Iron in PDB 6rfq: Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2

All present enzymatic activity of Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2:
1.6.5.3; 1.6.99.3; 7.1.1.2;

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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 (pdb code 6rfq). 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 A Respiratory Complex I Assembly Intermediate with NDUFAF2, PDB code: 6rfq:
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 A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:21.6 occ:1.00 FE1 A:SF4801 0.0 21.6 1.0 S2 A:SF4801 2.2 21.6 1.0 S3 A:SF4801 2.3 21.6 1.0 S4 A:SF4801 2.3 21.6 1.0 SG A:CYS142 2.3 27.0 1.0 FE3 A:SF4801 2.6 21.6 1.0 FE2 A:SF4801 2.7 21.6 1.0 FE4 A:SF4801 2.7 21.6 1.0 CB A:CYS142 3.0 27.0 1.0 O A:GLN138 3.7 27.7 1.0 S1 A:SF4801 3.8 21.6 1.0 OE1 A:GLN145 3.9 23.7 1.0 SG A:CYS136 4.3 26.1 1.0 CB A:GLN145 4.3 23.7 1.0 SG A:CYS133 4.4 21.3 1.0 CA A:CYS142 4.4 27.0 1.0 CD A:GLN145 4.6 23.7 1.0 NE2 A:HIS129 4.7 28.7 1.0 CB A:GLN138 4.7 27.7 1.0 C A:GLN138 4.8 27.7 1.0 CG A:GLN145 4.9 23.7 1.0

Iron binding site 2 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:21.6 occ:1.00 FE2 A:SF4801 0.0 21.6 1.0 S1 A:SF4801 2.2 21.6 1.0 S4 A:SF4801 2.3 21.6 1.0 S3 A:SF4801 2.3 21.6 1.0 SG A:CYS133 2.3 21.3 1.0 FE3 A:SF4801 2.6 21.6 1.0 FE1 A:SF4801 2.7 21.6 1.0 FE4 A:SF4801 2.7 21.6 1.0 CB A:CYS133 3.7 21.3 1.0 S2 A:SF4801 3.8 21.6 1.0 NE2 A:HIS129 3.8 28.7 1.0 CA A:CYS133 4.0 21.3 1.0 N A:CYS133 4.0 21.3 1.0 CE C:MET378 4.2 29.8 1.0 OE1 A:GLN145 4.6 23.7 1.0 CD2 A:HIS129 4.6 28.7 1.0 C A:ASP132 4.7 25.4 1.0 SG A:CYS142 4.7 27.0 1.0 CB A:CYS136 4.8 26.1 1.0 CD A:GLN145 4.8 23.7 1.0 SG A:CYS136 4.9 26.1 1.0 CE1 A:HIS129 4.9 28.7 1.0 N A:ASP132 5.0 25.4 1.0

Iron binding site 3 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:21.6 occ:1.00 FE3 A:SF4801 0.0 21.6 1.0 NE2 A:HIS129 2.1 28.7 1.0 S4 A:SF4801 2.2 21.6 1.0 S2 A:SF4801 2.3 21.6 1.0 S1 A:SF4801 2.3 21.6 1.0 FE2 A:SF4801 2.6 21.6 1.0 FE1 A:SF4801 2.6 21.6 1.0 CE1 A:HIS129 2.7 28.7 1.0 FE4 A:SF4801 2.7 21.6 1.0 CD2 A:HIS129 3.4 28.7 1.0 S3 A:SF4801 3.8 21.6 1.0 ND1 A:HIS129 3.9 28.7 1.0 SG A:CYS142 4.1 27.0 1.0 CG A:HIS129 4.3 28.7 1.0 CD2 A:LEU144 4.6 26.9 1.0 CD A:ARG182 4.6 29.2 1.0 CB A:VAL235 4.7 24.3 1.0 CG1 A:VAL235 4.7 24.3 1.0 SG A:CYS136 4.8 26.1 1.0 SG A:CYS133 4.9 21.3 1.0 CB A:ARG182 4.9 29.2 1.0

