Iron in PDB 6gcs: Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica

All present enzymatic activity of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica:
1.6.5.3; 1.6.99.3;

The structure of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica (pdb code 6gcs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica, PDB code: 6gcs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.3 occ:1.00 FE1 A:SF4801 0.0 0.3 1.0 S2 A:SF4801 2.2 0.3 1.0 S3 A:SF4801 2.3 0.3 1.0 SG A:CYS142 2.3 0.7 1.0 S4 A:SF4801 2.3 0.3 1.0 CB A:CYS142 2.4 0.7 1.0 FE2 A:SF4801 2.6 0.3 1.0 FE4 A:SF4801 2.7 0.3 1.0 FE3 A:SF4801 2.7 0.3 1.0 OE1 A:GLN145 3.0 0.8 1.0 S1 A:SF4801 3.8 0.3 1.0 O A:GLN138 3.9 0.5 1.0 CA A:CYS142 3.9 0.7 1.0 CD A:GLN145 4.0 0.8 1.0 CB A:GLN145 4.0 0.8 1.0 SG A:CYS136 4.3 0.1 1.0 SG A:CYS133 4.4 0.4 1.0 CG A:GLN145 4.7 0.8 1.0 N A:CYS142 4.7 0.7 1.0 CB A:CYS136 4.7 0.1 1.0 NE2 A:HIS129 4.8 0.4 1.0 CD2 A:LEU144 4.8 0.3 1.0 C A:CYS142 4.8 0.7 1.0 N A:GLN145 4.9 0.8 1.0 NE2 A:GLN145 4.9 0.8 1.0 C A:GLN138 4.9 0.5 1.0

Iron binding site 2 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.3 occ:1.00 FE2 A:SF4801 0.0 0.3 1.0 S1 A:SF4801 2.2 0.3 1.0 S3 A:SF4801 2.3 0.3 1.0 S4 A:SF4801 2.3 0.3 1.0 SG A:CYS133 2.3 0.4 1.0 FE1 A:SF4801 2.6 0.3 1.0 FE4 A:SF4801 2.6 0.3 1.0 FE3 A:SF4801 2.7 0.3 1.0 CA A:CYS133 2.8 0.4 1.0 CB A:CYS133 3.1 0.4 1.0 N A:CYS133 3.2 0.4 1.0 OE1 A:GLN145 3.4 0.8 1.0 S2 A:SF4801 3.8 0.3 1.0 CD A:GLN145 4.0 0.8 1.0 CB A:CYS136 4.1 0.1 1.0 C A:ASP132 4.1 0.7 1.0 C A:CYS133 4.1 0.4 1.0 NE2 A:GLN145 4.2 0.8 1.0 O A:CYS133 4.4 0.4 1.0 CE C:MET378 4.5 0.5 1.0 NE2 A:HIS129 4.5 0.4 1.0 SG A:CYS136 4.6 0.1 1.0 O A:ASP132 4.7 0.7 1.0 SG A:CYS142 4.7 0.7 1.0 CB A:CYS142 4.8 0.7 1.0 N A:ASP132 4.9 0.7 1.0 CA A:ASP132 5.0 0.7 1.0 CD2 A:HIS129 5.0 0.4 1.0

Iron binding site 3 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.3 occ:1.00 FE3 A:SF4801 0.0 0.3 1.0 NE2 A:HIS129 2.2 0.4 1.0 S4 A:SF4801 2.2 0.3 1.0 S2 A:SF4801 2.3 0.3 1.0 S1 A:SF4801 2.3 0.3 1.0 FE1 A:SF4801 2.7 0.3 1.0 FE2 A:SF4801 2.7 0.3 1.0 FE4 A:SF4801 2.7 0.3 1.0 CD2 A:HIS129 3.0 0.4 1.0 CE1 A:HIS129 3.1 0.4 1.0 SG A:CYS142 3.8 0.7 1.0 S3 A:SF4801 3.9 0.3 1.0 CG A:HIS129 4.2 0.4 1.0 ND1 A:HIS129 4.2 0.4 1.0 CD2 A:LEU144 4.2 0.3 1.0 CE C:MET378 4.3 0.5 1.0 SG A:CYS133 4.3 0.4 1.0 CD A:ARG182 4.4 0.2 1.0 CB A:CYS142 4.8 0.7 1.0 O A:PRO130 4.9 0.1 1.0 SG A:CYS136 4.9 0.1 1.0 OE1 A:GLN145 5.0 0.8 1.0 CG A:ARG182 5.0 0.2 1.0

