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Iron in PDB 5zzn: Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus

Enzymatic activity of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus

All present enzymatic activity of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus, PDB code: 5zzn was solved by Y.Nakajima, Y.Umena, R.Nagao, K.Endo, K.Kobayashi, F.Akita, M.Suga, H.Wada, T.Noguchi, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.250, 228.430, 287.120, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19.7

Other elements in 5zzn:

The structure of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 9 atoms
Chlorine (Cl) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus (pdb code 5zzn). 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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus, PDB code: 5zzn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5zzn

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Iron binding site 1 out of 6 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:41.5
occ:1.00
NE2 A:HIS215 2.3 41.2 1.0
O1 D:BCT402 2.3 24.5 0.4
NE2 D:HIS214 2.3 36.3 1.0
NE2 D:HIS268 2.3 34.8 1.0
O1 D:BCT402 2.4 50.8 0.6
NE2 A:HIS272 2.4 44.7 1.0
O2 D:BCT402 2.5 36.0 0.6
O2 D:BCT402 2.6 36.5 0.4
C D:BCT402 2.7 46.6 0.6
C D:BCT402 2.7 36.3 0.4
CE1 A:HIS215 3.1 37.8 1.0
CE1 D:HIS268 3.2 37.2 1.0
CE1 A:HIS272 3.2 35.6 1.0
CD2 D:HIS214 3.2 34.8 1.0
CE1 D:HIS214 3.3 35.7 1.0
CD2 A:HIS215 3.4 38.5 1.0
CD2 D:HIS268 3.4 36.1 1.0
CD2 A:HIS272 3.5 45.0 1.0
O3 D:BCT402 4.0 44.2 0.6
O3 D:BCT402 4.0 40.4 0.4
ND1 A:HIS215 4.3 38.9 1.0
ND1 D:HIS268 4.4 35.0 1.0
CG D:HIS214 4.4 33.8 1.0
ND1 A:HIS272 4.4 39.9 1.0
ND1 D:HIS214 4.4 38.5 1.0
CG A:HIS215 4.4 38.6 1.0
CG D:HIS268 4.5 34.8 1.0
CG A:HIS272 4.6 37.8 1.0
CG2 A:VAL219 4.7 33.6 1.0
CG2 D:VAL218 4.9 30.1 1.0

Iron binding site 2 out of 6 in 5zzn

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Iron binding site 2 out of 6 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:49.0
occ:1.00
FE F:HEM101 0.0 49.0 1.0
NB F:HEM101 1.9 48.7 1.0
ND F:HEM101 2.1 49.0 1.0
NA F:HEM101 2.1 56.1 1.0
NC F:HEM101 2.1 48.8 1.0
NE2 E:HIS23 2.2 56.0 1.0
NE2 F:HIS24 2.2 51.0 1.0
C4B F:HEM101 3.0 55.7 1.0
C1B F:HEM101 3.0 56.8 1.0
C4D F:HEM101 3.0 57.8 1.0
CD2 F:HIS24 3.0 53.6 1.0
C1A F:HEM101 3.1 53.5 1.0
CE1 E:HIS23 3.1 58.4 1.0
C1D F:HEM101 3.1 52.8 1.0
C1C F:HEM101 3.1 43.3 1.0
C4A F:HEM101 3.1 56.5 1.0
C4C F:HEM101 3.1 46.8 1.0
CD2 E:HIS23 3.2 58.5 1.0
CE1 F:HIS24 3.2 52.3 1.0
CHA F:HEM101 3.4 53.3 1.0
CHC F:HEM101 3.4 51.9 1.0
CHB F:HEM101 3.4 56.4 1.0
CHD F:HEM101 3.5 47.2 1.0
C3B F:HEM101 4.2 52.9 1.0
C2B F:HEM101 4.2 59.5 1.0
ND1 E:HIS23 4.2 55.7 1.0
CG F:HIS24 4.2 57.5 1.0
C3D F:HEM101 4.3 50.4 1.0
ND1 F:HIS24 4.3 53.8 1.0
C2D F:HEM101 4.3 52.5 1.0
CG E:HIS23 4.3 61.6 1.0
C2A F:HEM101 4.3 54.0 1.0
C2C F:HEM101 4.3 49.0 1.0
C3A F:HEM101 4.3 63.3 1.0
C3C F:HEM101 4.3 52.1 1.0
CE1 E:TYR19 4.9 64.2 1.0
NE1 F:TRP20 4.9 49.3 1.0

