Iron in PDB 8bee: Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)

All present enzymatic activity of Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core):
7.1.1.2;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) (pdb code 8bee). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core), PDB code: 8bee:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:12.1 occ:1.00 FE1 B:SF4500 0.0 12.1 1.0 S2 B:SF4500 2.3 5.8 1.0 SG B:CYS158 2.3 2.9 1.0 S4 B:SF4500 2.3 1.3 1.0 S3 B:SF4500 2.3 7.3 1.0 FE3 B:SF4500 2.7 11.6 1.0 FE4 B:SF4500 2.7 11.3 1.0 FE2 B:SF4500 2.7 12.1 1.0 CB B:CYS158 3.0 1.4 1.0 O B:HOH682 3.3 1.8 1.0 O B:HOH641 3.8 3.1 1.0 S1 B:SF4500 3.9 0.0 1.0 OG1 B:THR130 3.9 5.2 1.0 N B:CYS158 3.9 0.1 1.0 CA B:CYS158 4.1 3.8 1.0 SG B:CYS188 4.5 0.2 1.0 N B:THR130 4.6 2.3 1.0 SG B:CYS94 4.8 3.6 1.0 CE2 B:TYR165 4.8 3.8 1.0 SG B:CYS93 4.9 0.0 1.0 CA B:GLY129 4.9 0.9 1.0 C B:GLY129 4.9 1.0 1.0

Iron binding site 2 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:12.1 occ:1.00 FE2 B:SF4500 0.0 12.1 1.0 SG B:CYS94 2.3 3.6 1.0 S3 B:SF4500 2.3 7.3 1.0 S4 B:SF4500 2.3 1.3 1.0 S1 B:SF4500 2.3 0.0 1.0 FE4 B:SF4500 2.7 11.3 1.0 FE3 B:SF4500 2.7 11.6 1.0 FE1 B:SF4500 2.7 12.1 1.0 CB B:CYS94 3.4 2.8 1.0 O B:HOH641 3.5 3.1 1.0 N B:CYS94 3.6 1.7 1.0 S2 B:SF4500 3.9 5.8 1.0 CA B:CYS94 3.9 3.8 1.0 CA B:PRO189 4.3 0.7 1.0 CB B:PRO189 4.3 4.2 1.0 C B:CYS93 4.6 3.4 1.0 CA B:GLY156 4.6 1.0 1.0 SG B:CYS93 4.7 0.0 1.0 CB B:CYS93 4.7 0.0 1.0 N B:PRO189 4.7 4.3 1.0 CA B:CYS188 4.7 0.8 1.0 CA B:GLY129 4.8 0.9 1.0 SG B:CYS188 4.9 0.2 1.0 SG B:CYS158 4.9 2.9 1.0 N B:CYS93 4.9 0.3 1.0 CA B:CYS93 5.0 2.9 1.0 C B:CYS188 5.0 0.1 1.0 CB B:CYS158 5.0 1.4 1.0

Iron binding site 3 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:11.6 occ:1.00 FE3 B:SF4500 0.0 11.6 1.0 SG B:CYS188 2.3 0.2 1.0 S4 B:SF4500 2.3 1.3 1.0 S2 B:SF4500 2.3 5.8 1.0 S1 B:SF4500 2.3 0.0 1.0 FE1 B:SF4500 2.7 12.1 1.0 FE2 B:SF4500 2.7 12.1 1.0 FE4 B:SF4500 2.8 11.3 1.0 CB B:CYS188 3.4 0.6 1.0 CA B:CYS188 3.4 0.8 1.0 O B:HOH682 3.4 1.8 1.0 C B:CYS188 3.7 0.1 1.0 S3 B:SF4500 3.9 7.3 1.0 O B:CYS188 4.1 3.1 1.0 NE D:ARG69 4.1 0.0 1.0 N B:PRO189 4.1 4.3 1.0 CD2 D:HIS154 4.4 0.0 1.0 NE2 D:HIS154 4.5 0.0 1.0 CA B:PRO189 4.5 0.7 1.0 SG B:CYS158 4.6 2.9 1.0 NH2 D:ARG69 4.7 0.0 1.0 SG B:CYS94 4.8 3.6 1.0 N B:CYS188 4.8 0.0 1.0 SG B:CYS93 4.8 0.0 1.0 CZ D:ARG69 4.9 0.0 1.0 O B:GLY187 4.9 0.7 1.0 CD D:ARG69 4.9 0.0 1.0 CD B:PRO189 4.9 1.6 1.0

