Iron in PDB 6rfr: Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution

All present enzymatic activity of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution:
1.6.5.3; 1.6.99.3; 7.1.1.2;

The structure of Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution 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 at 3.2 A Resolution (pdb code 6rfr). 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 at 3.2 A Resolution, PDB code: 6rfr:
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 at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.5 occ:1.00 FE1 A:SF4801 0.0 25.5 1.0 S2 A:SF4801 2.2 25.5 1.0 S3 A:SF4801 2.3 25.5 1.0 S4 A:SF4801 2.3 25.5 1.0 SG A:CYS142 2.3 9.7 1.0 FE3 A:SF4801 2.7 25.5 1.0 FE2 A:SF4801 2.7 25.5 1.0 FE4 A:SF4801 2.7 25.5 1.0 CB A:CYS142 3.0 9.7 1.0 OE1 A:GLN145 3.7 9.2 1.0 O A:GLN138 3.7 13.4 1.0 S1 A:SF4801 3.9 25.5 1.0 CB A:GLN145 4.3 9.2 1.0 SG A:CYS136 4.4 17.0 1.0 CD A:GLN145 4.4 9.2 1.0 CA A:CYS142 4.4 9.7 1.0 SG A:CYS133 4.5 21.2 1.0 NE2 A:HIS129 4.7 8.5 1.0 C A:GLN138 4.8 13.4 1.0 CG A:GLN145 4.8 9.2 1.0 CB A:CYS136 5.0 17.0 1.0 CB A:GLN138 5.0 13.4 1.0

Iron binding site 2 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.5 occ:1.00 FE2 A:SF4801 0.0 25.5 1.0 S1 A:SF4801 2.2 25.5 1.0 S4 A:SF4801 2.3 25.5 1.0 S3 A:SF4801 2.3 25.5 1.0 SG A:CYS133 2.3 21.2 1.0 FE3 A:SF4801 2.6 25.5 1.0 FE4 A:SF4801 2.6 25.5 1.0 FE1 A:SF4801 2.7 25.5 1.0 CB A:CYS133 3.5 21.2 1.0 CA A:CYS133 3.6 21.2 1.0 S2 A:SF4801 3.8 25.5 1.0 N A:CYS133 3.8 21.2 1.0 NE2 A:HIS129 4.1 8.5 1.0 CE C:MET378 4.2 11.4 1.0 C A:ASP132 4.4 25.5 1.0 CB A:CYS136 4.5 17.0 1.0 OE1 A:GLN145 4.7 9.2 1.0 CD2 A:HIS129 4.7 8.5 1.0 SG A:CYS136 4.8 17.0 1.0 O A:ASP132 4.8 25.5 1.0 SG A:CYS142 4.9 9.7 1.0 CD A:GLN145 5.0 9.2 1.0 C A:CYS133 5.0 21.2 1.0

Iron binding site 3 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.5 occ:1.00 FE3 A:SF4801 0.0 25.5 1.0 NE2 A:HIS129 2.1 8.5 1.0 S4 A:SF4801 2.2 25.5 1.0 S2 A:SF4801 2.3 25.5 1.0 S1 A:SF4801 2.3 25.5 1.0 FE2 A:SF4801 2.6 25.5 1.0 FE1 A:SF4801 2.7 25.5 1.0 FE4 A:SF4801 2.7 25.5 1.0 CE1 A:HIS129 2.8 8.5 1.0 CD2 A:HIS129 3.3 8.5 1.0 S3 A:SF4801 3.8 25.5 1.0 SG A:CYS142 4.0 9.7 1.0 ND1 A:HIS129 4.0 8.5 1.0 CG A:HIS129 4.3 8.5 1.0 CD2 A:LEU144 4.5 8.6 1.0 CG1 A:VAL235 4.5 16.8 1.0 CB A:VAL235 4.7 16.8 1.0 CB A:ARG182 4.7 12.2 1.0 SG A:CYS133 4.8 21.2 1.0 SG A:CYS136 4.8 17.0 1.0 CD A:ARG182 4.8 12.2 1.0 CE C:MET378 5.0 11.4 1.0

