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Iron in PDB 5mdx: Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana

Enzymatic activity of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana

All present enzymatic activity of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana:
1.10.3.9;

Other elements in 5mdx:

The structure of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana also contains other interesting chemical elements:

Magnesium (Mg) 308 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana (pdb code 5mdx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana, PDB code: 5mdx:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5mdx

Go back to Iron Binding Sites List in 5mdx
Iron binding site 1 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:0.1
occ:1.00
NE2 D:HIS269 2.1 0.5 1.0
NE2 A:HIS272 2.1 0.9 1.0
NE2 A:HIS215 2.2 0.5 1.0
NE2 D:HIS215 2.2 0.4 1.0
CD2 A:HIS272 2.7 0.9 1.0
CE1 D:HIS269 2.8 0.5 1.0
CE1 D:HIS215 2.8 0.4 1.0
CE1 A:HIS215 3.0 0.5 1.0
CD2 D:HIS269 3.3 0.5 1.0
CD2 A:HIS215 3.3 0.5 1.0
CE1 A:HIS272 3.3 0.9 1.0
CD2 D:HIS215 3.3 0.4 1.0
ND1 D:HIS215 4.0 0.4 1.0
ND1 D:HIS269 4.0 0.5 1.0
CG A:HIS272 4.0 0.9 1.0
ND1 A:HIS215 4.2 0.5 1.0
CG2 A:VAL219 4.2 0.3 1.0
ND1 A:HIS272 4.2 0.9 1.0
CG D:HIS269 4.2 0.5 1.0
CG D:HIS215 4.3 0.4 1.0
CG A:HIS215 4.3 0.5 1.0
OH D:TYR245 4.4 0.2 1.0
CG2 D:VAL219 4.6 0.4 1.0

Iron binding site 2 out of 4 in 5mdx

Go back to Iron Binding Sites List in 5mdx
Iron binding site 2 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe101

b:0.1
occ:1.00
FE E:HEM101 0.0 0.1 1.0
ND E:HEM101 2.0 0.1 1.0
NA E:HEM101 2.0 0.1 1.0
NB E:HEM101 2.0 0.1 1.0
NE2 F:HIS18 2.1 0.6 1.0
NE2 E:HIS23 2.1 0.7 1.0
NC E:HEM101 2.1 0.1 1.0
CE1 F:HIS18 2.7 0.6 1.0
CE1 E:HIS23 2.9 0.7 1.0
C4D E:HEM101 3.0 0.1 1.0
C1A E:HEM101 3.0 0.1 1.0
C4A E:HEM101 3.0 0.1 1.0
C1B E:HEM101 3.0 0.1 1.0
C1D E:HEM101 3.0 0.1 1.0
C4B E:HEM101 3.1 0.1 1.0
C1C E:HEM101 3.1 0.1 1.0
C4C E:HEM101 3.1 0.1 1.0
CD2 E:HIS23 3.3 0.7 1.0
CD2 F:HIS18 3.4 0.6 1.0
CHA E:HEM101 3.4 0.1 1.0
CHB E:HEM101 3.4 0.1 1.0
CHD E:HEM101 3.5 0.1 1.0
CHC E:HEM101 3.5 0.1 1.0
ND1 F:HIS18 3.9 0.6 1.0
ND1 E:HIS23 4.1 0.7 1.0
NE1 F:TRP14 4.2 0.6 1.0
C3D E:HEM101 4.2 0.1 1.0
C2A E:HEM101 4.2 0.1 1.0
C3A E:HEM101 4.2 0.1 1.0
C2D E:HEM101 4.2 0.1 1.0
CG F:HIS18 4.2 0.6 1.0
C2B E:HEM101 4.3 0.1 1.0
CG E:HIS23 4.3 0.7 1.0
C3B E:HEM101 4.3 0.1 1.0
C2C E:HEM101 4.3 0.1 1.0
C3C E:HEM101 4.4 0.1 1.0
CD1 F:TRP14 4.6 0.6 1.0

