHE163 4.8 199.1 1.0 C G:GLY161 4.8 183.8 1.0 N H:GLY161 4.8 197.3 1.0 C H:CYS160 4.9 203.1 1.0 CA G:CYS160 4.9 190.4 1.0 CB G:PHE163 4.9 188.3 1.0

Iron binding site 4 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe301 b:227.2 occ:1.00 FE4 H:SF4301 0.0 227.2 1.0 S1 H:SF4301 2.3 227.2 1.0 S3 H:SF4301 2.3 227.2 1.0 S2 H:SF4301 2.3 227.2 1.0 O G:GLY161 2.6 183.8 1.0 FE1 H:SF4301 2.7 227.2 1.0 FE2 H:SF4301 2.7 227.2 1.0 FE3 H:SF4301 2.7 227.2 1.0 C G:GLY161 3.8 183.8 1.0 S4 H:SF4301 3.9 227.2 1.0 SG G:CYS160 4.3 190.4 1.0 CA G:GLY162 4.5 175.8 1.0 N G:GLY162 4.6 175.8 1.0 C G:GLY162 4.8 175.8 1.0 CA G:GLY161 4.8 183.8 1.0 SG H:CYS160 5.0 203.1 1.0

Iron binding site 5 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:119.2 occ:1.00 FE1 A:SF4501 0.0 119.2 1.0 SG A:CYS29 1.4 102.4 1.0 S2 A:SF4501 2.3 119.2 1.0 S3 A:SF4501 2.3 119.2 1.0 S4 A:SF4501 2.3 119.2 1.0 CB A:CYS29 2.4 102.4 1.0 FE3 A:SF4501 2.7 119.2 1.0 FE2 A:SF4501 2.7 119.2 1.0 FE4 A:SF4501 2.7 119.2 1.0 SG A:CYS54 3.7 81.6 1.0 SG A:CYS115 3.8 112.2 1.0 CA A:CYS29 3.9 102.4 1.0 S1 A:SF4501 3.9 119.2 1.0 OD1 B:ASP36 4.2 91.5 1.0 N A:CYS29 4.2 102.4 1.0 CD2 A:LEU57 4.3 74.3 1.0 N A:GLY148 4.3 107.9 1.0 C A:CYS29 4.7 102.4 1.0 CA A:GLY148 4.7 107.9 1.0 C B:GLY35 4.8 98.0 1.0 O B:GLY35 4.8 98.0 1.0 CD1 A:LEU31 4.9 96.0 1.0 O A:CYS29 5.0 102.4 1.0

Iron binding site 6 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:119.2 occ:1.00 FE2 A:SF4501 0.0 119.2 1.0 OD1 B:ASP36 1.8 91.5 1.0 S1 A:SF4501 2.3 119.2 1.0 S4 A:SF4501 2.3 119.2 1.0 S3 A:SF4501 2.3 119.2 1.0 FE3 A:SF4501 2.7 119.2 1.0 FE4 A:SF4501 2.7 119.2 1.0 FE1 A:SF4501 2.7 119.2 1.0 CG B:ASP36 3.0 91.5 1.0 OD2 B:ASP36 3.7 91.5 1.0 OG1 A:THR53 3.7 79.5 1.0 SG A:CYS54 3.8 81.6 1.0 S2 A:SF4501 3.9 119.2 1.0 SG A:CYS29 3.9 102.4 1.0 CG B:PRO33 3.9 106.2 1.0 SG A:CYS115 4.1 112.2 1.0 CB B:ASP36 4.1 91.5 1.0 CA B:ASP36 4.1 91.5 1.0 N B:ASP36 4.4 91.5 1.0 CB A:THR53 4.7 79.5 1.0 CD B:PRO33 4.8 106.2 1.0 C B:GLY35 4.8 98.0 1.0 CB A:CYS115 4.9 112.2 1.0 CB A:CYS29 4.9 102.4 1.0 N A:CYS54 5.0 81.6 1.0

Iron binding site 7 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:119.2 occ:1.00 FE3 A:SF4501 0.0 119.2 1.0 SG A:CYS54 1.2 81.6 1.0 S4 A:SF4501 2.3 119.2 1.0 S1 A:SF4501 2.3 119.2 1.0 S2 A:SF4501 2.3 119.2 1.0 FE2 A:SF4501 2.7 119.2 1.0 FE4 A:SF4501 2.7 119.2 1.0 FE1 A:SF4501 2.7 119.2 1.0 CB A:CYS54 2.8 81.6 1.0 CA A:CYS54 3.4 81.6 1.0 N A:CYS54 3.7 81.6 1.0 OG1 A:THR53 3.7 79.5 1.0 S3 A:SF4501 3.9 119.2 1.0 SG A:CYS29 3.9 102.4 1.0 SG A:CYS115 3.9 112.2 1.0 OD1 B:ASP36 4.4 91.5 1.0 CD1 A:LEU31 4.5 96.0 1.0 CB A:CYS115 4.5 112.2 1.0 C A:THR53 4.6 79.5 1.0 CD A:PRO116 4.6 113.9 1.0 N A:CYS115 4.8 112.2 1.0 C A:CYS54 4.8 81.6 1.0 CB A:CYS29 4.9 102.4 1.0

