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Iron in PDB 5mx2: Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution

Enzymatic activity of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution

All present enzymatic activity of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution, PDB code: 5mx2 was solved by M.Zhang, M.Bommer, R.Chatterjee, R.Hussain, J.Kern, J.Yano, H.Dau, H.Dobbek, A.Zouni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.65 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.326, 219.617, 304.043, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26

Other elements in 5mx2:

The structure of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution (pdb code 5mx2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution, PDB code: 5mx2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5mx2

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Iron binding site 1 out of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe414

b:26.9
occ:1.00
 O2 A:BCT415 2.0 25.8 1.0
O1 A:BCT415 2.1 29.4 1.0
NE2 A:HIS215 2.2 25.9 1.0
NE2 D:HIS214 2.2 21.9 1.0
C A:BCT415 2.4 31.3 1.0
NE2 D:HIS268 2.4 26.9 1.0
NE2 A:HIS272 2.5 27.1 1.0
CE1 D:HIS214 3.0 19.3 1.0
CE1 A:HIS215 3.0 24.6 1.0
CD2 A:HIS215 3.2 26.4 1.0
CD2 D:HIS214 3.2 17.2 1.0
CE1 D:HIS268 3.3 24.7 1.0
CD2 D:HIS268 3.4 23.6 1.0
CE1 A:HIS272 3.4 26.2 1.0
CD2 A:HIS272 3.5 26.0 1.0
O3 A:BCT415 3.7 32.6 1.0
ND1 D:HIS214 4.2 18.5 1.0
ND1 A:HIS215 4.2 25.9 1.0
CG D:HIS214 4.3 18.8 1.0
CG A:HIS215 4.3 27.0 1.0
ND1 D:HIS268 4.5 24.8 1.0
CG D:HIS268 4.5 23.9 1.0
ND1 A:HIS272 4.6 27.9 1.0
CG A:HIS272 4.6 28.2 1.0
OH D:TYR244 4.7 32.7 1.0
CG2 D:VAL218 4.8 23.4 1.0
CG2 A:VAL219 4.9 25.0 1.0
OH A:TYR246 5.0 38.4 1.0

Iron binding site 2 out of 6 in 5mx2

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Iron binding site 2 out of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe102

b:42.0
occ:1.00
 FE E:HEM102 0.0 42.0 1.0
NC E:HEM102 2.0 38.1 1.0
NE2 E:HIS23 2.0 44.6 1.0
NB E:HEM102 2.0 42.6 1.0
NA E:HEM102 2.0 46.8 1.0
ND E:HEM102 2.0 37.8 1.0
NE2 F:HIS24 2.1 43.0 1.0
CE1 F:HIS24 2.9 39.8 1.0
CE1 E:HIS23 3.0 43.0 1.0
C1C E:HEM102 3.0 37.4 1.0
C1D E:HEM102 3.0 37.4 1.0
C4B E:HEM102 3.0 43.0 1.0
C4A E:HEM102 3.0 46.0 1.0
C4C E:HEM102 3.1 36.7 1.0
C4D E:HEM102 3.1 41.1 1.0
C1B E:HEM102 3.1 44.5 1.0
C1A E:HEM102 3.1 45.0 1.0
CD2 E:HIS23 3.1 43.8 1.0
CD2 F:HIS24 3.1 40.1 1.0
CHC E:HEM102 3.4 37.7 1.0
CHB E:HEM102 3.4 45.3 1.0
CHD E:HEM102 3.4 34.5 1.0
CHA E:HEM102 3.4 42.6 1.0
ND1 F:HIS24 4.0 39.5 1.0
ND1 E:HIS23 4.1 45.3 1.0
CG F:HIS24 4.2 44.7 1.0
CG E:HIS23 4.2 44.8 1.0
C2C E:HEM102 4.2 40.5 1.0
C2D E:HEM102 4.2 40.0 1.0
C2B E:HEM102 4.2 49.1 1.0
C3C E:HEM102 4.3 43.1 1.0
C3D E:HEM102 4.3 42.0 1.0
C3A E:HEM102 4.3 49.3 1.0
C2A E:HEM102 4.3 50.8 1.0
C3B E:HEM102 4.3 48.2 1.0
CE1 E:TYR19 4.9 46.0 1.0

