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

Enzymatic activity of Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)

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

Other elements in 8bed:

The structure of Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip) (pdb code 8bed). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip), PDB code: 8bed:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8bed

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Iron binding site 1 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:38.0
occ:1.00
 FE1 E:FES500 0.0 38.0 1.0
S1 E:FES500 2.2 32.9 1.0
S2 E:FES500 2.2 27.6 1.0
SD E:MET169 2.3 15.6 1.0
SG E:CYS171 2.3 29.6 1.0
FE2 E:FES500 2.7 38.8 1.0
CE E:MET169 2.8 10.9 1.0
O E:HOH685 3.3 11.8 1.0
CG E:MET169 3.4 13.1 1.0
CA E:GLY131 3.4 19.6 1.0
SG E:CYS135 3.5 28.4 1.0
CB E:CYS171 4.0 17.9 1.0
O E:MET180 4.0 17.9 1.0
N E:GLY131 4.1 19.2 1.0
O E:HOH638 4.2 14.4 1.0
CB E:CYS135 4.3 27.9 1.0
C E:GLY131 4.6 22.2 1.0
N E:THR132 4.6 22.1 1.0
CA E:CYS171 4.7 17.2 1.0
C E:MET180 4.7 15.1 1.0
SG E:CYS175 4.7 28.4 1.0
N E:MET180 4.8 16.5 1.0
CB E:MET169 4.8 12.1 1.0
CB E:MET180 4.9 15.6 1.0

Iron binding site 2 out of 16 in 8bed

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Iron binding site 2 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:38.8
occ:1.00
 FE2 E:FES500 0.0 38.8 1.0
CB E:CYS135 2.1 27.9 1.0
S1 E:FES500 2.2 32.9 1.0
S2 E:FES500 2.2 27.6 1.0
SG E:CYS175 2.3 28.4 1.0
SG E:CYS135 2.3 28.4 1.0
FE1 E:FES500 2.7 38.0 1.0
CA E:CYS135 3.4 26.1 1.0
SG E:CYS171 3.5 29.6 1.0
CB E:CYS175 3.6 20.6 1.0
N E:CYS135 3.7 25.9 1.0
O E:HOH685 4.2 11.8 1.0
C E:CYS135 4.5 27.5 1.0
CB E:CYS171 4.6 17.9 1.0
CA E:CYS175 4.6 20.6 1.0
C E:PRO134 4.7 24.2 1.0
O E:THR132 4.7 24.3 1.0
CA E:GLY131 4.8 19.6 1.0
N E:MET180 4.8 16.5 1.0
CE E:MET180 4.9 14.3 1.0
CG E:PRO134 4.9 25.0 1.0
N E:THR132 4.9 22.1 1.0
SD E:MET169 4.9 15.6 1.0
O E:ALA178 5.0 22.0 1.0

Iron binding site 3 out of 16 in 8bed

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Iron binding site 3 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:6.1
occ:1.00
 FE1 F:SF4501 0.0 6.1 1.0
SG F:CYS405 2.3 0.0 1.0
S3 F:SF4501 2.3 0.0 1.0
S4 F:SF4501 2.3 0.0 1.0
S2 F:SF4501 2.3 0.0 1.0
FE2 F:SF4501 2.7 22.9 1.0
FE3 F:SF4501 2.7 0.0 1.0
FE4 F:SF4501 2.7 0.0 1.0
CB F:CYS405 3.5 0.0 1.0
N F:CYS405 3.8 0.0 1.0
CB F:CYS408 3.8 0.0 1.0
S1 F:SF4501 3.9 0.0 1.0
CA F:CYS405 4.1 0.0 1.0
N F:ILE447 4.2 1.8 1.0
CB F:ILE447 4.3 0.0 1.0
O F:CYS405 4.4 0.0 1.0
SG F:CYS408 4.5 0.0 1.0
CB F:THR446 4.5 0.0 1.0
N F:CYS448 4.7 0.0 1.0
C F:CYS405 4.7 0.0 1.0
CB F:GLN404 4.7 0.9 1.0
SG F:CYS402 4.8 0.0 1.0
N F:GLN404 4.8 0.0 1.0
SG F:CYS448 4.8 0.0 1.0
CA F:ILE447 4.8 0.0 1.0
C F:GLN404 4.8 0.0 1.0
CG1 F:ILE447 4.9 0.0 1.0
CD1 F:ILE447 4.9 0.0 1.0