Iron binding site 8 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:119.2 occ:1.00 FE4 A:SF4501 0.0 119.2 1.0 SG A:CYS115 1.4 112.2 1.0 S3 A:SF4501 2.3 119.2 1.0 S2 A:SF4501 2.3 119.2 1.0 S1 A:SF4501 2.3 119.2 1.0 CB A:CYS115 2.7 112.2 1.0 FE3 A:SF4501 2.7 119.2 1.0 FE2 A:SF4501 2.7 119.2 1.0 FE1 A:SF4501 2.7 119.2 1.0 SG A:CYS54 3.6 81.6 1.0 N A:GLY148 3.8 107.9 1.0 CA A:CYS115 3.8 112.2 1.0 N A:CYS115 3.8 112.2 1.0 S4 A:SF4501 3.9 119.2 1.0 SG A:CYS29 4.0 102.4 1.0 OG A:SER147 4.1 109.4 1.0 CG B:PRO33 4.1 106.2 1.0 CB A:CYS29 4.2 102.4 1.0 OD1 B:ASP36 4.3 91.5 1.0 CA A:GLY148 4.4 107.9 1.0 CB B:PRO33 4.6 106.2 1.0 CD A:PRO116 4.7 113.9 1.0 CA A:SER147 4.8 109.4 1.0 C A:SER147 4.8 109.4 1.0 CB A:SER147 5.0 109.4 1.0 C A:CYS115 5.0 112.2 1.0

Iron binding site 9 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:99.8 occ:1.00 FE1 C:SF4501 0.0 99.8 1.0 SG C:CYS29 1.2 60.6 1.0 S2 C:SF4501 2.3 99.8 1.0 S4 C:SF4501 2.3 99.8 1.0 S3 C:SF4501 2.3 99.8 1.0 CB C:CYS29 2.6 60.6 1.0 FE4 C:SF4501 2.7 99.8 1.0 FE2 C:SF4501 2.7 99.8 1.0 FE3 C:SF4501 2.7 99.8 1.0 SG C:CYS115 3.6 69.9 1.0 OD1 D:ASP36 3.9 71.0 1.0 S1 C:SF4501 3.9 99.8 1.0 CA C:CYS29 3.9 60.6 1.0 SG C:CYS54 3.9 58.8 1.0 N C:CYS29 4.2 60.6 1.0 N C:GLY148 4.3 73.6 1.0 CA C:GLY148 4.6 73.6 1.0 C D:GLY35 4.6 63.5 1.0 CD1 C:LEU57 4.6 52.0 1.0 CA D:GLY35 4.8 63.5 1.0 O D:GLY35 4.8 63.5 1.0 N D:ASP36 4.8 71.0 1.0 O D:GLN34 4.9 71.7 1.0

Iron binding site 10 out of 16 in the Cryoem Structure of Dpor in the Presence of Adp-ALF3


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 Dpor in the Presence of Adp-ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:99.8 occ:1.00 FE2 C:SF4501 0.0 99.8 1.0 OD1 D:ASP36 1.6 71.0 1.0 S1 C:SF4501 2.3 99.8 1.0 S3 C:SF4501 2.3 99.8 1.0 S4 C:SF4501 2.3 99.8 1.0 FE4 C:SF4501 2.7 99.8 1.0 FE1 C:SF4501 2.7 99.8 1.0 FE3 C:SF4501 2.7 99.8 1.0 CG D:ASP36 2.7 71.0 1.0 OD2 D:ASP36 3.3 71.0 1.0 SG C:CYS29 3.6 60.6 1.0 CG D:PRO33 3.8 74.7 1.0 S2 C:SF4501 3.9 99.8 1.0 CB D:ASP36 3.9 71.0 1.0 SG C:CYS115 3.9 69.9 1.0 SG C:CYS54 4.0 58.8 1.0 CA D:ASP36 4.1 71.0 1.0 N D:ASP36 4.2 71.0 1.0 SG D:CYS95 4.4 84.7 1.0 CG2 C:THR53 4.6 58.4 1.0 C D:GLY35 4.7 63.5 1.0 CD D:PRO33 4.8 74.7 1.0 CB C:CYS115 4.8 69.9 1.0 CB D:PRO33 4.9 74.7 1.0 CB C:THR53 4.9 58.4 1.0

R.Kashyap, N.Walsh, J.Deveryshetty, M.Tokmina-Lukaszewska, K.Zhao, Y.J.Gan, B.M.Hoffman, R.Sarangi, B.Bothner, B.Bennett, E.Antony. Cryo-Em Captures the Coordination of Asymmetric Electron Transfer Through A Di-Copper Site in Dpor. Nat Commun V. 16 3866 2025.
ISSN: ESSN 2041-1723
PubMed: 40274796
DOI: 10.1038/S41467-025-59158-7