Iron binding site 3 out of 6 in 5mx2

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Iron binding site 3 out of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:34.7
occ:1.00
 FE V:HEM201 0.0 34.7 1.0
NE2 V:HIS41 1.9 35.7 1.0
NC V:HEM201 2.0 35.0 1.0
NB V:HEM201 2.0 35.8 1.0
NA V:HEM201 2.0 33.9 1.0
ND V:HEM201 2.1 35.0 1.0
NE2 V:HIS92 2.1 34.7 1.0
CD2 V:HIS41 2.9 35.0 1.0
CE1 V:HIS41 2.9 31.7 1.0
C1C V:HEM201 3.0 37.9 1.0
CE1 V:HIS92 3.0 34.9 1.0
C4A V:HEM201 3.0 36.3 1.0
C4B V:HEM201 3.0 37.9 1.0
C1B V:HEM201 3.0 37.0 1.0
C4C V:HEM201 3.1 32.5 1.0
C4D V:HEM201 3.1 35.8 1.0
C1D V:HEM201 3.1 32.9 1.0
C1A V:HEM201 3.1 34.5 1.0
CD2 V:HIS92 3.1 33.2 1.0
CHC V:HEM201 3.4 34.8 1.0
CHB V:HEM201 3.4 36.7 1.0
CHA V:HEM201 3.4 34.7 1.0
CHD V:HEM201 3.4 32.1 1.0
ND1 V:HIS41 4.0 30.9 1.0
CG V:HIS41 4.0 34.1 1.0
ND1 V:HIS92 4.1 34.5 1.0
CG V:HIS92 4.2 33.6 1.0
C2C V:HEM201 4.2 37.8 1.0
C2B V:HEM201 4.2 38.4 1.0
C3A V:HEM201 4.3 40.7 1.0
C3B V:HEM201 4.3 36.8 1.0
C3C V:HEM201 4.3 38.7 1.0
C2D V:HEM201 4.3 31.4 1.0
C2A V:HEM201 4.3 41.3 1.0
C3D V:HEM201 4.3 36.5 1.0
CE1 V:TYR75 4.9 37.5 1.0
OH V:TYR75 4.9 37.8 1.0

Iron binding site 4 out of 6 in 5mx2

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Iron binding site 4 out of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:40.0
occ:1.00
 O2 a:BCT413 2.0 33.3 1.0
O1 a:BCT413 2.0 31.3 1.0
NE2 d:HIS214 2.1 27.1 1.0
NE2 a:HIS215 2.2 30.1 1.0
C a:BCT413 2.4 34.1 1.0
NE2 d:HIS268 2.4 28.6 1.0
NE2 a:HIS272 2.4 37.3 1.0
CE1 a:HIS215 2.9 33.4 1.0
CE1 d:HIS214 3.0 24.1 1.0
CD2 d:HIS214 3.1 25.5 1.0
CE1 d:HIS268 3.3 28.9 1.0
CD2 a:HIS215 3.3 33.0 1.0
CD2 a:HIS272 3.4 33.5 1.0
CD2 d:HIS268 3.4 26.8 1.0
CE1 a:HIS272 3.4 34.9 1.0
O3 a:BCT413 3.7 40.6 1.0
ND1 d:HIS214 4.1 22.1 1.0
ND1 a:HIS215 4.1 34.2 1.0
CG d:HIS214 4.2 23.0 1.0
CG a:HIS215 4.3 32.5 1.0
ND1 d:HIS268 4.4 28.3 1.0
CG d:HIS268 4.5 30.9 1.0
CG a:HIS272 4.5 30.9 1.0
ND1 a:HIS272 4.5 31.8 1.0
OH d:TYR244 4.8 35.7 1.0
CG2 a:VAL219 4.8 33.5 1.0
CG2 d:VAL218 4.8 26.1 1.0

