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Iron in PDB 4pj0: Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing

Enzymatic activity of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing

All present enzymatic activity of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing:
1.10.3.9;

Protein crystallography data

The structure of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing, PDB code: 4pj0 was solved by J.Hellmich, M.Bommer, A.Burkhardt, M.Ibrahim, J.Kern, A.Meents, F.Mueh, H.Dobbek, A.Zouni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.12 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.447, 218.889, 302.202, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.6

Other elements in 4pj0:

The structure of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 4 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing (pdb code 4pj0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing, PDB code: 4pj0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4pj0

Go back to Iron Binding Sites List in 4pj0
Iron binding site 1 out of 6 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:34.2
occ:1.00
 O2 A:BCT616 2.1 33.4 1.0
O1 A:BCT616 2.1 28.9 1.0
NE2 D:HIS214 2.1 25.7 1.0
NE2 A:HIS215 2.2 34.5 1.0
NE2 A:HIS272 2.3 33.1 1.0
NE2 D:HIS268 2.3 26.7 1.0
C A:BCT616 2.4 33.9 1.0
CE1 D:HIS214 3.0 26.8 1.0
CD2 D:HIS214 3.1 24.2 1.0
CE1 D:HIS268 3.1 28.3 1.0
CE1 A:HIS272 3.2 31.7 1.0
CE1 A:HIS215 3.2 33.4 1.0
CD2 A:HIS215 3.2 30.9 1.0
CD2 A:HIS272 3.3 34.7 1.0
CD2 D:HIS268 3.4 31.8 1.0
O3 A:BCT616 3.7 38.4 1.0
ND1 D:HIS214 4.2 31.8 1.0
CG D:HIS214 4.2 26.4 1.0
ND1 A:HIS272 4.3 34.2 1.0
ND1 A:HIS215 4.3 34.0 1.0
ND1 D:HIS268 4.3 33.5 1.0
CG A:HIS272 4.4 35.2 1.0
CG A:HIS215 4.4 31.9 1.0
CG D:HIS268 4.5 35.6 1.0
CG2 D:VAL218 4.8 35.6 1.0
OH D:TYR244 4.8 43.8 1.0
CG2 A:VAL219 4.8 35.9 1.0

Iron binding site 2 out of 6 in 4pj0

Go back to Iron Binding Sites List in 4pj0
Iron binding site 2 out of 6 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe102

b:50.7
occ:1.00
 FE E:HEM102 0.0 50.7 1.0
NC E:HEM102 2.0 48.3 1.0
NB E:HEM102 2.0 53.7 1.0
NA E:HEM102 2.1 50.7 1.0
ND E:HEM102 2.1 46.2 1.0
NE2 E:HIS23 2.1 57.4 1.0
NE2 F:HIS24 2.2 55.7 1.0
CE1 E:HIS23 2.9 58.4 1.0
C1C E:HEM102 3.0 50.1 1.0
C4B E:HEM102 3.1 56.0 1.0
C4A E:HEM102 3.1 55.6 1.0
C1B E:HEM102 3.1 55.1 1.0
C1D E:HEM102 3.1 49.2 1.0
C4C E:HEM102 3.1 45.3 1.0
CE1 F:HIS24 3.1 53.7 1.0
C1A E:HEM102 3.1 52.5 1.0
CD2 F:HIS24 3.1 49.4 1.0
C4D E:HEM102 3.1 50.8 1.0
CD2 E:HIS23 3.2 56.3 1.0
CHC E:HEM102 3.4 46.3 1.0
CHB E:HEM102 3.4 54.8 1.0
CHD E:HEM102 3.4 42.7 1.0
CHA E:HEM102 3.5 52.8 1.0
ND1 E:HIS23 4.1 58.5 1.0
ND1 F:HIS24 4.2 49.8 1.0
CG F:HIS24 4.2 50.4 1.0
CG E:HIS23 4.3 56.4 1.0
C2C E:HEM102 4.3 51.1 1.0
C3B E:HEM102 4.3 59.6 1.0
C2B E:HEM102 4.3 57.4 1.0
C3C E:HEM102 4.3 46.6 1.0
C3A E:HEM102 4.3 54.5 1.0
C2D E:HEM102 4.3 51.6 1.0
C2A E:HEM102 4.3 51.3 1.0
C3D E:HEM102 4.3 53.2 1.0
CE1 E:TYR19 4.8 55.6 1.0