Iron binding site 3 out of 6 in 5zzn

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Iron binding site 3 out of 6 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:33.2
occ:1.00
FE V:HEC201 0.0 33.2 1.0
NA V:HEC201 1.9 33.5 1.0
NC V:HEC201 2.0 28.3 1.0
NE2 V:HIS41 2.0 28.1 1.0
NB V:HEC201 2.1 32.4 1.0
ND V:HEC201 2.1 32.9 1.0
NE2 V:HIS92 2.1 39.8 1.0
C4A V:HEC201 3.0 35.1 1.0
CE1 V:HIS41 3.0 31.3 1.0
C4C V:HEC201 3.0 32.8 1.0
C1C V:HEC201 3.0 32.6 1.0
C1A V:HEC201 3.0 31.3 1.0
C1D V:HEC201 3.0 31.5 1.0
CD2 V:HIS41 3.0 30.1 1.0
CD2 V:HIS92 3.1 38.8 1.0
C1B V:HEC201 3.1 32.2 1.0
C4D V:HEC201 3.1 32.8 1.0
C4B V:HEC201 3.1 32.3 1.0
CE1 V:HIS92 3.1 34.5 1.0
CHB V:HEC201 3.4 32.8 1.0
CHD V:HEC201 3.4 31.6 1.0
CHC V:HEC201 3.4 30.4 1.0
CHA V:HEC201 3.4 31.1 1.0
ND1 V:HIS41 4.1 31.5 1.0
CG V:HIS41 4.2 30.8 1.0
C3A V:HEC201 4.2 35.4 1.0
C2A V:HEC201 4.2 34.6 1.0
ND1 V:HIS92 4.2 38.0 1.0
CG V:HIS92 4.2 38.6 1.0
C2C V:HEC201 4.2 33.5 1.0
C3C V:HEC201 4.2 31.6 1.0
C2D V:HEC201 4.3 35.1 1.0
C3D V:HEC201 4.3 31.3 1.0
C2B V:HEC201 4.3 34.3 1.0
C3B V:HEC201 4.3 36.7 1.0
CE2 V:TYR75 4.8 35.6 1.0

Iron binding site 4 out of 6 in 5zzn

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Iron binding site 4 out of 6 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe403

b:40.9
occ:1.00
NE2 a:HIS215 2.2 38.9 1.0
O1 d:BCT401 2.3 31.6 0.4
NE2 d:HIS214 2.3 33.1 1.0
O2 d:BCT401 2.3 22.0 0.4
NE2 a:HIS272 2.3 41.1 1.0
NE2 d:HIS268 2.4 30.8 1.0
O1 d:BCT401 2.6 50.8 0.6
C d:BCT401 2.6 31.7 0.4
O2 d:BCT401 2.7 68.0 0.6
C d:BCT401 3.0 55.5 0.6
CE1 a:HIS215 3.0 39.8 1.0
CE1 a:HIS272 3.1 38.0 1.0
CD2 d:HIS214 3.2 33.3 1.0
CE1 d:HIS268 3.2 29.7 1.0
CD2 a:HIS215 3.3 35.5 1.0
CE1 d:HIS214 3.3 34.4 1.0
CD2 a:HIS272 3.4 40.1 1.0
CD2 d:HIS268 3.5 32.6 1.0
O3 d:BCT401 3.9 38.5 0.4
ND1 a:HIS215 4.2 38.7 1.0
O3 d:BCT401 4.3 52.1 0.6
ND1 a:HIS272 4.3 41.6 1.0
CG a:HIS215 4.4 36.7 1.0
CG d:HIS214 4.4 36.8 1.0
ND1 d:HIS268 4.4 32.4 1.0
ND1 d:HIS214 4.4 38.4 1.0
CG a:HIS272 4.5 43.2 1.0
CG d:HIS268 4.6 28.2 1.0
CG2 a:VAL219 4.7 34.9 1.0
CG2 d:VAL218 4.9 30.9 1.0

