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Iron in PDB 4ub6: Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6 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) 62.29 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.744, 229.989, 288.337, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.8

Other elements in 4ub6:

The structure of Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser (pdb code 4ub6). 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-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4ub6

Go back to Iron Binding Sites List in 4ub6
Iron binding site 1 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.9
occ:1.00
 NE2 D:HIS214 2.2 16.0 1.0
O2 A:BCT404 2.3 21.6 1.0
NE2 A:HIS215 2.3 20.6 1.0
NE2 D:HIS268 2.3 18.9 1.0
O1 A:BCT404 2.4 24.6 1.0
NE2 A:HIS272 2.4 29.8 1.0
C A:BCT404 2.7 36.1 1.0
CE1 D:HIS268 3.2 20.3 1.0
CE1 A:HIS215 3.2 19.6 1.0
CD2 D:HIS214 3.2 18.2 1.0
CE1 D:HIS214 3.2 20.1 1.0
CD2 A:HIS215 3.4 15.7 1.0
CD2 A:HIS272 3.4 26.4 1.0
CD2 D:HIS268 3.4 17.2 1.0
CE1 A:HIS272 3.4 20.3 1.0
O3 A:BCT404 4.0 48.0 1.0
ND1 D:HIS214 4.3 21.0 1.0
ND1 A:HIS215 4.3 24.6 1.0
ND1 D:HIS268 4.3 19.9 1.0
CG D:HIS214 4.4 21.9 1.0
CG A:HIS215 4.5 21.1 1.0
CG D:HIS268 4.5 20.3 1.0
ND1 A:HIS272 4.5 25.4 1.0
CG A:HIS272 4.5 23.6 1.0
CG2 A:VAL219 4.6 20.1 1.0
CG2 D:VAL218 4.6 21.3 1.0
OH D:TYR244 4.7 28.9 1.0
OH A:TYR246 4.9 43.5 1.0

Iron binding site 2 out of 6 in 4ub6

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Iron binding site 2 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:32.2
occ:1.00
 FE E:HEM103 0.0 32.2 1.0
ND E:HEM103 2.0 30.4 1.0
NA E:HEM103 2.0 33.4 1.0
NC E:HEM103 2.1 26.4 1.0
NE2 F:HIS24 2.1 35.6 1.0
NB E:HEM103 2.1 25.0 1.0
NE2 E:HIS23 2.1 43.4 1.0
C4D E:HEM103 2.9 34.6 1.0
C1A E:HEM103 2.9 42.3 1.0
C1D E:HEM103 3.0 27.6 1.0
CD2 F:HIS24 3.0 35.0 1.0
CD2 E:HIS23 3.0 36.7 1.0
C4C E:HEM103 3.0 23.5 1.0
C4A E:HEM103 3.1 37.8 1.0
C4B E:HEM103 3.1 38.3 1.0
C1B E:HEM103 3.1 39.7 1.0
CE1 F:HIS24 3.1 40.5 1.0
C1C E:HEM103 3.1 25.3 1.0
CE1 E:HIS23 3.1 34.9 1.0
CHA E:HEM103 3.3 41.0 1.0
CHD E:HEM103 3.4 23.8 1.0
CHB E:HEM103 3.5 37.5 1.0
CHC E:HEM103 3.5 24.3 1.0
C3D E:HEM103 4.1 28.2 1.0
C2A E:HEM103 4.1 43.8 1.0
C2D E:HEM103 4.2 23.6 1.0
CG F:HIS24 4.2 34.5 1.0
CG E:HIS23 4.2 44.0 1.0
ND1 F:HIS24 4.2 34.1 1.0
C3A E:HEM103 4.2 40.5 1.0
ND1 E:HIS23 4.2 28.6 1.0
C3C E:HEM103 4.3 23.2 1.0
C2C E:HEM103 4.3 27.4 1.0
C2B E:HEM103 4.3 33.2 1.0
C3B E:HEM103 4.3 36.6 1.0
CE2 E:TYR19 4.8 39.5 1.0
NE1 F:TRP20 5.0 44.0 1.0

