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Iron in PDB 4ub8: Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8 was solved by M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.90 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.807, 230.001, 288.502, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.5

Other elements in 4ub8:

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 6 atoms
Calcium (Ca) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser (pdb code 4ub8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4ub8

Go back to Iron Binding Sites List in 4ub8
Iron binding site 1 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:27.4
occ:1.00
 NE2 D:HIS214 2.3 19.8 1.0
NE2 A:HIS215 2.3 28.5 1.0
O2 A:BCT404 2.3 27.4 1.0
NE2 D:HIS268 2.4 20.1 1.0
O1 A:BCT404 2.4 30.8 1.0
NE2 A:HIS272 2.4 28.7 1.0
C A:BCT404 2.7 40.1 1.0
CE1 A:HIS215 3.0 26.0 1.0
CE1 D:HIS214 3.2 20.1 1.0
CD2 D:HIS214 3.2 18.1 1.0
CD2 D:HIS268 3.3 18.1 1.0
CE1 D:HIS268 3.3 18.4 1.0
CD2 A:HIS272 3.4 27.1 1.0
CE1 A:HIS272 3.4 26.1 1.0
CD2 A:HIS215 3.4 18.1 1.0
O3 A:BCT404 4.0 39.8 1.0
ND1 A:HIS215 4.3 25.7 1.0
ND1 D:HIS214 4.3 23.3 1.0
CG D:HIS214 4.4 20.7 1.0
ND1 D:HIS268 4.5 24.8 1.0
CG A:HIS215 4.5 34.4 1.0
ND1 A:HIS272 4.5 27.4 1.0
CG D:HIS268 4.5 19.5 1.0
CG A:HIS272 4.5 26.2 1.0
CG2 A:VAL219 4.7 21.1 1.0
CG2 D:VAL218 4.8 19.6 1.0
OH D:TYR244 4.8 30.3 1.0
OH A:TYR246 5.0 52.1 1.0

Iron binding site 2 out of 6 in 4ub8

Go back to Iron Binding Sites List in 4ub8
Iron binding site 2 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:36.3
occ:1.00
 FE E:HEM103 0.0 36.3 1.0
ND E:HEM103 2.0 33.7 1.0
NA E:HEM103 2.0 36.7 1.0
NC E:HEM103 2.1 33.8 1.0
NE2 F:HIS24 2.1 42.8 1.0
NB E:HEM103 2.1 32.1 1.0
NE2 E:HIS23 2.1 39.0 1.0
C4D E:HEM103 2.9 44.0 1.0
C1A E:HEM103 2.9 37.8 1.0
C1D E:HEM103 3.0 29.5 1.0
CD2 F:HIS24 3.0 38.7 1.0
C4C E:HEM103 3.1 34.5 1.0
C4A E:HEM103 3.1 40.8 1.0
CE1 E:HIS23 3.1 40.3 1.0
C4B E:HEM103 3.1 40.6 1.0
C1B E:HEM103 3.1 41.3 1.0
CE1 F:HIS24 3.1 41.7 1.0
C1C E:HEM103 3.1 27.5 1.0
CD2 E:HIS23 3.1 34.9 1.0
CHA E:HEM103 3.3 36.8 1.0
CHD E:HEM103 3.4 33.8 1.0
CHB E:HEM103 3.5 40.0 1.0
CHC E:HEM103 3.5 27.0 1.0
C3D E:HEM103 4.1 34.1 1.0
C2A E:HEM103 4.2 50.1 1.0
C2D E:HEM103 4.2 32.2 1.0
ND1 E:HIS23 4.2 42.0 1.0
CG F:HIS24 4.2 39.5 1.0
ND1 F:HIS24 4.2 39.5 1.0
C3A E:HEM103 4.2 45.5 1.0
CG E:HIS23 4.2 44.8 1.0
C3C E:HEM103 4.3 28.9 1.0
C2C E:HEM103 4.3 29.1 1.0
C2B E:HEM103 4.3 38.3 1.0
C3B E:HEM103 4.3 42.9 1.0
NE1 F:TRP20 4.9 41.9 1.0
CE2 E:TYR19 4.9 37.1 1.0

