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Iron in PDB 5h2f: Crystal Structure of the Psbm-Deletion Mutant of Photosystem II

Enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II

All present enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f was solved by S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.954, 226.993, 285.886, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 22.6

Other elements in 5h2f:

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 7 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II (pdb code 5h2f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5h2f

Go back to Iron Binding Sites List in 5h2f
Iron binding site 1 out of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:40.0
occ:1.00
NE2 A:HIS215 2.0 36.8 1.0
NE2 D:HIS214 2.2 33.3 1.0
O3 A:BCT421 2.3 27.7 0.5
NE2 A:HIS272 2.3 43.8 1.0
O3 A:BCT421 2.3 34.4 0.5
NE2 D:HIS268 2.4 31.1 1.0
O2 A:BCT421 2.5 35.0 0.5
O2 A:BCT421 2.5 36.4 0.5
C A:BCT421 2.7 30.1 0.5
C A:BCT421 2.8 39.4 0.5
CE1 A:HIS215 2.8 34.7 1.0
CD2 D:HIS214 3.0 29.3 1.0
CE1 A:HIS272 3.1 33.1 1.0
CD2 A:HIS215 3.2 33.4 1.0
CE1 D:HIS214 3.3 29.1 1.0
CD2 D:HIS268 3.3 27.7 1.0
CE1 D:HIS268 3.4 28.3 1.0
CD2 A:HIS272 3.4 36.2 1.0
O1 A:BCT421 3.9 29.9 0.5
ND1 A:HIS215 4.1 33.0 1.0
O1 A:BCT421 4.1 39.5 0.5
CG A:HIS215 4.2 35.2 1.0
CG D:HIS214 4.2 29.1 1.0
ND1 D:HIS214 4.4 27.9 1.0
ND1 A:HIS272 4.4 35.8 1.0
ND1 D:HIS268 4.5 32.1 1.0
CG2 A:VAL219 4.5 31.8 1.0
CG A:HIS272 4.5 33.7 1.0
CG D:HIS268 4.5 30.7 1.0
O A:HOH501 4.6 40.1 1.0
CG2 D:VAL218 4.8 26.5 1.0

Iron binding site 2 out of 6 in 5h2f

Go back to Iron Binding Sites List in 5h2f
Iron binding site 2 out of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe102

b:52.2
occ:1.00
FE E:HEM102 0.0 52.2 1.0
NB E:HEM102 2.0 53.1 1.0
NE2 E:HIS23 2.0 63.1 1.0
NC E:HEM102 2.1 54.6 1.0
ND E:HEM102 2.1 52.6 1.0
NE2 F:HIS24 2.1 47.9 1.0
NA E:HEM102 2.1 56.9 1.0
CD2 F:HIS24 3.0 45.8 1.0
CE1 E:HIS23 3.0 56.8 1.0
C1B E:HEM102 3.0 57.8 1.0
CD2 E:HIS23 3.0 62.2 1.0
C4B E:HEM102 3.0 57.8 1.0
C4D E:HEM102 3.1 57.8 1.0
C1C E:HEM102 3.1 52.3 1.0
C1A E:HEM102 3.1 58.0 1.0
C4C E:HEM102 3.1 49.5 1.0
C1D E:HEM102 3.1 55.3 1.0
C4A E:HEM102 3.1 56.6 1.0
CE1 F:HIS24 3.2 45.3 1.0
CHC E:HEM102 3.4 50.8 1.0
CHA E:HEM102 3.4 58.2 1.0
CHB E:HEM102 3.4 59.5 1.0
CHD E:HEM102 3.5 51.3 1.0
ND1 E:HIS23 4.1 56.1 1.0
CG E:HIS23 4.2 59.8 1.0
CG F:HIS24 4.2 50.1 1.0
C2B E:HEM102 4.2 57.0 1.0
ND1 F:HIS24 4.3 46.7 1.0
C3B E:HEM102 4.3 56.5 1.0
C2C E:HEM102 4.3 51.1 1.0
C3D E:HEM102 4.3 57.7 1.0
C2A E:HEM102 4.3 59.7 1.0
C3C E:HEM102 4.3 50.6 1.0
C3A E:HEM102 4.3 61.9 1.0
C2D E:HEM102 4.3 56.3 1.0
NE1 F:TRP20 4.7 50.0 1.0
CE2 E:TYR19 4.8 56.5 1.0