Iron binding site 3 out of 4 in 5mdx

Go back to Iron Binding Sites List in 5mdx
Iron binding site 3 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:0.1
occ:1.00
NE2 d:HIS215 2.2 0.9 1.0
NE2 a:HIS215 2.2 0.4 1.0
NE2 a:HIS272 2.3 0.8 1.0
NE2 d:HIS269 2.3 0.6 1.0
CE1 d:HIS215 2.9 0.9 1.0
CE1 a:HIS215 3.0 0.4 1.0
CD2 a:HIS272 3.0 0.8 1.0
CE1 d:HIS269 3.1 0.6 1.0
CD2 d:HIS215 3.2 0.9 1.0
CD2 a:HIS215 3.3 0.4 1.0
CD2 d:HIS269 3.4 0.6 1.0
CE1 a:HIS272 3.4 0.8 1.0
CG2 a:VAL219 3.9 0.5 1.0
ND1 d:HIS215 4.1 0.9 1.0
ND1 a:HIS215 4.2 0.4 1.0
CG d:HIS215 4.2 0.9 1.0
ND1 d:HIS269 4.3 0.6 1.0
CG a:HIS272 4.3 0.8 1.0
CG a:HIS215 4.4 0.4 1.0
ND1 a:HIS272 4.4 0.8 1.0
CG d:HIS269 4.4 0.6 1.0
CG2 d:VAL219 4.7 0.0 1.0
OH d:TYR245 4.7 0.1 1.0
CB a:VAL219 4.9 0.5 1.0

Iron binding site 4 out of 4 in 5mdx

Go back to Iron Binding Sites List in 5mdx
Iron binding site 4 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe101

b:0.1
occ:1.00
FE e:HEM101 0.0 0.1 1.0
ND e:HEM101 2.0 0.1 1.0
NC e:HEM101 2.0 0.1 1.0
NA e:HEM101 2.1 0.1 1.0
NB e:HEM101 2.1 0.1 1.0
NE2 e:HIS23 2.1 0.6 1.0
NE2 f:HIS18 2.1 0.1 1.0
CD2 e:HIS23 2.7 0.6 1.0
CD2 f:HIS18 2.8 0.1 1.0
C1D e:HEM101 3.0 0.1 1.0
C4C e:HEM101 3.0 0.1 1.0
C4D e:HEM101 3.0 0.1 1.0
C1C e:HEM101 3.0 0.1 1.0
C4A e:HEM101 3.1 0.1 1.0
C1A e:HEM101 3.1 0.1 1.0
C1B e:HEM101 3.1 0.1 1.0
C4B e:HEM101 3.1 0.1 1.0
CE1 f:HIS18 3.3 0.1 1.0
CE1 e:HIS23 3.3 0.6 1.0
CHD e:HEM101 3.4 0.1 1.0
CHC e:HEM101 3.4 0.1 1.0
CHA e:HEM101 3.4 0.1 1.0
CHB e:HEM101 3.4 0.1 1.0
CG e:HIS23 3.9 0.6 1.0
CG f:HIS18 4.1 0.1 1.0
C2D e:HEM101 4.2 0.1 1.0
C3D e:HEM101 4.2 0.1 1.0
ND1 e:HIS23 4.2 0.6 1.0
C2C e:HEM101 4.2 0.1 1.0
ND1 f:HIS18 4.2 0.1 1.0
C3C e:HEM101 4.2 0.1 1.0
NE1 f:TRP14 4.3 0.6 1.0
C3A e:HEM101 4.3 0.1 1.0
C2A e:HEM101 4.3 0.1 1.0
C2B e:HEM101 4.3 0.1 1.0
C3B e:HEM101 4.3 0.1 1.0

Reference:

L.S.Van Bezouwen, S.Caffarri, R.S.Kale, R.Kouril, A.W.H.Thunnissen, G.T.Oostergetel, E.J.Boekema. Subunit and Chlorophyll Organization of the Plant Photosystem II Supercomplex. Nat Plants V. 3 17080 2017.
ISSN: ESSN 2055-0278
PubMed: 28604725
DOI: 10.1038/NPLANTS.2017.80
Page generated: Sun Dec 13 16:08:38 2020

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