Iron binding site 4 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:25.5 occ:1.00 FE4 A:SF4801 0.0 25.5 1.0 S3 A:SF4801 2.2 25.5 1.0 S1 A:SF4801 2.3 25.5 1.0 SG A:CYS136 2.3 17.0 1.0 S2 A:SF4801 2.3 25.5 1.0 FE2 A:SF4801 2.6 25.5 1.0 CB A:CYS136 2.7 17.0 1.0 FE3 A:SF4801 2.7 25.5 1.0 FE1 A:SF4801 2.7 25.5 1.0 S4 A:SF4801 3.9 25.5 1.0 CD A:ARG182 4.0 12.2 1.0 CA A:CYS136 4.2 17.0 1.0 NE A:ARG182 4.4 12.2 1.0 O A:GLN138 4.4 13.4 1.0 O A:ASP132 4.5 25.5 1.0 CA A:CYS133 4.6 21.2 1.0 NE2 A:HIS129 4.6 8.5 1.0 SG A:CYS142 4.6 9.7 1.0 SG A:CYS133 4.7 21.2 1.0 C A:ASP132 4.7 25.5 1.0 N A:GLY236 4.7 25.5 1.0 N A:CYS133 4.8 21.2 1.0 C A:CYS136 5.0 17.0 1.0 N A:CYS136 5.0 17.0 1.0

Iron binding site 5 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:8.8 occ:1.00 FE1 A:SF4802 0.0 8.8 1.0 S2 A:SF4802 2.2 8.8 1.0 S3 A:SF4802 2.3 8.8 1.0 S4 A:SF4802 2.3 8.8 1.0 SG A:CYS186 2.3 10.0 1.0 FE4 A:SF4802 2.6 8.8 1.0 FE2 A:SF4802 2.6 8.8 1.0 FE3 A:SF4802 2.7 8.8 1.0 N A:CYS186 3.6 10.0 1.0 CB A:CYS186 3.7 10.0 1.0 S1 A:SF4802 3.8 8.8 1.0 SG A:CYS233 3.9 25.5 1.0 CA A:CYS186 4.1 10.0 1.0 N A:THR187 4.3 8.4 1.0 CD A:PRO234 4.3 12.2 1.0 SG A:CYS183 4.4 13.2 1.0 C A:CYS186 4.4 10.0 1.0 N A:ARG188 4.5 6.1 1.0 N A:HIS185 4.6 15.0 1.0 C A:HIS185 4.7 15.0 1.0 CA A:HIS185 4.8 15.0 1.0 CB A:ARG188 4.8 6.1 1.0 CB A:CYS233 4.8 25.5 1.0 CG1 A:ILE184 4.8 25.5 1.0 CA A:CYS233 4.9 25.5 1.0 SG A:CYS189 4.9 9.4 1.0 N A:CYS189 4.9 9.4 1.0

Iron binding site 6 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:8.8 occ:1.00 FE2 A:SF4802 0.0 8.8 1.0 S1 A:SF4802 2.2 8.8 1.0 S4 A:SF4802 2.3 8.8 1.0 S3 A:SF4802 2.3 8.8 1.0 SG A:CYS183 2.3 13.2 1.0 FE4 A:SF4802 2.6 8.8 1.0 FE1 A:SF4802 2.6 8.8 1.0 FE3 A:SF4802 2.6 8.8 1.0 S2 A:SF4802 3.8 8.8 1.0 CB A:CYS183 3.9 13.2 1.0 CG1 A:ILE213 4.1 14.7 1.0 N A:HIS185 4.1 15.0 1.0 CE A:MET180 4.2 11.5 1.0 CA A:HIS185 4.3 15.0 1.0 CB A:ILE213 4.3 14.7 1.0 N A:CYS186 4.5 10.0 1.0 CG2 A:ILE213 4.5 14.7 1.0 N A:ILE184 4.6 25.5 1.0 CA A:CYS183 4.6 13.2 1.0 SG A:CYS233 4.6 25.5 1.0 SG A:CYS189 4.7 9.4 1.0 SG A:CYS186 4.8 10.0 1.0 C A:HIS185 5.0 15.0 1.0

Iron binding site 7 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:8.8 occ:1.00 FE3 A:SF4802 0.0 8.8 1.0 S4 A:SF4802 2.2 8.8 1.0 S2 A:SF4802 2.3 8.8 1.0 SG A:CYS189 2.3 9.4 1.0 S1 A:SF4802 2.3 8.8 1.0 FE2 A:SF4802 2.6 8.8 1.0 FE4 A:SF4802 2.7 8.8 1.0 FE1 A:SF4802 2.7 8.8 1.0 CB A:CYS189 3.2 9.4 1.0 N A:CYS189 3.7 9.4 1.0 S3 A:SF4802 3.9 8.8 1.0 CG2 A:ILE213 4.0 14.7 1.0 CA A:CYS189 4.0 9.4 1.0 N A:ARG188 4.4 6.1 1.0 SG A:CYS186 4.5 10.0 1.0 N A:THR187 4.6 8.4 1.0 N A:VAL190 4.7 10.1 1.0 CB A:ILE213 4.7 14.7 1.0 C A:THR187 4.7 8.4 1.0 CD1 A:LEU238 4.7 10.6 1.0 CG1 A:ILE213 4.8 14.7 1.0 C A:ARG188 4.8 6.1 1.0 SG A:CYS233 4.8 25.5 1.0 CA A:THR187 4.9 8.4 1.0 C A:CYS189 4.9 9.4 1.0 SG A:CYS183 4.9 13.2 1.0