Iron binding site 5 out of 6 in 5zzn

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Iron binding site 5 out of 6 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:48.6
occ:1.00
FE f:HEM101 0.0 48.6 1.0
NA f:HEM101 2.0 48.5 1.0
ND f:HEM101 2.0 48.1 1.0
NE2 e:HIS23 2.0 55.5 1.0
NC f:HEM101 2.1 44.1 1.0
NB f:HEM101 2.1 42.0 1.0
NE2 f:HIS24 2.2 54.5 1.0
CE1 e:HIS23 2.9 51.6 1.0
C1A f:HEM101 3.0 49.3 1.0
C4D f:HEM101 3.0 50.7 1.0
C1D f:HEM101 3.0 50.7 1.0
C4A f:HEM101 3.0 52.1 1.0
C4C f:HEM101 3.1 46.9 1.0
CD2 f:HIS24 3.1 45.4 1.0
C1B f:HEM101 3.1 53.2 1.0
CD2 e:HIS23 3.1 57.0 1.0
C1C f:HEM101 3.1 46.1 1.0
C4B f:HEM101 3.1 46.1 1.0
CE1 f:HIS24 3.2 48.3 1.0
CHA f:HEM101 3.3 53.3 1.0
CHD f:HEM101 3.4 48.5 1.0
CHB f:HEM101 3.4 54.6 1.0
CHC f:HEM101 3.5 47.1 1.0
ND1 e:HIS23 4.1 47.3 1.0
CG e:HIS23 4.2 54.2 1.0
C2A f:HEM101 4.2 51.3 1.0
C2D f:HEM101 4.2 49.5 1.0
C3D f:HEM101 4.2 48.2 1.0
C3A f:HEM101 4.3 52.4 1.0
CG f:HIS24 4.3 53.0 1.0
ND1 f:HIS24 4.3 52.5 1.0
C3C f:HEM101 4.3 44.5 1.0
C2C f:HEM101 4.3 48.6 1.0
C2B f:HEM101 4.4 52.6 1.0
C3B f:HEM101 4.4 49.2 1.0
CE1 e:TYR19 4.7 55.6 1.0
NE1 f:TRP20 5.0 50.2 1.0

Iron binding site 6 out of 6 in 5zzn

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Iron binding site 6 out of 6 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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 Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe202

b:41.7
occ:1.00
FE v:HEC202 0.0 41.7 1.0
NC v:HEC202 2.0 48.2 1.0
NB v:HEC202 2.0 40.1 1.0
NE2 v:HIS41 2.1 50.1 1.0
NA v:HEC202 2.1 43.4 1.0
ND v:HEC202 2.1 45.1 1.0
NE2 v:HIS92 2.1 39.3 1.0
C1C v:HEC202 3.0 44.7 1.0
C4B v:HEC202 3.0 44.0 1.0
CE1 v:HIS41 3.0 45.1 1.0
C4D v:HEC202 3.1 42.7 1.0
CD2 v:HIS41 3.1 43.4 1.0
C1A v:HEC202 3.1 43.0 1.0
CD2 v:HIS92 3.1 41.1 1.0
C4C v:HEC202 3.1 53.2 1.0
C1B v:HEC202 3.1 45.3 1.0
CE1 v:HIS92 3.1 41.5 1.0
C1D v:HEC202 3.2 47.4 1.0
C4A v:HEC202 3.2 44.2 1.0
CHC v:HEC202 3.3 47.0 1.0
CHA v:HEC202 3.4 42.6 1.0
CHB v:HEC202 3.5 44.0 1.0
CHD v:HEC202 3.5 44.3 1.0
ND1 v:HIS41 4.1 42.2 1.0
CG v:HIS41 4.2 44.1 1.0
ND1 v:HIS92 4.2 43.9 1.0
CG v:HIS92 4.2 39.3 1.0
C2C v:HEC202 4.2 43.7 1.0
C3B v:HEC202 4.3 44.4 1.0
C3D v:HEC202 4.3 41.7 1.0
C2B v:HEC202 4.3 46.6 1.0
C3C v:HEC202 4.3 44.3 1.0
C2A v:HEC202 4.3 47.5 1.0
C2D v:HEC202 4.3 40.6 1.0
C3A v:HEC202 4.4 45.6 1.0
CE2 v:TYR75 4.9 48.2 1.0

Reference:

Y.Nakajima, Y.Umena, R.Nagao, K.Endo, K.Kobayashi, F.Akita, M.Suga, H.Wada, T.Noguchi, J.R.Shen. Thylakoid Membrane Lipid Sulfoquinovosyl-Diacylglycerol (Sqdg) Is Required For Full Functioning of Photosystem II Inthermosynechococcus Elongatus. J. Biol. Chem. V. 293 14786 2018.
ISSN: ESSN 1083-351X
PubMed: 30076221
DOI: 10.1074/JBC.RA118.004304
Page generated: Sun Dec 13 16:19:50 2020

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