Iron binding site 4 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:11.3 occ:1.00 FE4 B:SF4500 0.0 11.3 1.0 S1 B:SF4500 2.3 0.0 1.0 S3 B:SF4500 2.3 7.3 1.0 SG B:CYS93 2.3 0.0 1.0 S2 B:SF4500 2.3 5.8 1.0 FE2 B:SF4500 2.7 12.1 1.0 FE1 B:SF4500 2.7 12.1 1.0 FE3 B:SF4500 2.8 11.6 1.0 CB B:CYS93 3.2 0.0 1.0 N B:CYS93 3.9 0.3 1.0 NE2 D:HIS154 3.9 0.0 1.0 S4 B:SF4500 3.9 1.3 1.0 CA B:CYS93 4.0 2.9 1.0 N B:CYS94 4.2 1.7 1.0 C B:CYS93 4.5 3.4 1.0 CG D:ARG69 4.6 0.0 1.0 CB B:ALA92 4.6 4.3 1.0 CD2 D:HIS154 4.6 0.0 1.0 SG B:CYS158 4.8 2.9 1.0 SG B:CYS188 4.8 0.2 1.0 SG B:CYS94 4.8 3.6 1.0 CE1 D:HIS154 4.9 0.0 1.0 NE D:ARG69 4.9 0.0 1.0 NH1 D:ARG49 4.9 0.0 1.0 C B:ALA92 4.9 5.0 1.0 CD D:ARG69 5.0 0.0 1.0

Iron binding site 5 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe500 b:10.2 occ:1.00 FE1 I:SF4500 0.0 10.2 1.0 S4 I:SF4500 2.3 0.0 1.0 S3 I:SF4500 2.3 0.0 1.0 SG I:CYS168 2.3 0.0 1.0 S2 I:SF4500 2.3 2.7 1.0 NE2 I:HIS111 2.5 6.9 1.0 FE2 I:SF4500 2.7 2.7 1.0 FE3 I:SF4500 2.8 9.7 1.0 FE4 I:SF4500 2.8 10.6 1.0 CB I:CYS168 3.3 0.0 1.0 CE1 I:HIS111 3.5 4.0 1.0 CD2 I:HIS111 3.5 2.0 1.0 S1 I:SF4500 3.9 0.0 1.0 N I:CYS168 4.0 0.0 1.0 CA I:CYS168 4.3 0.0 1.0 SG I:CYS162 4.6 0.0 1.0 CD1 I:ILE138 4.6 0.0 1.0 ND1 I:HIS111 4.6 8.0 1.0 CG I:HIS111 4.7 6.0 1.0 N I:GLY166 4.8 0.0 1.0 SG I:CYS165 4.8 0.0 1.0 OE2 I:GLU179 4.9 7.4 1.0 N I:PHE167 4.9 0.0 1.0

Iron binding site 6 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe500 b:2.7 occ:1.00 FE2 I:SF4500 0.0 2.7 1.0 SG I:CYS162 2.3 0.0 1.0 S4 I:SF4500 2.3 0.0 1.0 S3 I:SF4500 2.3 0.0 1.0 S1 I:SF4500 2.3 0.0 1.0 FE1 I:SF4500 2.7 10.2 1.0 FE4 I:SF4500 2.7 10.6 1.0 FE3 I:SF4500 2.7 9.7 1.0 CB I:CYS162 3.1 0.0 1.0 CE1 I:HIS111 3.5 4.0 1.0 NE2 I:HIS111 3.5 6.9 1.0 CA I:CYS162 3.7 0.0 1.0 N I:TYR164 3.8 0.0 1.0 N I:ILE163 3.8 0.0 1.0 S2 I:SF4500 3.9 2.7 1.0 C I:CYS162 4.2 0.0 1.0 CA I:TYR164 4.4 0.0 1.0 SG I:CYS133 4.6 0.0 1.0 ND1 I:HIS111 4.7 8.0 1.0 N I:CYS165 4.7 0.0 1.0 C I:ILE163 4.8 0.0 1.0 CD2 I:HIS111 4.8 2.0 1.0 CA I:ILE163 4.9 0.0 1.0 SG I:CYS165 4.9 0.0 1.0 SG I:CYS168 4.9 0.0 1.0 N I:CYS162 5.0 1.7 1.0 CB I:ALA137 5.0 0.0 1.0

Iron binding site 7 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe500 b:9.7 occ:1.00 FE3 I:SF4500 0.0 9.7 1.0 S2 I:SF4500 2.3 2.7 1.0 S1 I:SF4500 2.3 0.0 1.0 SG I:CYS165 2.3 0.0 1.0 S4 I:SF4500 2.3 0.0 1.0 FE2 I:SF4500 2.7 2.7 1.0 FE4 I:SF4500 2.7 10.6 1.0 FE1 I:SF4500 2.8 10.2 1.0 N I:CYS165 3.5 0.0 1.0 CB I:CYS165 3.7 0.0 1.0 N I:GLY166 3.8 0.0 1.0 S3 I:SF4500 3.9 0.0 1.0 CA I:CYS165 4.0 0.0 1.0 N I:PHE167 4.1 0.0 1.0 CD I:PRO134 4.3 0.0 1.0 C I:CYS165 4.3 0.8 1.0 N I:TYR164 4.4 0.0 1.0 CG1 I:ILE163 4.5 0.0 1.0 SG I:CYS168 4.5 0.0 1.0 C I:TYR164 4.6 0.0 1.0 N I:CYS168 4.6 0.0 1.0 SG I:CYS162 4.6 0.0 1.0 SG I:CYS133 4.7 0.0 1.0 CA I:GLY166 4.7 0.0 1.0 CA I:TYR164 4.7 0.0 1.0 NE2 I:HIS111 4.7 6.9 1.0 CB I:PHE167 4.7 0.0 1.0 C I:GLY166 4.8 0.0 1.0 N I:ILE163 4.9 0.0 1.0 CA I:PHE167 4.9 0.0 1.0