Iron binding site 8 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:8.8 occ:1.00 FE4 A:SF4802 0.0 8.8 1.0 S3 A:SF4802 2.2 8.8 1.0 S1 A:SF4802 2.3 8.8 1.0 S2 A:SF4802 2.3 8.8 1.0 SG A:CYS233 2.3 25.5 1.0 FE1 A:SF4802 2.6 8.8 1.0 FE2 A:SF4802 2.6 8.8 1.0 FE3 A:SF4802 2.7 8.8 1.0 CB A:CYS233 3.3 25.5 1.0 S4 A:SF4802 3.8 8.8 1.0 CD1 A:LEU238 4.2 10.6 1.0 CA A:CYS233 4.2 25.5 1.0 CG A:LEU238 4.3 10.6 1.0 CB A:ALA237 4.4 13.0 1.0 SG A:CYS183 4.4 13.2 1.0 SG A:CYS189 4.5 9.4 1.0 CB A:CYS189 4.7 9.4 1.0 SG A:CYS186 4.7 10.0 1.0 N A:LEU238 4.9 10.6 1.0 CB A:LEU238 4.9 10.6 1.0

Iron binding site 9 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:9.3 occ:1.00 FE1 A:FES803 0.0 9.3 1.0 S1 A:FES803 2.2 9.3 1.0 S2 A:FES803 2.2 9.3 1.0 SG A:CYS69 2.3 7.4 1.0 SG A:CYS80 2.3 6.3 1.0 FE2 A:FES803 3.1 9.3 1.0 N A:CYS80 3.2 6.3 1.0 CB A:CYS80 3.4 6.3 1.0 N A:ARG81 3.6 6.8 1.0 CA A:CYS80 3.7 6.3 1.0 CB A:CYS69 3.7 7.4 1.0 N A:CYS69 3.9 7.4 1.0 N A:ASN79 4.0 8.0 1.0 C A:CYS80 4.0 6.3 1.0 O A:ALA77 4.0 7.3 1.0 CA A:CYS69 4.2 7.4 1.0 C A:ASN79 4.2 8.0 1.0 C A:GLY78 4.3 8.4 1.0 C A:CYS69 4.5 7.4 1.0 CA A:GLY78 4.5 8.4 1.0 SG A:CYS97 4.5 8.6 1.0 N A:MET82 4.5 7.5 1.0 CA A:ASN79 4.6 8.0 1.0 CA A:ARG81 4.7 6.8 1.0 N A:TYR68 4.8 7.2 1.0 SG A:CYS83 4.8 8.9 1.0 N A:TYR70 4.8 9.5 1.0 O A:CYS69 4.9 7.4 1.0 C A:ALA77 4.9 7.3 1.0 O A:GLY78 5.0 8.4 1.0 C A:TYR68 5.0 7.2 1.0 O A:CYS80 5.0 6.3 1.0

Iron binding site 10 out of 28 in the Cryo-Em Structure of Respiratory Complex I From Yarrowia Lipolytica at 3.2 A Resolution


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 at 3.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:9.3 occ:1.00 FE2 A:FES803 0.0 9.3 1.0 S1 A:FES803 2.2 9.3 1.0 S2 A:FES803 2.2 9.3 1.0 SG A:CYS83 2.3 8.9 1.0 SG A:CYS97 2.3 8.6 1.0 CB A:CYS97 3.0 8.6 1.0 FE1 A:FES803 3.1 9.3 1.0 CB A:CYS83 3.9 8.9 1.0 N A:CYS97 3.9 8.6 1.0 CA A:CYS97 4.1 8.6 1.0 O A:ALA77 4.4 7.3 1.0 N A:CYS83 4.5 8.9 1.0 CB A:ALA95 4.6 9.9 1.0 SG A:CYS80 4.7 6.3 1.0 SG A:CYS69 4.7 7.4 1.0 CA A:CYS83 4.7 8.9 1.0 N A:SER96 4.9 9.4 1.0

K.Parey, O.Haapanen, V.Sharma, H.Kofeler, T.Zullig, S.Prinz, K.Siegmund, I.Wittig, D.J.Mills, J.Vonck, W.Kuhlbrandt, V.Zickermann. High-Resolution Cryo-Em Structures of Respiratory Complex I: Mechanism, Assembly, and Disease. Sci Adv V. 5 X9484 2019.
ISSN: ESSN 2375-2548
PubMed: 31844670
DOI: 10.1126/SCIADV.AAX9484