Iron binding site 3 out of 6 in 4pj0

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Iron binding site 3 out of 6 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:31.4
occ:1.00
 FE V:HEM201 0.0 31.4 1.0
NC V:HEM201 2.0 41.5 1.0
NB V:HEM201 2.0 33.1 1.0
NA V:HEM201 2.1 42.4 1.0
ND V:HEM201 2.1 33.9 1.0
NE2 V:HIS41 2.2 37.1 1.0
NE2 V:HIS92 2.2 39.9 1.0
C1C V:HEM201 3.0 40.8 1.0
CD2 V:HIS41 3.0 41.8 1.0
C4B V:HEM201 3.1 40.8 1.0
CD2 V:HIS92 3.1 36.5 1.0
C1B V:HEM201 3.1 34.2 1.0
C4A V:HEM201 3.1 41.0 1.0
C4C V:HEM201 3.1 36.5 1.0
C1D V:HEM201 3.1 39.4 1.0
C1A V:HEM201 3.1 41.5 1.0
C4D V:HEM201 3.1 37.5 1.0
CE1 V:HIS92 3.2 33.2 1.0
CE1 V:HIS41 3.2 40.0 1.0
CHC V:HEM201 3.4 37.0 1.0
CHB V:HEM201 3.4 37.3 1.0
CHD V:HEM201 3.4 38.8 1.0
CHA V:HEM201 3.5 36.3 1.0
CG V:HIS41 4.2 40.8 1.0
CG V:HIS92 4.2 36.8 1.0
C2C V:HEM201 4.3 39.4 1.0
C2B V:HEM201 4.3 38.9 1.0
C3B V:HEM201 4.3 38.0 1.0
ND1 V:HIS41 4.3 44.6 1.0
C3C V:HEM201 4.3 36.0 1.0
ND1 V:HIS92 4.3 35.2 1.0
C3A V:HEM201 4.3 37.3 1.0
C2D V:HEM201 4.3 37.3 1.0
C2A V:HEM201 4.3 34.7 1.0
C3D V:HEM201 4.3 37.2 1.0
CE1 V:TYR75 5.0 31.1 1.0

Iron binding site 4 out of 6 in 4pj0

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Iron binding site 4 out of 6 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:38.0
occ:1.00
 O2 a:BCT618 2.1 43.2 1.0
O1 a:BCT618 2.1 38.1 1.0
NE2 a:HIS215 2.3 37.2 1.0
NE2 a:HIS272 2.3 41.6 1.0
NE2 d:HIS214 2.3 32.5 1.0
NE2 d:HIS268 2.3 37.5 1.0
C a:BCT618 2.4 36.4 1.0
CE1 a:HIS215 3.2 43.9 1.0
CE1 a:HIS272 3.2 44.4 1.0
CE1 d:HIS268 3.3 37.2 1.0
CE1 d:HIS214 3.3 35.6 1.0
CD2 a:HIS272 3.3 41.3 1.0
CD2 d:HIS268 3.3 38.4 1.0
CD2 d:HIS214 3.3 32.5 1.0
CD2 a:HIS215 3.4 39.0 1.0
O3 a:BCT618 3.8 45.0 1.0
ND1 a:HIS215 4.3 44.7 1.0
ND1 a:HIS272 4.4 36.0 1.0
ND1 d:HIS268 4.4 35.9 1.0
ND1 d:HIS214 4.4 31.5 1.0
CG a:HIS272 4.4 40.0 1.0
CG a:HIS215 4.5 36.8 1.0
CG d:HIS268 4.5 39.4 1.0
CG d:HIS214 4.5 30.8 1.0
OH d:TYR244 4.7 50.5 1.0
CG2 a:VAL219 4.8 47.7 1.0
CG2 d:VAL218 4.8 34.3 1.0