Iron binding site 3 out of 6 in 4ub6

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Iron binding site 3 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:26.9
occ:1.00
 FE V:HEM201 0.0 26.9 1.0
NA V:HEM201 2.0 27.2 1.0
ND V:HEM201 2.0 39.5 1.0
NE2 V:HIS41 2.1 27.8 1.0
NC V:HEM201 2.1 29.0 1.0
NE2 V:HIS92 2.1 25.7 1.0
NB V:HEM201 2.1 28.0 1.0
C1D V:HEM201 3.0 29.5 1.0
C4D V:HEM201 3.0 24.3 1.0
C1A V:HEM201 3.0 26.4 1.0
CD2 V:HIS92 3.0 25.2 1.0
CD2 V:HIS41 3.0 29.0 1.0
C4A V:HEM201 3.0 27.9 1.0
C4C V:HEM201 3.1 22.6 1.0
C1B V:HEM201 3.1 23.7 1.0
C4B V:HEM201 3.1 23.4 1.0
CE1 V:HIS41 3.1 26.4 1.0
CE1 V:HIS92 3.1 24.4 1.0
C1C V:HEM201 3.1 34.7 1.0
CHD V:HEM201 3.4 22.5 1.0
CHA V:HEM201 3.4 23.5 1.0
CHB V:HEM201 3.4 28.9 1.0
CHC V:HEM201 3.5 26.5 1.0
CG V:HIS92 4.2 31.8 1.0
CG V:HIS41 4.2 21.9 1.0
C2A V:HEM201 4.2 23.9 1.0
ND1 V:HIS92 4.2 25.4 1.0
ND1 V:HIS41 4.2 21.8 1.0
C3A V:HEM201 4.2 34.2 1.0
C2D V:HEM201 4.2 30.1 1.0
C3D V:HEM201 4.2 27.7 1.0
C3C V:HEM201 4.3 22.4 1.0
C2B V:HEM201 4.3 26.4 1.0
C2C V:HEM201 4.3 28.5 1.0
C3B V:HEM201 4.4 25.7 1.0
CE1 V:TYR75 4.8 26.6 1.0
OH V:TYR75 4.9 26.6 1.0

Iron binding site 4 out of 6 in 4ub6

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Iron binding site 4 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe403

b:28.7
occ:1.00
 NE2 a:HIS215 2.3 23.3 1.0
NE2 d:HIS214 2.3 23.1 1.0
O2 a:BCT419 2.3 32.9 1.0
NE2 d:HIS268 2.4 21.6 1.0
O1 a:BCT419 2.4 21.3 1.0
NE2 a:HIS272 2.4 30.1 1.0
C a:BCT419 2.7 41.3 1.0
CE1 a:HIS215 3.2 26.1 1.0
CD2 d:HIS214 3.3 20.4 1.0
CE1 d:HIS268 3.3 21.8 1.0
CE1 d:HIS214 3.3 26.9 1.0
CD2 a:HIS215 3.3 19.8 1.0
CD2 d:HIS268 3.3 23.3 1.0
CD2 a:HIS272 3.4 21.7 1.0
CE1 a:HIS272 3.4 24.6 1.0
O3 a:BCT419 4.0 50.9 1.0
ND1 a:HIS215 4.3 26.1 1.0
ND1 d:HIS214 4.4 22.5 1.0
CG d:HIS214 4.4 24.2 1.0
CG a:HIS215 4.4 26.5 1.0
ND1 d:HIS268 4.4 20.8 1.0
CG d:HIS268 4.5 21.6 1.0
ND1 a:HIS272 4.5 24.6 1.0
CG a:HIS272 4.6 23.0 1.0
CG2 a:VAL219 4.6 20.5 1.0
CG2 d:VAL218 4.8 20.4 1.0
OH d:TYR244 4.9 28.0 1.0