Iron binding site 4 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.3 occ:1.00 FE4 A:SF4801 0.0 0.3 1.0 S3 A:SF4801 2.2 0.3 1.0 S1 A:SF4801 2.3 0.3 1.0 S2 A:SF4801 2.3 0.3 1.0 SG A:CYS136 2.3 0.1 1.0 CB A:CYS136 2.5 0.1 1.0 FE2 A:SF4801 2.6 0.3 1.0 FE1 A:SF4801 2.7 0.3 1.0 FE3 A:SF4801 2.7 0.3 1.0 CD A:ARG182 3.4 0.2 1.0 S4 A:SF4801 3.8 0.3 1.0 NE A:ARG182 3.9 0.2 1.0 CA A:CYS136 4.0 0.1 1.0 NE2 A:HIS129 4.2 0.4 1.0 N A:CYS133 4.4 0.4 1.0 CA A:CYS133 4.5 0.4 1.0 N A:GLY236 4.5 0.9 1.0 C A:ASP132 4.5 0.7 1.0 CB A:ASP132 4.5 0.7 1.0 SG A:CYS142 4.6 0.7 1.0 CG A:ARG182 4.6 0.2 1.0 C A:CYS136 4.7 0.1 1.0 CB A:CYS142 4.7 0.7 1.0 CZ A:ARG182 4.8 0.2 1.0 O A:ASP132 4.8 0.7 1.0 N A:CYS136 4.8 0.1 1.0 SG A:CYS133 4.9 0.4 1.0 CA A:GLY236 4.9 0.9 1.0 O A:GLN138 4.9 0.5 1.0 OE1 A:GLN145 5.0 0.8 1.0 CE1 A:HIS129 5.0 0.4 1.0

Iron binding site 5 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:0.8 occ:1.00 FE1 A:SF4802 0.0 0.8 1.0 S2 A:SF4802 2.2 0.8 1.0 S3 A:SF4802 2.3 0.8 1.0 S4 A:SF4802 2.3 0.8 1.0 SG A:CYS186 2.3 0.5 1.0 FE4 A:SF4802 2.6 0.8 1.0 FE3 A:SF4802 2.7 0.8 1.0 FE2 A:SF4802 2.7 0.8 1.0 CB A:CYS186 3.5 0.5 1.0 SG A:CYS233 3.5 0.9 1.0 N A:CYS186 3.6 0.5 1.0 SG A:CYS183 3.8 0.8 1.0 S1 A:SF4802 3.9 0.8 1.0 CA A:CYS186 4.0 0.5 1.0 N A:THR187 4.1 0.9 1.0 CB A:CYS233 4.3 0.9 1.0 CD A:PRO234 4.3 0.2 1.0 N A:HIS185 4.4 0.8 1.0 C A:CYS186 4.5 0.5 1.0 CA A:CYS233 4.6 0.9 1.0 C A:HIS185 4.6 0.8 1.0 CA A:HIS185 4.7 0.8 1.0 N A:ILE184 4.8 0.9 1.0 N A:ARG188 4.8 0.8 1.0 SG A:CYS189 4.9 0.6 1.0 CB A:CYS183 4.9 0.8 1.0 CG1 A:ILE184 5.0 0.9 1.0

Iron binding site 6 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:0.8 occ:1.00 FE2 A:SF4802 0.0 0.8 1.0 S1 A:SF4802 2.2 0.8 1.0 S4 A:SF4802 2.3 0.8 1.0 SG A:CYS183 2.3 0.8 1.0 S3 A:SF4802 2.3 0.8 1.0 FE3 A:SF4802 2.6 0.8 1.0 FE4 A:SF4802 2.6 0.8 1.0 FE1 A:SF4802 2.7 0.8 1.0 CB A:CYS183 3.3 0.8 1.0 S2 A:SF4802 3.8 0.8 1.0 CE A:MET180 4.1 0.6 1.0 SG A:CYS189 4.1 0.6 1.0 CG1 A:ILE213 4.2 0.8 1.0 CA A:CYS183 4.2 0.8 1.0 CB A:ILE213 4.3 0.8 1.0 CG2 A:ILE213 4.5 0.8 1.0 SG A:CYS233 4.6 0.9 1.0 N A:HIS185 4.7 0.8 1.0 SG A:CYS186 4.8 0.5 1.0 CA A:HIS185 4.8 0.8 1.0 CB A:CYS189 4.9 0.6 1.0 C A:CYS183 4.9 0.8 1.0 N A:CYS186 5.0 0.5 1.0

Iron binding site 7 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:0.8 occ:1.00 FE3 A:SF4802 0.0 0.8 1.0 S4 A:SF4802 2.2 0.8 1.0 S2 A:SF4802 2.3 0.8 1.0 SG A:CYS189 2.3 0.6 1.0 S1 A:SF4802 2.3 0.8 1.0 CB A:CYS189 2.6 0.6 1.0 FE2 A:SF4802 2.6 0.8 1.0 FE1 A:SF4802 2.7 0.8 1.0 FE4 A:SF4802 2.7 0.8 1.0 N A:CYS189 3.3 0.6 1.0 CA A:CYS189 3.5 0.6 1.0 SG A:CYS186 3.8 0.5 1.0 S3 A:SF4802 3.8 0.8 1.0 N A:ARG188 4.2 0.8 1.0 N A:THR187 4.2 0.9 1.0 CA A:THR187 4.5 0.9 1.0 C A:ARG188 4.5 0.8 1.0 N A:VAL190 4.6 0.4 1.0 C A:CYS189 4.6 0.6 1.0 CB A:CYS233 4.6 0.9 1.0 SG A:CYS233 4.7 0.9 1.0 C A:THR187 4.7 0.9 1.0 SG A:CYS183 4.7 0.8 1.0 CG2 A:ILE213 4.8 0.8 1.0 CA A:ARG188 4.9 0.8 1.0

