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Iron in PDB 7d1t: Cryo-Em Structure of Psii at 1.95 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution:
1.10.3.9;

Other elements in 7d1t:

The structure of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Chlorine (Cl) 4 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution (pdb code 7d1t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution, PDB code: 7d1t:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7d1t

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Iron binding site 1 out of 6 in the Cryo-Em Structure of Psii at 1.95 Angstrom 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 Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:5.4
occ:1.00
NE2 D:HIS214 2.0 6.5 1.0
NE2 A:HIS215 2.1 8.6 1.0
NE2 D:HIS268 2.2 7.5 1.0
NE2 A:HIS272 2.3 9.9 1.0
O3 D:BCT403 2.4 11.0 1.0
O2 D:BCT403 2.4 11.0 1.0
C D:BCT403 2.8 11.0 1.0
CE1 D:HIS214 2.9 6.5 1.0
CD2 D:HIS214 3.0 6.5 1.0
CE1 A:HIS215 3.0 8.6 1.0
CE1 D:HIS268 3.1 7.5 1.0
CD2 A:HIS215 3.1 8.6 1.0
CE1 A:HIS272 3.1 9.9 1.0
CD2 D:HIS268 3.3 7.5 1.0
CD2 A:HIS272 3.3 9.9 1.0
O1 D:BCT403 4.0 11.1 1.0
ND1 D:HIS214 4.0 6.5 1.0
CG D:HIS214 4.1 6.5 1.0
ND1 A:HIS215 4.1 8.6 1.0
CG A:HIS215 4.2 8.6 1.0
ND1 D:HIS268 4.3 7.5 1.0
ND1 A:HIS272 4.3 9.9 1.0
CG D:HIS268 4.4 7.5 1.0
CG A:HIS272 4.4 10.0 1.0
CG2 A:VAL219 4.7 10.2 1.0
CG2 D:VAL218 4.8 8.0 1.0
OH D:TYR244 4.8 13.1 1.0
OH A:TYR246 4.9 18.4 1.0

Iron binding site 2 out of 6 in 7d1t

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Iron binding site 2 out of 6 in the Cryo-Em Structure of Psii at 1.95 Angstrom 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 Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:19.0
occ:1.00
FE E:HEM103 0.0 19.0 1.0
NE2 E:HIS23 2.0 23.5 1.0
NC E:HEM103 2.0 19.0 1.0
NB E:HEM103 2.0 19.0 1.0
ND E:HEM103 2.0 19.0 1.0
NA E:HEM103 2.1 19.0 1.0
NE2 F:HIS24 2.1 18.2 1.0
CE1 E:HIS23 2.9 23.5 1.0
CD2 F:HIS24 3.0 18.2 1.0
CD2 E:HIS23 3.0 23.6 1.0
C4C E:HEM103 3.0 18.9 1.0
C1C E:HEM103 3.0 18.9 1.0
C4D E:HEM103 3.0 19.0 1.0
C1A E:HEM103 3.0 19.0 1.0
C4B E:HEM103 3.0 19.0 1.0
C1D E:HEM103 3.0 19.0 1.0
C1B E:HEM103 3.1 19.0 1.0
C4A E:HEM103 3.1 19.0 1.0
CE1 F:HIS24 3.2 18.2 1.0
CHA E:HEM103 3.4 19.0 1.0
CHC E:HEM103 3.4 18.9 1.0
CHD E:HEM103 3.4 19.0 1.0
CHB E:HEM103 3.5 19.0 1.0
ND1 E:HIS23 4.0 23.6 1.0
CG E:HIS23 4.1 23.7 1.0
CG F:HIS24 4.2 18.2 1.0
C2C E:HEM103 4.2 18.9 1.0
C3C E:HEM103 4.2 19.0 1.0
C3D E:HEM103 4.2 19.1 1.0
ND1 F:HIS24 4.2 18.2 1.0
C2D E:HEM103 4.2 19.0 1.0
C2A E:HEM103 4.2 19.1 1.0
C2B E:HEM103 4.3 19.0 1.0
C3B E:HEM103 4.3 19.0 1.0
C3A E:HEM103 4.3 19.1 1.0
CE1 E:TYR19 4.6 24.5 1.0
NE1 F:TRP20 4.9 20.6 1.0