Iron binding site 3 out of 6 in 4ub8

Go back to Iron Binding Sites List in 4ub8
Iron binding site 3 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe203

b:27.4
occ:1.00
 FE V:HEM203 0.0 27.4 1.0
ND V:HEM203 2.0 31.8 1.0
NA V:HEM203 2.0 25.5 1.0
NE2 V:HIS41 2.1 26.8 1.0
NC V:HEM203 2.1 26.9 1.0
NE2 V:HIS92 2.1 30.0 1.0
NB V:HEM203 2.1 27.7 1.0
C4D V:HEM203 3.0 24.7 1.0
C1D V:HEM203 3.0 29.0 1.0
C1A V:HEM203 3.0 25.2 1.0
C4A V:HEM203 3.0 32.1 1.0
CE1 V:HIS92 3.0 29.6 1.0
CD2 V:HIS41 3.1 25.2 1.0
C4C V:HEM203 3.1 26.2 1.0
C1B V:HEM203 3.1 26.5 1.0
CE1 V:HIS41 3.1 32.6 1.0
C4B V:HEM203 3.1 27.1 1.0
CD2 V:HIS92 3.1 34.8 1.0
C1C V:HEM203 3.1 28.5 1.0
CHA V:HEM203 3.4 25.0 1.0
CHD V:HEM203 3.4 25.6 1.0
CHB V:HEM203 3.5 25.5 1.0
CHC V:HEM203 3.5 26.3 1.0
ND1 V:HIS92 4.2 29.7 1.0
C2A V:HEM203 4.2 28.0 1.0
ND1 V:HIS41 4.2 23.4 1.0
C3D V:HEM203 4.2 30.1 1.0
C3A V:HEM203 4.2 30.1 1.0
C2D V:HEM203 4.2 35.3 1.0
CG V:HIS41 4.2 23.5 1.0
CG V:HIS92 4.2 38.7 1.0
C3C V:HEM203 4.3 31.4 1.0
C2C V:HEM203 4.3 36.1 1.0
C2B V:HEM203 4.3 25.5 1.0
C3B V:HEM203 4.4 25.4 1.0
CE1 V:TYR75 4.7 27.6 1.0

Iron binding site 4 out of 6 in 4ub8

Go back to Iron Binding Sites List in 4ub8
Iron binding site 4 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe403

b:30.0
occ:1.00
 O2 a:BCT418 2.3 33.0 1.0
NE2 d:HIS214 2.3 24.3 1.0
NE2 a:HIS215 2.3 28.1 1.0
NE2 a:HIS272 2.3 26.8 1.0
O1 a:BCT418 2.4 30.8 1.0
NE2 d:HIS268 2.4 26.1 1.0
C a:BCT418 2.7 44.0 1.0
CE1 a:HIS272 3.2 24.6 1.0
CE1 d:HIS214 3.2 24.0 1.0
CE1 a:HIS215 3.2 23.0 1.0
CD2 d:HIS268 3.3 24.5 1.0
CD2 d:HIS214 3.3 21.1 1.0
CD2 a:HIS215 3.4 21.6 1.0
CD2 a:HIS272 3.4 23.6 1.0
CE1 d:HIS268 3.5 24.1 1.0
O3 a:BCT418 3.9 42.7 1.0
ND1 d:HIS214 4.4 27.6 1.0
ND1 a:HIS272 4.4 27.9 1.0
ND1 a:HIS215 4.4 31.3 1.0
CG d:HIS214 4.5 23.4 1.0
CG d:HIS268 4.5 21.0 1.0
CG a:HIS215 4.5 35.4 1.0
CG a:HIS272 4.5 28.3 1.0
ND1 d:HIS268 4.5 28.2 1.0
CG2 a:VAL219 4.7 22.4 1.0
CG2 d:VAL218 4.8 23.8 1.0
OH d:TYR244 4.9 34.3 1.0