Iron binding site 5 out of 6 in 5mx2

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Iron binding site 5 out of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:47.2
occ:1.00
 FE e:HEM102 0.0 47.2 1.0
NE2 e:HIS23 1.9 50.3 1.0
NC e:HEM102 2.0 44.9 1.0
NB e:HEM102 2.0 48.6 1.0
NA e:HEM102 2.0 47.0 1.0
ND e:HEM102 2.1 45.7 1.0
NE2 f:HIS24 2.2 45.6 1.0
CE1 e:HIS23 2.8 48.4 1.0
CD2 e:HIS23 2.9 48.4 1.0
C1C e:HEM102 3.0 46.9 1.0
C4B e:HEM102 3.0 49.7 1.0
C4A e:HEM102 3.0 50.1 1.0
C4C e:HEM102 3.1 42.1 1.0
C1B e:HEM102 3.1 47.7 1.0
C1D e:HEM102 3.1 46.2 1.0
C1A e:HEM102 3.1 46.3 1.0
C4D e:HEM102 3.1 49.6 1.0
CE1 f:HIS24 3.1 46.8 1.0
CD2 f:HIS24 3.2 44.2 1.0
CHC e:HEM102 3.3 48.8 1.0
CHB e:HEM102 3.4 46.9 1.0
CHD e:HEM102 3.4 44.7 1.0
CHA e:HEM102 3.5 51.0 1.0
ND1 e:HIS23 3.9 52.4 1.0
CG e:HIS23 4.0 50.0 1.0
C2C e:HEM102 4.2 44.8 1.0
ND1 f:HIS24 4.2 48.4 1.0
C3B e:HEM102 4.2 48.8 1.0
C2B e:HEM102 4.3 48.0 1.0
C3C e:HEM102 4.3 42.3 1.0
C3A e:HEM102 4.3 53.6 1.0
CG f:HIS24 4.3 44.9 1.0
C2D e:HEM102 4.3 47.9 1.0
C2A e:HEM102 4.3 50.0 1.0
C3D e:HEM102 4.3 48.5 1.0
CE2 e:TYR19 4.9 48.1 1.0

Iron binding site 6 out of 6 in 5mx2

Go back to Iron Binding Sites List in 5mx2
Iron binding site 6 out of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:35.2
occ:1.00
 FE v:HEM201 0.0 35.2 1.0
NE2 v:HIS41 1.9 38.2 1.0
NB v:HEM201 2.0 36.1 1.0
NC v:HEM201 2.0 38.1 1.0
ND v:HEM201 2.0 33.0 1.0
NA v:HEM201 2.1 37.1 1.0
NE2 v:HIS92 2.1 34.0 1.0
CE1 v:HIS41 2.8 38.1 1.0
CE1 v:HIS92 2.9 33.9 1.0
CD2 v:HIS41 3.0 37.2 1.0
C1C v:HEM201 3.0 39.8 1.0
C4B v:HEM201 3.0 37.6 1.0
C1D v:HEM201 3.0 33.5 1.0
C1B v:HEM201 3.1 33.8 1.0
C4A v:HEM201 3.1 32.6 1.0
C4C v:HEM201 3.1 34.6 1.0
C4D v:HEM201 3.1 34.6 1.0
C1A v:HEM201 3.1 37.0 1.0
CD2 v:HIS92 3.1 37.0 1.0
CHC v:HEM201 3.3 37.9 1.0
CHB v:HEM201 3.4 31.3 1.0
CHD v:HEM201 3.4 32.7 1.0
CHA v:HEM201 3.5 33.9 1.0
ND1 v:HIS41 3.9 39.1 1.0
ND1 v:HIS92 4.0 36.6 1.0
CG v:HIS41 4.0 41.6 1.0
CG v:HIS92 4.2 34.5 1.0
C2C v:HEM201 4.2 33.1 1.0
C3B v:HEM201 4.2 41.1 1.0
C2B v:HEM201 4.2 35.7 1.0
C2D v:HEM201 4.3 35.7 1.0
C3C v:HEM201 4.3 31.9 1.0
C3D v:HEM201 4.3 36.8 1.0
C3A v:HEM201 4.3 33.9 1.0
C2A v:HEM201 4.3 34.8 1.0
CE1 v:TYR75 5.0 37.1 1.0

Reference:

M.Zhang, M.Bommer, R.Chatterjee, R.Hussein, J.Yano, H.Dau, J.Kern, H.Dobbek, A.Zouni. Structural Insights Into the Light-Driven Auto-Assembly Process of the Water-Oxidizing MN4CAO5-Cluster in Photosystem II. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28718766
DOI: 10.7554/ELIFE.26933
Page generated: Tue Aug 6 06:01:42 2024

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