Iron binding site 4 out of 16 in 8bed

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Iron binding site 4 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:22.9
occ:1.00
 FE2 F:SF4501 0.0 22.9 1.0
SG F:CYS408 2.3 0.0 1.0
S3 F:SF4501 2.3 0.0 1.0
S1 F:SF4501 2.3 0.0 1.0
S4 F:SF4501 2.3 0.0 1.0
FE1 F:SF4501 2.7 6.1 1.0
FE4 F:SF4501 2.7 0.0 1.0
FE3 F:SF4501 2.7 0.0 1.0
CB F:CYS408 2.8 0.0 1.0
OG F:SER401 3.5 0.0 1.0
S2 F:SF4501 3.9 0.0 1.0
CD2 F:LEU450 3.9 0.0 1.0
CA F:CYS408 4.3 0.0 1.0
SG F:CYS405 4.4 0.0 1.0
CB F:SER401 4.4 0.0 1.0
CB F:LEU450 4.4 0.0 1.0
N F:CYS402 4.4 0.0 1.0
CA F:SER401 4.6 0.0 1.0
CG F:LEU450 4.7 0.0 1.0
SG F:CYS448 4.7 0.0 1.0
N F:GLY451 4.7 0.0 1.0
N F:GLY403 4.8 0.0 1.0
SG F:CYS402 4.8 0.0 1.0
C F:CYS408 4.8 0.0 1.0
C F:SER401 5.0 0.0 1.0
N F:ARG409 5.0 0.0 1.0

Iron binding site 5 out of 16 in 8bed

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Iron binding site 5 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:0.0
occ:1.00
 FE3 F:SF4501 0.0 0.0 1.0
SG F:CYS402 2.3 0.0 1.0
S4 F:SF4501 2.3 0.0 1.0
S1 F:SF4501 2.3 0.0 1.0
S2 F:SF4501 2.3 0.0 1.0
FE4 F:SF4501 2.7 0.0 1.0
FE1 F:SF4501 2.7 6.1 1.0
FE2 F:SF4501 2.7 22.9 1.0
CB F:CYS402 3.4 0.0 1.0
N F:CYS402 3.8 0.0 1.0
N F:GLN404 3.8 0.0 1.0
N F:GLY403 3.8 0.0 1.0
S3 F:SF4501 3.9 0.0 1.0
CA F:CYS402 4.0 2.3 1.0
CB F:GLN404 4.1 0.9 1.0
C F:CYS402 4.2 0.0 1.0
CD F:PRO246 4.3 0.0 1.0
CA F:GLN404 4.5 0.0 1.0
N F:CYS405 4.6 0.0 1.0
OG F:SER401 4.7 0.0 1.0
CG F:PRO246 4.7 0.9 1.0
C F:GLY403 4.7 0.0 1.0
CA F:GLY403 4.8 0.0 1.0
NE2 F:GLN404 4.8 0.0 1.0
SG F:CYS448 4.8 0.0 1.0
SG F:CYS405 4.8 0.0 1.0
SG F:CYS408 4.9 0.0 1.0
C F:SER401 4.9 0.0 1.0
CG1 F:ILE228 4.9 0.0 1.0

Iron binding site 6 out of 16 in 8bed

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Iron binding site 6 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:0.0
occ:1.00
 FE4 F:SF4501 0.0 0.0 1.0
SG F:CYS448 2.3 0.0 1.0
S3 F:SF4501 2.3 0.0 1.0
S1 F:SF4501 2.3 0.0 1.0
S2 F:SF4501 2.3 0.0 1.0
FE3 F:SF4501 2.7 0.0 1.0
FE1 F:SF4501 2.7 6.1 1.0
FE2 F:SF4501 2.7 22.9 1.0
CB F:CYS448 3.4 0.0 1.0
S4 F:SF4501 3.9 0.0 1.0
N F:CYS448 3.9 0.0 1.0
CB F:LEU450 4.1 0.0 1.0
CA F:CYS448 4.1 2.1 1.0
CG F:PRO246 4.1 0.9 1.0
C F:CYS448 4.4 0.0 1.0
CD1 F:ILE228 4.4 0.0 1.0
O F:CYS448 4.4 0.1 1.0
CD F:PRO246 4.6 0.0 1.0
N F:LEU450 4.6 0.4 1.0
SG F:CYS402 4.7 0.0 1.0
SG F:CYS408 4.8 0.0 1.0
SG F:CYS405 4.8 0.0 1.0
CA F:LEU450 4.9 0.0 1.0
CB F:PRO246 5.0 0.0 1.0
N F:GLY451 5.0 0.0 1.0

Iron binding site 7 out of 16 in 8bed

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Iron binding site 7 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe801