Iron binding site 3 out of 6 in 5h2f

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Iron binding site 3 out of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe202

b:30.1
occ:1.00
FE V:HEC202 0.0 30.1 1.0
NA V:HEC202 1.9 29.9 1.0
NE2 V:HIS41 2.0 32.2 1.0
NE2 V:HIS92 2.0 31.6 1.0
NC V:HEC202 2.0 28.3 1.0
NB V:HEC202 2.1 29.8 1.0
ND V:HEC202 2.1 29.2 1.0
CD2 V:HIS92 3.0 32.9 1.0
C1A V:HEC202 3.0 29.8 1.0
CE1 V:HIS41 3.0 29.7 1.0
C4A V:HEC202 3.0 31.8 1.0
CD2 V:HIS41 3.0 29.9 1.0
CE1 V:HIS92 3.0 30.8 1.0
C4C V:HEC202 3.1 28.8 1.0
C4D V:HEC202 3.1 30.7 1.0
C1C V:HEC202 3.1 29.7 1.0
C1B V:HEC202 3.1 30.1 1.0
C1D V:HEC202 3.1 29.4 1.0
C4B V:HEC202 3.1 30.3 1.0
CHA V:HEC202 3.4 29.3 1.0
CHB V:HEC202 3.4 31.6 1.0
CHD V:HEC202 3.5 27.4 1.0
CHC V:HEC202 3.5 27.6 1.0
ND1 V:HIS41 4.1 28.2 1.0
ND1 V:HIS92 4.2 28.1 1.0
CG V:HIS92 4.2 30.5 1.0
CG V:HIS41 4.2 29.7 1.0
C3A V:HEC202 4.2 31.1 1.0
C2A V:HEC202 4.2 30.0 1.0
C3C V:HEC202 4.3 27.2 1.0
C2C V:HEC202 4.3 28.2 1.0
C3D V:HEC202 4.3 28.6 1.0
C2B V:HEC202 4.3 30.3 1.0
C2D V:HEC202 4.4 29.8 1.0
C3B V:HEC202 4.4 31.1 1.0
CE1 V:TYR75 4.6 30.8 1.0
OH V:TYR75 5.0 29.4 1.0

Iron binding site 4 out of 6 in 5h2f

Go back to Iron Binding Sites List in 5h2f
Iron binding site 4 out of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe404

b:42.7
occ:1.00
NE2 a:HIS215 2.0 36.2 1.0
NE2 d:HIS214 2.1 36.0 1.0
NE2 a:HIS272 2.3 37.8 1.0
NE2 d:HIS268 2.3 28.3 1.0
O2 a:BCT422 2.4 51.2 1.0
O3 a:BCT422 2.6 52.3 1.0
C a:BCT422 2.9 57.5 1.0
CE1 a:HIS215 2.9 35.0 1.0
CD2 d:HIS214 3.0 32.3 1.0
CD2 a:HIS215 3.1 35.1 1.0
CE1 d:HIS214 3.1 33.5 1.0
CE1 d:HIS268 3.2 26.6 1.0
CE1 a:HIS272 3.3 33.4 1.0
CD2 a:HIS272 3.3 35.5 1.0
CD2 d:HIS268 3.4 30.7 1.0
ND1 a:HIS215 4.1 32.9 1.0
CG d:HIS214 4.2 34.7 1.0
CG a:HIS215 4.2 32.5 1.0
O1 a:BCT422 4.2 56.6 1.0
ND1 d:HIS214 4.2 35.0 1.0
ND1 a:HIS272 4.4 37.5 1.0
ND1 d:HIS268 4.4 28.6 1.0
CG a:HIS272 4.4 35.8 1.0
CG d:HIS268 4.5 30.4 1.0
CG2 a:VAL219 4.7 33.5 1.0
CG2 d:VAL218 4.8 28.8 1.0