Iron binding site 4 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:21.6 occ:1.00 FE4 A:SF4801 0.0 21.6 1.0 S3 A:SF4801 2.2 21.6 1.0 S1 A:SF4801 2.3 21.6 1.0 S2 A:SF4801 2.3 21.6 1.0 SG A:CYS136 2.3 26.1 1.0 FE1 A:SF4801 2.7 21.6 1.0 FE3 A:SF4801 2.7 21.6 1.0 FE2 A:SF4801 2.7 21.6 1.0 CB A:CYS136 2.8 26.1 1.0 CD A:ARG182 3.7 29.2 1.0 S4 A:SF4801 3.9 21.6 1.0 NE A:ARG182 4.3 29.2 1.0 CA A:CYS136 4.3 26.1 1.0 NE2 A:HIS129 4.5 28.7 1.0 SG A:CYS133 4.5 21.3 1.0 O A:GLN138 4.5 27.7 1.0 N A:CYS133 4.6 21.3 1.0 CA A:CYS133 4.7 21.3 1.0 C A:ASP132 4.7 25.4 1.0 N A:GLY236 4.7 26.2 1.0 CB A:ASP132 4.7 25.4 1.0 O A:ASP132 4.7 25.4 1.0 CG A:ARG182 4.8 29.2 1.0 SG A:CYS142 4.8 27.0 1.0 CE1 A:HIS129 4.9 28.7 1.0

Iron binding site 5 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:30.9 occ:1.00 FE1 A:SF4802 0.0 30.9 1.0 S2 A:SF4802 2.2 30.9 1.0 S3 A:SF4802 2.3 30.9 1.0 S4 A:SF4802 2.3 30.9 1.0 SG A:CYS186 2.3 29.2 1.0 FE4 A:SF4802 2.6 30.9 1.0 FE2 A:SF4802 2.7 30.9 1.0 FE3 A:SF4802 2.7 30.9 1.0 N A:CYS186 3.7 29.2 1.0 CB A:CYS186 3.7 29.2 1.0 S1 A:SF4802 3.8 30.9 1.0 SG A:CYS233 3.9 26.8 1.0 CD A:PRO234 4.1 25.0 1.0 CA A:CYS186 4.1 29.2 1.0 N A:THR187 4.3 30.3 1.0 SG A:CYS183 4.4 29.6 1.0 C A:CYS186 4.4 29.2 1.0 N A:ARG188 4.5 27.1 1.0 CB A:CYS233 4.7 26.8 1.0 CB A:ARG188 4.7 27.1 1.0 N A:HIS185 4.7 32.0 1.0 CA A:CYS233 4.8 26.8 1.0 C A:HIS185 4.8 32.0 1.0 CG A:PRO234 4.8 25.0 1.0 N A:CYS189 4.8 32.1 1.0 CA A:HIS185 4.9 32.0 1.0 CG1 A:ILE184 5.0 27.9 1.0 SG A:CYS189 5.0 32.1 1.0

Iron binding site 6 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:30.9 occ:1.00 FE2 A:SF4802 0.0 30.9 1.0 S1 A:SF4802 2.3 30.9 1.0 S3 A:SF4802 2.3 30.9 1.0 S4 A:SF4802 2.3 30.9 1.0 SG A:CYS183 2.3 29.6 1.0 FE3 A:SF4802 2.7 30.9 1.0 FE1 A:SF4802 2.7 30.9 1.0 FE4 A:SF4802 2.7 30.9 1.0 CB A:CYS183 3.7 29.6 1.0 S2 A:SF4802 3.8 30.9 1.0 N A:HIS185 4.1 32.0 1.0 CG1 A:ILE213 4.3 41.2 1.0 CA A:HIS185 4.3 32.0 1.0 CA A:CYS183 4.4 29.6 1.0 N A:CYS186 4.5 29.2 1.0 SG A:CYS189 4.5 32.1 1.0 N A:ILE184 4.6 27.9 1.0 CB A:ILE213 4.6 41.2 1.0 SG A:CYS233 4.7 26.8 1.0 CE A:MET180 4.7 37.5 1.0 SG A:CYS186 4.8 29.2 1.0 CG2 A:ILE213 4.8 41.2 1.0 C A:CYS183 5.0 29.6 1.0

Iron binding site 7 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:30.9 occ:1.00 FE3 A:SF4802 0.0 30.9 1.0 S4 A:SF4802 2.2 30.9 1.0 S2 A:SF4802 2.3 30.9 1.0 SG A:CYS189 2.3 32.1 1.0 S1 A:SF4802 2.3 30.9 1.0 FE2 A:SF4802 2.7 30.9 1.0 FE1 A:SF4802 2.7 30.9 1.0 FE4 A:SF4802 2.7 30.9 1.0 CB A:CYS189 2.9 32.1 1.0 N A:CYS189 3.4 32.1 1.0 CA A:CYS189 3.8 32.1 1.0 S3 A:SF4802 3.9 30.9 1.0 N A:ARG188 4.2 27.1 1.0 SG A:CYS186 4.4 29.2 1.0 CG2 A:ILE213 4.5 41.2 1.0 C A:ARG188 4.5 27.1 1.0 N A:THR187 4.6 30.3 1.0 C A:THR187 4.7 30.3 1.0 N A:VAL190 4.7 33.9 1.0 C A:CYS189 4.8 32.1 1.0 CD1 A:LEU238 4.8 33.6 1.0 CA A:ARG188 4.8 27.1 1.0 CA A:THR187 4.9 30.3 1.0 SG A:CYS233 4.9 26.8 1.0 SG A:CYS183 5.0 29.6 1.0