b:38.5
occ:1.00
 FE1 G:FES801 0.0 38.5 1.0
S2 G:FES801 2.2 0.0 1.0
S1 G:FES801 2.2 0.0 1.0
SG G:CYS117 2.3 0.0 1.0
SG G:CYS106 2.3 0.0 1.0
FE2 G:FES801 2.7 44.9 1.0
CB G:CYS117 3.4 0.0 1.0
N G:CYS117 3.5 0.0 1.0
CB G:CYS106 3.6 0.0 1.0
N G:ARG118 3.7 0.0 1.0
N G:CYS106 3.7 0.0 1.0
CA G:CYS117 3.8 0.1 1.0
CA G:CYS106 4.1 3.2 1.0
C G:CYS117 4.1 0.0 1.0
N G:TYR107 4.2 0.0 1.0
O G:HOH1137 4.2 0.0 1.0
N G:ASN116 4.3 0.0 1.0
N G:MET119 4.3 0.0 1.0
SG G:CYS134 4.4 0.0 1.0
N G:PHE105 4.5 1.7 1.0
C G:CYS106 4.5 0.0 1.0
CA G:GLY115 4.5 0.0 1.0
SG G:CYS120 4.6 0.0 1.0
C G:ASN116 4.6 0.0 1.0
C G:GLY115 4.6 0.0 1.0
CA G:ARG118 4.6 0.0 1.0
C G:PHE105 4.8 0.0 1.0
N G:GLY115 4.8 0.0 1.0
N G:CYS120 4.9 0.0 1.0

Iron binding site 8 out of 16 in 8bed

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Iron binding site 8 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe801

b:44.9
occ:1.00
 FE2 G:FES801 0.0 44.9 1.0
S2 G:FES801 2.2 0.0 1.0
S1 G:FES801 2.2 0.0 1.0
SG G:CYS120 2.3 0.0 1.0
SG G:CYS134 2.3 0.0 1.0
FE1 G:FES801 2.7 38.5 1.0
CB G:CYS134 3.2 0.0 1.0
CB G:CYS120 3.4 0.0 1.0
O G:HOH1137 4.1 0.0 1.0
N G:CYS134 4.2 2.7 1.0
SG G:CYS106 4.2 0.0 1.0
CA G:CYS134 4.3 0.0 1.0
N G:CYS120 4.3 0.0 1.0
CA G:GLY115 4.4 0.0 1.0
CA G:CYS120 4.5 0.0 1.0
SG G:CYS117 4.6 0.0 1.0
CB G:ALA132 4.7 0.0 1.0
CB G:TYR107 4.7 0.0 1.0
N G:ARG118 5.0 0.0 1.0
N G:GLY115 5.0 0.0 1.0

Iron binding site 9 out of 16 in 8bed

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Iron binding site 9 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe802

b:2.9
occ:1.00
 FE1 G:SF4802 0.0 2.9 1.0
SG G:CYS179 2.3 2.7 1.0
S2 G:SF4802 2.3 0.0 1.0
S3 G:SF4802 2.3 0.0 1.0
S4 G:SF4802 2.3 0.0 1.0
FE2 G:SF4802 2.7 19.2 1.0
FE4 G:SF4802 2.7 20.8 1.0
FE3 G:SF4802 2.7 20.2 1.0
CB G:CYS179 3.3 0.0 1.0
CG G:GLN182 3.8 0.0 1.0
S1 G:SF4802 3.9 0.0 1.0
CD G:GLN182 4.3 0.0 1.0
CB G:LEU181 4.3 0.0 1.0
NE2 G:HIS166 4.5 0.0 1.0
CB G:GLN175 4.5 0.0 1.0
N G:GLN182 4.6 0.0 1.0
CA G:CYS179 4.7 0.0 1.0
CG G:GLN175 4.7 1.7 1.0
SG G:CYS173 4.7 0.0 1.0
NE2 G:GLN182 4.7 0.0 1.0
CD2 G:LEU181 4.8 0.0 1.0
OE1 G:GLN182 4.8 0.5 1.0
CB G:GLN182 4.8 0.0 1.0
SG G:CYS170 4.9 0.0 1.0

Iron binding site 10 out of 16 in 8bed

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Iron binding site 10 out of 16 in the Cryo-Em Structure of the Arabidopsis Thaliana I+III2 Supercomplex (Ci Peripheral Tip)


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 Tip) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe802

b:19.2
occ:1.00
 FE2 G:SF4802 0.0 19.2 1.0
NE2 G:HIS166 2.0 0.0 1.0
S1 G:SF4802 2.3 0.0 1.0
S4 G:SF4802 2.3 0.0 1.0
S3 G:SF4802 2.3 0.0 1.0
FE3 G:SF4802 2.7 20.2 1.0
FE1 G:SF4802 2.7 2.9 1.0
FE4 G:SF4802 2.7 20.8 1.0
CD2 G:HIS166 2.9 0.0 1.0
CE1 G:HIS166 3.1 0.0 1.0
S2 G:SF4802 3.9 0.0 1.0
CG G:HIS166 4.1 0.0 1.0
ND1 G:HIS166 4.2 0.0 1.0
CD2 G:LEU181 4.2 0.0 1.0
SG G:CYS170 4.7 0.0 1.0
SG G:CYS179 4.7 2.7 1.0
OD1 G:ASP169 4.8 18.8 1.0
O G:PRO167 4.8 0.0 1.0
SG G:CYS173 4.8 0.0 1.0
CG G:ARG217 4.9 4.1 1.0

Reference:

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
Page generated: Fri Aug 9 18:58:32 2024

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