Iron binding site 5 out of 6 in 4ub6

Go back to Iron Binding Sites List in 4ub6
Iron binding site 5 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:40.0
occ:1.00
 FE e:HEM102 0.0 40.0 1.0
ND e:HEM102 2.0 40.4 1.0
NA e:HEM102 2.0 46.6 1.0
NC e:HEM102 2.1 50.5 1.0
NE2 f:HIS24 2.1 34.4 1.0
NE2 e:HIS23 2.1 46.2 1.0
NB e:HEM102 2.1 39.4 1.0
C4D e:HEM102 2.9 47.5 1.0
C1A e:HEM102 2.9 53.8 1.0
C1D e:HEM102 3.0 37.9 1.0
CD2 f:HIS24 3.0 37.6 1.0
C4A e:HEM102 3.0 47.5 1.0
CE1 e:HIS23 3.1 40.3 1.0
C4C e:HEM102 3.1 38.8 1.0
C4B e:HEM102 3.1 45.9 1.0
CD2 e:HIS23 3.1 39.6 1.0
C1B e:HEM102 3.1 50.8 1.0
C1C e:HEM102 3.1 43.3 1.0
CE1 f:HIS24 3.1 37.5 1.0
CHA e:HEM102 3.3 45.9 1.0
CHD e:HEM102 3.4 47.0 1.0
CHB e:HEM102 3.5 44.1 1.0
CHC e:HEM102 3.5 38.5 1.0
C2A e:HEM102 4.1 49.1 1.0
CG f:HIS24 4.2 32.6 1.0
C3D e:HEM102 4.2 46.0 1.0
ND1 e:HIS23 4.2 35.2 1.0
C3A e:HEM102 4.2 43.9 1.0
C2D e:HEM102 4.2 45.6 1.0
ND1 f:HIS24 4.2 39.4 1.0
CG e:HIS23 4.2 43.2 1.0
C3C e:HEM102 4.3 40.5 1.0
C2C e:HEM102 4.3 46.1 1.0
C2B e:HEM102 4.3 48.0 1.0
C3B e:HEM102 4.3 52.7 1.0
CE2 e:TYR19 4.8 46.9 1.0

Iron binding site 6 out of 6 in 4ub6

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Iron binding site 6 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe202

b:30.3
occ:1.00
 FE v:HEM202 0.0 30.3 1.0
ND v:HEM202 2.0 34.4 1.0
NA v:HEM202 2.0 30.8 1.0
NE2 v:HIS41 2.1 29.5 1.0
NE2 v:HIS92 2.1 31.1 1.0
NC v:HEM202 2.1 29.8 1.0
NB v:HEM202 2.1 35.4 1.0
C4D v:HEM202 2.9 35.2 1.0
C1D v:HEM202 3.0 41.0 1.0
C1A v:HEM202 3.0 40.5 1.0
CE1 v:HIS92 3.0 31.6 1.0
CD2 v:HIS41 3.0 29.8 1.0
C4C v:HEM202 3.0 29.3 1.0
C4A v:HEM202 3.1 31.2 1.0
C1B v:HEM202 3.1 40.4 1.0
C4B v:HEM202 3.1 44.3 1.0
CE1 v:HIS41 3.1 29.8 1.0
CD2 v:HIS92 3.1 31.0 1.0
C1C v:HEM202 3.1 39.9 1.0
CHA v:HEM202 3.4 30.4 1.0
CHD v:HEM202 3.4 29.1 1.0
CHB v:HEM202 3.5 31.4 1.0
CHC v:HEM202 3.5 36.5 1.0
ND1 v:HIS92 4.1 32.0 1.0
C3D v:HEM202 4.2 34.7 1.0
CG v:HIS41 4.2 28.9 1.0
C2D v:HEM202 4.2 29.3 1.0
ND1 v:HIS41 4.2 28.7 1.0
C2A v:HEM202 4.2 38.4 1.0
CG v:HIS92 4.2 31.6 1.0
C3A v:HEM202 4.2 46.7 1.0
C3C v:HEM202 4.3 34.5 1.0
C2C v:HEM202 4.3 29.5 1.0
C2B v:HEM202 4.3 31.4 1.0
C3B v:HEM202 4.4 31.2 1.0
CE1 v:TYR75 4.9 32.6 1.0
OH v:TYR75 5.0 33.5 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 12:02:09 2024

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