Iron binding site 3 out of 6 in 7d1t

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Iron binding site 3 out of 6 in the Cryo-Em Structure of Psii at 1.95 Angstrom 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 Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:20.8
occ:1.00
FE V:HEC201 0.0 20.8 1.0
ND V:HEC201 2.0 20.9 1.0
NA V:HEC201 2.0 20.9 1.0
NB V:HEC201 2.0 20.9 1.0
NE2 V:HIS92 2.1 23.9 1.0
NC V:HEC201 2.1 20.9 1.0
NE2 V:HIS41 2.2 18.6 1.0
CD2 V:HIS92 2.9 23.9 1.0
C4D V:HEC201 2.9 20.9 1.0
C1A V:HEC201 3.0 20.9 1.0
C1B V:HEC201 3.0 20.9 1.0
C4A V:HEC201 3.0 20.9 1.0
C1D V:HEC201 3.0 20.9 1.0
C4B V:HEC201 3.0 20.9 1.0
C1C V:HEC201 3.1 20.9 1.0
CE1 V:HIS41 3.1 18.6 1.0
C4C V:HEC201 3.1 20.9 1.0
CD2 V:HIS41 3.2 18.6 1.0
CE1 V:HIS92 3.2 23.9 1.0
CHA V:HEC201 3.3 20.9 1.0
CHB V:HEC201 3.4 20.9 1.0
CHC V:HEC201 3.4 20.9 1.0
CHD V:HEC201 3.5 20.9 1.0
CG V:HIS92 4.1 24.1 1.0
C3D V:HEC201 4.2 21.0 1.0
C2A V:HEC201 4.2 21.0 1.0
ND1 V:HIS92 4.2 24.0 1.0
C3A V:HEC201 4.2 20.9 1.0
C2D V:HEC201 4.2 21.0 1.0
ND1 V:HIS41 4.2 18.6 1.0
C2B V:HEC201 4.2 21.0 1.0
C3B V:HEC201 4.3 21.0 1.0
CG V:HIS41 4.3 18.6 1.0
C2C V:HEC201 4.3 21.0 1.0
C3C V:HEC201 4.3 21.0 1.0
CE2 V:TYR75 4.8 25.3 1.0

Iron binding site 4 out of 6 in 7d1t

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Psii at 1.95 Angstrom 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 Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe402

b:5.4
occ:1.00
NE2 d:HIS214 2.0 6.5 1.0
NE2 a:HIS215 2.1 8.6 1.0
NE2 d:HIS268 2.2 7.5 1.0
NE2 a:HIS272 2.3 9.9 1.0
O3 d:BCT403 2.4 11.0 1.0
O2 d:BCT403 2.4 11.0 1.0
C d:BCT403 2.8 11.0 1.0
CE1 d:HIS214 2.9 6.5 1.0
CD2 d:HIS214 3.0 6.5 1.0
CE1 a:HIS215 3.0 8.6 1.0
CE1 d:HIS268 3.1 7.5 1.0
CD2 a:HIS215 3.1 8.6 1.0
CE1 a:HIS272 3.1 9.9 1.0
CD2 d:HIS268 3.3 7.5 1.0
CD2 a:HIS272 3.3 9.9 1.0
O1 d:BCT403 4.0 11.1 1.0
ND1 d:HIS214 4.0 6.5 1.0
CG d:HIS214 4.1 6.5 1.0
ND1 a:HIS215 4.1 8.6 1.0
CG a:HIS215 4.2 8.6 1.0
ND1 d:HIS268 4.3 7.5 1.0
ND1 a:HIS272 4.3 9.9 1.0
CG d:HIS268 4.4 7.5 1.0
CG a:HIS272 4.4 10.0 1.0
CG2 a:VAL219 4.7 10.2 1.0
CG2 d:VAL218 4.8 8.0 1.0
OH d:TYR244 4.8 13.1 1.0
OH a:TYR246 4.9 18.4 1.0