Iron binding site 5 out of 6 in 4pj0

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Iron binding site 5 out of 6 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe101

b:55.9
occ:1.00
 FE e:HEM101 0.0 55.9 1.0
NC e:HEM101 2.0 59.3 1.0
NB e:HEM101 2.0 56.9 1.0
NA e:HEM101 2.1 52.9 1.0
ND e:HEM101 2.1 51.9 1.0
NE2 f:HIS24 2.2 62.7 1.0
NE2 e:HIS23 2.2 63.7 1.0
CE1 e:HIS23 3.0 61.5 1.0
C1C e:HEM101 3.0 57.1 1.0
C4B e:HEM101 3.0 56.7 1.0
C4A e:HEM101 3.1 52.6 1.0
C1B e:HEM101 3.1 57.9 1.0
C1D e:HEM101 3.1 57.5 1.0
CE1 f:HIS24 3.1 59.8 1.0
C4C e:HEM101 3.1 56.0 1.0
C1A e:HEM101 3.1 58.7 1.0
C4D e:HEM101 3.1 59.1 1.0
CD2 f:HIS24 3.1 58.3 1.0
CD2 e:HIS23 3.3 63.2 1.0
CHC e:HEM101 3.4 58.9 1.0
CHB e:HEM101 3.4 51.8 1.0
CHD e:HEM101 3.5 54.9 1.0
CHA e:HEM101 3.5 62.2 1.0
ND1 e:HIS23 4.2 64.1 1.0
ND1 f:HIS24 4.2 56.7 1.0
CG f:HIS24 4.2 59.5 1.0
C2C e:HEM101 4.3 57.2 1.0
C2B e:HEM101 4.3 58.6 1.0
C3B e:HEM101 4.3 54.3 1.0
C3A e:HEM101 4.3 62.2 1.0
C3C e:HEM101 4.3 50.4 1.0
C2D e:HEM101 4.3 62.3 1.0
CG e:HIS23 4.3 63.5 1.0
C2A e:HEM101 4.3 63.1 1.0
C3D e:HEM101 4.3 62.7 1.0
CE1 e:TYR19 4.9 61.1 1.0

Iron binding site 6 out of 6 in 4pj0

Go back to Iron Binding Sites List in 4pj0
Iron binding site 6 out of 6 in the Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of T.Elongatus Photosystem II, Rows of Dimers Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:44.6
occ:1.00
 FE v:HEM201 0.0 44.6 1.0
NE2 v:HIS41 2.0 42.0 1.0
NC v:HEM201 2.0 39.1 1.0
NB v:HEM201 2.0 36.5 1.0
NA v:HEM201 2.1 39.2 1.0
ND v:HEM201 2.1 39.9 1.0
NE2 v:HIS92 2.2 40.3 1.0
CD2 v:HIS41 2.9 40.9 1.0
C1C v:HEM201 3.0 41.8 1.0
CE1 v:HIS92 3.0 37.5 1.0
C4B v:HEM201 3.0 37.1 1.0
C4A v:HEM201 3.1 38.6 1.0
C1B v:HEM201 3.1 34.9 1.0
C4C v:HEM201 3.1 39.9 1.0
C1D v:HEM201 3.1 40.9 1.0
CE1 v:HIS41 3.1 42.1 1.0
C1A v:HEM201 3.1 37.9 1.0
C4D v:HEM201 3.1 41.1 1.0
CD2 v:HIS92 3.2 44.6 1.0
CHC v:HEM201 3.3 39.5 1.0
CHB v:HEM201 3.4 35.9 1.0
CHD v:HEM201 3.4 39.4 1.0
CHA v:HEM201 3.5 39.8 1.0
CG v:HIS41 4.1 40.4 1.0
ND1 v:HIS92 4.1 46.7 1.0
ND1 v:HIS41 4.1 45.1 1.0
CG v:HIS92 4.2 45.4 1.0
C2C v:HEM201 4.2 41.0 1.0
C3B v:HEM201 4.3 33.4 1.0
C2B v:HEM201 4.3 29.6 1.0
C3C v:HEM201 4.3 40.3 1.0
C3A v:HEM201 4.3 42.9 1.0
C2D v:HEM201 4.3 37.1 1.0
C2A v:HEM201 4.3 40.9 1.0
C3D v:HEM201 4.3 37.4 1.0

Reference:

J.Hellmich, M.Bommer, A.Burkhardt, M.Ibrahim, J.Kern, A.Meents, F.Mueh, H.Dobbek, A.Zouni. Native-Like Photosystem II Superstructure at 2.44 A Resolution Through Detergent Extraction From the Protein Crystal Structure 2014.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2014.09.007
Page generated: Mon Aug 5 08:27:15 2024

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