Iron binding site 5 out of 6 in 5h2f

Go back to Iron Binding Sites List in 5h2f
Iron binding site 5 out of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe101

b:51.2
occ:1.00
FE e:HEM101 0.0 51.2 1.0
NB e:HEM101 2.0 51.7 1.0
NE2 f:HIS24 2.1 60.8 1.0
ND e:HEM101 2.1 50.6 1.0
NE2 e:HIS23 2.1 61.1 1.0
NC e:HEM101 2.1 50.4 1.0
NA e:HEM101 2.1 57.5 1.0
CD2 f:HIS24 2.9 52.5 1.0
C4B e:HEM101 3.0 53.5 1.0
C1B e:HEM101 3.0 56.6 1.0
CE1 e:HIS23 3.1 60.4 1.0
C4D e:HEM101 3.1 55.6 1.0
CD2 e:HIS23 3.1 59.2 1.0
C1C e:HEM101 3.1 47.0 1.0
C1A e:HEM101 3.1 60.9 1.0
C4A e:HEM101 3.1 56.2 1.0
C1D e:HEM101 3.1 50.7 1.0
CE1 f:HIS24 3.1 54.5 1.0
C4C e:HEM101 3.2 46.7 1.0
CHC e:HEM101 3.4 48.1 1.0
CHA e:HEM101 3.4 57.5 1.0
CHB e:HEM101 3.4 59.0 1.0
CHD e:HEM101 3.5 48.0 1.0
CG f:HIS24 4.2 56.2 1.0
ND1 e:HIS23 4.2 55.9 1.0
CG e:HIS23 4.2 59.8 1.0
C3B e:HEM101 4.2 52.2 1.0
ND1 f:HIS24 4.2 55.7 1.0
C2B e:HEM101 4.2 55.0 1.0
C3D e:HEM101 4.3 54.0 1.0
C3A e:HEM101 4.3 63.1 1.0
C2C e:HEM101 4.3 48.6 1.0
C2A e:HEM101 4.3 63.2 1.0
C2D e:HEM101 4.4 53.6 1.0
C3C e:HEM101 4.4 46.8 1.0
CE2 e:TYR19 5.0 64.1 1.0

Iron binding site 6 out of 6 in 5h2f

Go back to Iron Binding Sites List in 5h2f
Iron binding site 6 out of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe202

b:38.5
occ:1.00
FE v:HEC202 0.0 38.5 1.0
NE2 v:HIS92 1.9 36.4 1.0
NA v:HEC202 2.0 37.4 1.0
NE2 v:HIS41 2.0 40.4 1.0
NB v:HEC202 2.1 37.6 1.0
NC v:HEC202 2.1 40.3 1.0
ND v:HEC202 2.1 41.7 1.0
CE1 v:HIS92 2.8 38.2 1.0
CE1 v:HIS41 2.9 35.0 1.0
C1A v:HEC202 2.9 38.0 1.0
CD2 v:HIS92 3.0 35.4 1.0
C4D v:HEC202 3.0 38.8 1.0
C1C v:HEC202 3.0 37.7 1.0
CD2 v:HIS41 3.0 38.7 1.0
C4B v:HEC202 3.0 37.3 1.0
C4A v:HEC202 3.1 38.0 1.0
C1B v:HEC202 3.1 35.4 1.0
C4C v:HEC202 3.1 39.9 1.0
C1D v:HEC202 3.1 38.7 1.0
CHA v:HEC202 3.3 35.2 1.0
CHC v:HEC202 3.4 37.9 1.0
CHB v:HEC202 3.5 36.7 1.0
CHD v:HEC202 3.5 38.2 1.0
ND1 v:HIS92 4.0 34.5 1.0
ND1 v:HIS41 4.1 38.0 1.0
CG v:HIS92 4.1 33.7 1.0
CG v:HIS41 4.2 38.6 1.0
C2A v:HEC202 4.2 38.4 1.0
C3D v:HEC202 4.3 38.4 1.0
C3A v:HEC202 4.3 35.5 1.0
C2C v:HEC202 4.3 37.1 1.0
C3B v:HEC202 4.3 35.3 1.0
C2B v:HEC202 4.3 35.3 1.0
C3C v:HEC202 4.3 36.8 1.0
C2D v:HEC202 4.3 37.9 1.0
CE1 v:TYR75 4.8 39.2 1.0

Reference:

S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya. Mutual Relationships Between Structural and Functional Changes in A Psbm-Deletion Mutant of Photosystem II. Faraday Discuss. V. 198 107 2017.
ISSN: ISSN 1359-6640
PubMed: 28272640
DOI: 10.1039/C6FD00213G
Page generated: Sun Dec 13 16:02:55 2020

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