Iron binding site 5 out of 6 in 4ub8

Go back to Iron Binding Sites List in 4ub8
Iron binding site 5 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:44.8
occ:1.00
 FE e:HEM102 0.0 44.8 1.0
ND e:HEM102 2.0 42.8 1.0
NA e:HEM102 2.0 54.0 1.0
NE2 e:HIS23 2.1 43.4 1.0
NC e:HEM102 2.1 57.6 1.0
NE2 f:HIS24 2.1 45.3 1.0
NB e:HEM102 2.1 38.6 1.0
C4D e:HEM102 2.9 40.7 1.0
C1A e:HEM102 2.9 47.8 1.0
C1D e:HEM102 3.0 44.4 1.0
CD2 f:HIS24 3.0 36.9 1.0
CD2 e:HIS23 3.0 35.7 1.0
C4A e:HEM102 3.0 53.1 1.0
C4C e:HEM102 3.1 48.1 1.0
C4B e:HEM102 3.1 46.8 1.0
C1B e:HEM102 3.1 55.1 1.0
CE1 e:HIS23 3.1 41.1 1.0
CE1 f:HIS24 3.1 41.7 1.0
C1C e:HEM102 3.1 51.1 1.0
CHA e:HEM102 3.3 42.5 1.0
CHD e:HEM102 3.4 44.6 1.0
CHB e:HEM102 3.5 50.7 1.0
CHC e:HEM102 3.5 38.4 1.0
C2A e:HEM102 4.1 49.4 1.0
C3D e:HEM102 4.2 39.4 1.0
C2D e:HEM102 4.2 49.0 1.0
CG f:HIS24 4.2 39.8 1.0
CG e:HIS23 4.2 46.0 1.0
ND1 e:HIS23 4.2 39.1 1.0
C3A e:HEM102 4.2 46.1 1.0
ND1 f:HIS24 4.2 42.6 1.0
C3C e:HEM102 4.3 48.5 1.0
C2C e:HEM102 4.3 45.8 1.0
C2B e:HEM102 4.3 48.7 1.0
C3B e:HEM102 4.4 52.4 1.0
CE2 e:TYR19 4.8 46.4 1.0
NE1 f:TRP20 4.9 45.8 1.0

Iron binding site 6 out of 6 in 4ub8

Go back to Iron Binding Sites List in 4ub8
Iron binding site 6 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe202

b:32.2
occ:1.00
 FE v:HEM202 0.0 32.2 1.0
ND v:HEM202 2.0 32.7 1.0
NA v:HEM202 2.0 32.0 1.0
NE2 v:HIS41 2.1 30.8 1.0
NC v:HEM202 2.1 35.7 1.0
NB v:HEM202 2.1 38.3 1.0
NE2 v:HIS92 2.1 32.4 1.0
C4D v:HEM202 2.9 31.9 1.0
C1D v:HEM202 3.0 32.0 1.0
C1A v:HEM202 3.0 35.0 1.0
CE1 v:HIS41 3.1 33.1 1.0
CD2 v:HIS92 3.1 32.4 1.0
C4C v:HEM202 3.1 34.5 1.0
C4A v:HEM202 3.1 35.6 1.0
C4B v:HEM202 3.1 36.1 1.0
CD2 v:HIS41 3.1 38.7 1.0
C1B v:HEM202 3.1 43.4 1.0
CE1 v:HIS92 3.1 33.0 1.0
C1C v:HEM202 3.1 35.2 1.0
CHA v:HEM202 3.4 31.7 1.0
CHD v:HEM202 3.4 30.4 1.0
CHC v:HEM202 3.5 31.7 1.0
CHB v:HEM202 3.5 33.6 1.0
ND1 v:HIS41 4.2 29.9 1.0
C3D v:HEM202 4.2 38.2 1.0
C2D v:HEM202 4.2 30.6 1.0
ND1 v:HIS92 4.2 33.3 1.0
CG v:HIS41 4.2 32.4 1.0
C2A v:HEM202 4.2 40.5 1.0
CG v:HIS92 4.2 37.8 1.0
C3A v:HEM202 4.2 39.8 1.0
C3C v:HEM202 4.3 32.0 1.0
C2C v:HEM202 4.3 30.8 1.0
C2B v:HEM202 4.3 33.0 1.0
C3B v:HEM202 4.3 33.8 1.0
CE1 v:TYR75 4.9 33.9 1.0

Reference:

M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen. Native Structure of Photosystem II at 1.95A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13991
Page generated: Mon Aug 5 12:02:21 2024

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