Iron binding site 8 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:30.9 occ:1.00 FE4 A:SF4802 0.0 30.9 1.0 S3 A:SF4802 2.2 30.9 1.0 SG A:CYS233 2.3 26.8 1.0 S1 A:SF4802 2.3 30.9 1.0 S2 A:SF4802 2.3 30.9 1.0 FE1 A:SF4802 2.6 30.9 1.0 FE2 A:SF4802 2.7 30.9 1.0 FE3 A:SF4802 2.7 30.9 1.0 CB A:CYS233 3.1 26.8 1.0 S4 A:SF4802 3.8 30.9 1.0 CA A:CYS233 4.0 26.8 1.0 CB A:ALA237 4.3 30.0 1.0 CD1 A:LEU238 4.3 33.6 1.0 CG A:LEU238 4.5 33.6 1.0 SG A:CYS183 4.5 29.6 1.0 SG A:CYS189 4.7 32.1 1.0 CB A:CYS189 4.7 32.1 1.0 SG A:CYS186 4.8 29.2 1.0 CD A:PRO234 4.9 25.0 1.0 C A:CYS233 4.9 26.8 1.0 CG2 A:VAL235 4.9 24.3 1.0 N A:LEU238 4.9 33.6 1.0

Iron binding site 9 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:32.8 occ:1.00 FE1 A:FES803 0.0 32.8 1.0 S2 A:FES803 2.2 32.8 1.0 S1 A:FES803 2.2 32.8 1.0 SG A:CYS69 2.3 29.3 1.0 SG A:CYS80 2.3 29.8 1.0 FE2 A:FES803 3.0 32.8 1.0 N A:CYS80 3.3 29.8 1.0 CB A:CYS80 3.4 29.8 1.0 O A:ALA77 3.7 30.1 1.0 N A:ARG81 3.8 31.0 1.0 CB A:CYS69 3.8 29.3 1.0 CA A:CYS80 3.8 29.8 1.0 N A:CYS69 4.0 29.3 1.0 N A:ASN79 4.1 32.2 1.0 SG A:CYS97 4.1 34.9 1.0 C A:CYS80 4.2 29.8 1.0 C A:GLY78 4.2 30.9 1.0 CA A:GLY78 4.2 30.9 1.0 CA A:CYS69 4.3 29.3 1.0 C A:ASN79 4.4 32.2 1.0 C A:CYS69 4.5 29.3 1.0 C A:ALA77 4.6 30.1 1.0 N A:TYR70 4.7 33.1 1.0 N A:MET82 4.8 32.6 1.0 CA A:ASN79 4.8 32.2 1.0 CA A:ARG81 4.8 31.0 1.0 O A:GLY78 4.8 30.9 1.0 N A:GLY78 4.9 30.9 1.0 O A:CYS69 4.9 29.3 1.0 N A:TYR68 5.0 30.4 1.0 SG A:CYS83 5.0 34.3 1.0

Iron binding site 10 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Assembly Intermediate with NDUFAF2


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 A Respiratory Complex I Assembly Intermediate with NDUFAF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:32.8 occ:1.00 FE2 A:FES803 0.0 32.8 1.0 S1 A:FES803 2.2 32.8 1.0 S2 A:FES803 2.2 32.8 1.0 SG A:CYS83 2.3 34.3 1.0 SG A:CYS97 2.3 34.9 1.0 CB A:CYS97 2.9 34.9 1.0 FE1 A:FES803 3.0 32.8 1.0 N A:CYS97 3.8 34.9 1.0 CB A:CYS83 3.8 34.3 1.0 CA A:CYS97 3.9 34.9 1.0 N A:CYS83 4.4 34.3 1.0 SG A:CYS80 4.5 29.8 1.0 CB A:ALA95 4.6 34.1 1.0 O A:ALA77 4.7 30.1 1.0 CA A:CYS83 4.7 34.3 1.0 N A:SER96 4.8 35.6 1.0 C A:SER96 4.9 35.6 1.0 C A:CYS97 4.9 34.9 1.0 SG A:CYS69 4.9 29.3 1.0 CB A:TYR70 5.0 33.1 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