Iron binding site 8 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe500 b:10.6 occ:1.00 FE4 I:SF4500 0.0 10.6 1.0 S1 I:SF4500 2.3 0.0 1.0 S2 I:SF4500 2.3 2.7 1.0 S3 I:SF4500 2.3 0.0 1.0 SG I:CYS133 2.3 0.0 1.0 FE2 I:SF4500 2.7 2.7 1.0 FE3 I:SF4500 2.7 9.7 1.0 FE1 I:SF4500 2.8 10.2 1.0 CB I:CYS133 3.2 0.0 1.0 CA I:CYS133 3.8 0.0 1.0 S4 I:SF4500 3.9 0.0 1.0 CD1 I:ILE138 4.3 0.0 1.0 CD I:PRO134 4.3 0.0 1.0 C I:CYS133 4.5 0.0 1.0 N I:PRO134 4.6 2.1 1.0 SG I:CYS168 4.7 0.0 1.0 SG I:CYS165 4.7 0.0 1.0 CB I:ALA137 4.8 0.0 1.0 CB I:CYS168 4.8 0.0 1.0 CG1 I:ILE138 4.8 6.1 1.0 NE2 I:HIS111 4.9 6.9 1.0 SG I:CYS162 4.9 0.0 1.0

Iron binding site 9 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe501 b:11.3 occ:1.00 FE1 I:SF4501 0.0 11.3 1.0 S4 I:SF4501 2.3 0.2 1.0 S3 I:SF4501 2.3 3.1 1.0 S2 I:SF4501 2.3 0.9 1.0 SG I:CYS172 2.3 0.0 1.0 FE3 I:SF4501 2.7 9.0 1.0 FE2 I:SF4501 2.7 9.9 1.0 FE4 I:SF4501 2.7 13.8 1.0 CB I:CYS172 3.2 0.0 1.0 CA I:CYS172 3.8 0.0 1.0 S1 I:SF4501 3.9 0.0 1.0 CB I:ALA176 3.9 0.0 1.0 CD I:PRO173 4.2 0.0 1.0 CG2 I:ILE177 4.2 0.0 1.0 N I:ILE177 4.5 1.3 1.0 CG2 I:VAL174 4.5 0.0 1.0 SG I:CYS126 4.6 1.3 1.0 C I:CYS172 4.6 0.0 1.0 N I:ALA176 4.7 0.0 1.0 N I:PRO173 4.7 0.3 1.0 CA I:ALA176 4.8 0.0 1.0 SG I:CYS129 4.8 0.0 1.0 SG I:CYS123 4.8 0.0 1.0 CB I:ILE177 4.9 0.0 1.0

Iron binding site 10 out of 12 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core)


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 the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Core) within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe501 b:9.9 occ:1.00 FE2 I:SF4501 0.0 9.9 1.0 S3 I:SF4501 2.3 3.1 1.0 S4 I:SF4501 2.3 0.2 1.0 S1 I:SF4501 2.3 0.0 1.0 SG I:CYS123 2.3 0.0 1.0 FE3 I:SF4501 2.7 9.0 1.0 FE4 I:SF4501 2.7 13.8 1.0 FE1 I:SF4501 2.7 11.3 1.0 CB I:CYS123 3.3 0.0 1.0 CA I:CYS123 3.7 0.0 1.0 S2 I:SF4501 3.9 0.9 1.0 N I:ALA125 3.9 0.0 1.0 N I:ILE124 4.0 0.0 1.0 C I:CYS123 4.3 0.0 1.0 CE2 I:TYR155 4.4 0.0 1.0 CA I:ALA125 4.4 7.6 1.0 CB I:ALA176 4.4 0.0 1.0 N I:CYS126 4.5 0.1 1.0 SG I:CYS129 4.8 0.0 1.0 SG I:CYS172 4.8 0.0 1.0 C I:ILE124 4.9 1.4 1.0 O I:HOH673 4.9 1.5 1.0 SG I:CYS126 5.0 1.3 1.0 CD2 I:TYR155 5.0 0.5 1.0 C I:ALA125 5.0 0.1 1.0

N.Klusch, M.Dreimann, J.Senkler, N.Rugen, W.Kuhlbrandt, H.P.Braun. Cryo-Em Structure of the Respiratory I + III 2 Supercomplex From Arabidopsis Thaliana at 2 Angstrom Resolution. Nat.Plants 2022.
ISSN: ESSN 2055-0278
PubMed: 36585502
DOI: 10.1038/S41477-022-01308-6