Iron binding site 8 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:0.8 occ:1.00 FE4 A:SF4802 0.0 0.8 1.0 S3 A:SF4802 2.2 0.8 1.0 S1 A:SF4802 2.3 0.8 1.0 SG A:CYS233 2.3 0.9 1.0 S2 A:SF4802 2.3 0.8 1.0 FE2 A:SF4802 2.6 0.8 1.0 FE1 A:SF4802 2.6 0.8 1.0 FE3 A:SF4802 2.7 0.8 1.0 CB A:CYS233 2.8 0.9 1.0 S4 A:SF4802 3.8 0.8 1.0 CA A:CYS233 3.9 0.9 1.0 CD1 A:LEU238 4.2 0.2 1.0 CG A:LEU238 4.2 0.2 1.0 CB A:ALA237 4.3 0.7 1.0 CB A:CYS189 4.4 0.6 1.0 SG A:CYS183 4.5 0.8 1.0 SG A:CYS186 4.6 0.5 1.0 SG A:CYS189 4.7 0.6 1.0 N A:LEU238 4.7 0.2 1.0 CB A:LEU238 4.8 0.2 1.0 C A:CYS233 4.8 0.9 1.0 CB A:CYS183 4.9 0.8 1.0 N A:CYS233 4.9 0.9 1.0

Iron binding site 9 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:0.1 occ:1.00 FE1 A:FES803 0.0 0.1 1.0 S1 A:FES803 2.2 0.1 1.0 S2 A:FES803 2.2 0.1 1.0 SG A:CYS69 2.3 0.9 1.0 SG A:CYS80 2.3 0.6 1.0 N A:CYS80 2.8 0.6 1.0 FE2 A:FES803 3.1 0.1 1.0 CB A:CYS80 3.1 0.6 1.0 N A:ARG81 3.2 0.2 1.0 CA A:CYS80 3.3 0.6 1.0 C A:CYS80 3.6 0.6 1.0 N A:ASN79 3.8 0.2 1.0 O A:ALA77 3.8 0.9 1.0 CB A:CYS69 3.8 0.9 1.0 C A:GLY78 3.8 0.8 1.0 C A:ASN79 3.9 0.2 1.0 SG A:CYS97 4.1 0.3 1.0 O A:GLY78 4.1 0.8 1.0 N A:CYS69 4.2 0.9 1.0 CA A:ARG81 4.3 0.2 1.0 CA A:GLY78 4.3 0.8 1.0 CA A:CYS69 4.4 0.9 1.0 CA A:ASN79 4.4 0.2 1.0 N A:TYR70 4.4 0.9 1.0 C A:CYS69 4.5 0.9 1.0 N A:MET82 4.5 0.7 1.0 C A:ALA77 4.7 0.9 1.0 O A:CYS80 4.8 0.6 1.0 O A:ASN79 4.8 0.2 1.0 CB A:CYS97 4.9 0.3 1.0 C A:ARG81 5.0 0.2 1.0 SG A:CYS83 5.0 0.1 1.0 N A:GLY78 5.0 0.8 1.0

Iron binding site 10 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:0.1 occ:1.00 FE2 A:FES803 0.0 0.1 1.0 S2 A:FES803 2.2 0.1 1.0 S1 A:FES803 2.2 0.1 1.0 SG A:CYS83 2.3 0.1 1.0 SG A:CYS97 2.3 0.3 1.0 CB A:CYS97 2.5 0.3 1.0 FE1 A:FES803 3.1 0.1 1.0 CB A:CYS83 3.5 0.1 1.0 N A:CYS97 3.6 0.3 1.0 CA A:CYS97 3.6 0.3 1.0 CD1 A:ILE55 4.1 0.2 1.0 SG A:CYS80 4.1 0.6 1.0 N A:CYS83 4.4 0.1 1.0 CA A:CYS83 4.5 0.1 1.0 CB A:TYR70 4.6 0.9 1.0 CB A:ALA95 4.7 0.0 1.0 O A:ALA77 4.7 0.9 1.0 C A:CYS97 4.8 0.3 1.0 C A:SER96 4.8 0.3 1.0 N A:TYR70 4.8 0.9 1.0 SG A:CYS69 4.8 0.9 1.0 N A:SER96 4.9 0.3 1.0

K.Parey, U.Brandt, H.Xie, D.J.Mills, K.Siegmund, J.Vonck, W.Kuehlbrandt, V.Zickermann. Cryo-Em Structure of Respiratory Complex I at Work. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30277212
DOI: 10.7554/ELIFE.39213