Iron binding site 5 out of 6 in 7d1t

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Iron binding site 5 out of 6 in the Cryo-Em Structure of Psii at 1.95 Angstrom 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 Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe103

b:19.0
occ:1.00
FE e:HEM103 0.0 19.0 1.0
NE2 e:HIS23 2.0 23.5 1.0
NC e:HEM103 2.0 19.0 1.0
NB e:HEM103 2.0 19.0 1.0
ND e:HEM103 2.0 19.0 1.0
NA e:HEM103 2.1 19.0 1.0
NE2 f:HIS24 2.1 18.2 1.0
CE1 e:HIS23 2.9 23.5 1.0
CD2 f:HIS24 3.0 18.2 1.0
CD2 e:HIS23 3.0 23.6 1.0
C4C e:HEM103 3.0 18.9 1.0
C1C e:HEM103 3.0 18.9 1.0
C4D e:HEM103 3.0 19.0 1.0
C1A e:HEM103 3.0 19.0 1.0
C4B e:HEM103 3.0 19.0 1.0
C1D e:HEM103 3.0 19.0 1.0
C1B e:HEM103 3.1 19.0 1.0
C4A e:HEM103 3.1 19.0 1.0
CE1 f:HIS24 3.2 18.2 1.0
CHA e:HEM103 3.4 19.0 1.0
CHC e:HEM103 3.4 18.9 1.0
CHD e:HEM103 3.4 19.0 1.0
CHB e:HEM103 3.5 19.0 1.0
ND1 e:HIS23 4.0 23.6 1.0
CG e:HIS23 4.1 23.7 1.0
CG f:HIS24 4.2 18.2 1.0
C2C e:HEM103 4.2 18.9 1.0
C3C e:HEM103 4.2 19.0 1.0
C3D e:HEM103 4.2 19.1 1.0
ND1 f:HIS24 4.2 18.2 1.0
C2D e:HEM103 4.2 19.0 1.0
C2A e:HEM103 4.2 19.1 1.0
C2B e:HEM103 4.3 19.0 1.0
C3B e:HEM103 4.3 19.0 1.0
C3A e:HEM103 4.3 19.1 1.0
CE1 e:TYR19 4.6 24.5 1.0
NE1 f:TRP20 4.9 20.6 1.0

Iron binding site 6 out of 6 in 7d1t

Go back to Iron Binding Sites List in 7d1t
Iron binding site 6 out of 6 in the Cryo-Em Structure of Psii at 1.95 Angstrom 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 Psii at 1.95 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:20.8
occ:1.00
FE v:HEC201 0.0 20.8 1.0
ND v:HEC201 2.0 20.9 1.0
NA v:HEC201 2.0 20.9 1.0
NB v:HEC201 2.0 20.9 1.0
NE2 v:HIS92 2.1 23.9 1.0
NC v:HEC201 2.1 20.9 1.0
NE2 v:HIS41 2.2 18.6 1.0
CD2 v:HIS92 2.9 23.9 1.0
C4D v:HEC201 2.9 20.9 1.0
C1A v:HEC201 3.0 20.9 1.0
C1B v:HEC201 3.0 20.9 1.0
C4A v:HEC201 3.0 20.9 1.0
C4B v:HEC201 3.0 20.9 1.0
C1D v:HEC201 3.0 20.9 1.0
CE1 v:HIS41 3.1 18.6 1.0
C1C v:HEC201 3.1 20.9 1.0
C4C v:HEC201 3.1 20.9 1.0
CD2 v:HIS41 3.2 18.6 1.0
CE1 v:HIS92 3.2 23.9 1.0
CHA v:HEC201 3.3 20.9 1.0
CHB v:HEC201 3.4 20.9 1.0
CHC v:HEC201 3.4 20.9 1.0
CHD v:HEC201 3.5 20.9 1.0
CG v:HIS92 4.1 24.1 1.0
C3D v:HEC201 4.2 21.0 1.0
C2A v:HEC201 4.2 21.0 1.0
ND1 v:HIS92 4.2 24.0 1.0
C3A v:HEC201 4.2 20.9 1.0
ND1 v:HIS41 4.2 18.6 1.0
C2D v:HEC201 4.2 21.0 1.0
C2B v:HEC201 4.2 21.0 1.0
C3B v:HEC201 4.3 21.0 1.0
CG v:HIS41 4.3 18.6 1.0
C2C v:HEC201 4.3 21.0 1.0
C3C v:HEC201 4.3 21.0 1.0
CE2 v:TYR75 4.8 25.3 1.0

Reference:

K.Kato, N.Miyazaki, T.Hamaguchi, Y.Nakajima, F.Akita, K.Yonekura, J.R.Shen. High-Resolution Cryo-Em Structure of Photosystem II Reveals Damage From High-Dose Electron Beams Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01919-3
Page generated: Thu Aug 8 03:33:04 2024

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