Chlorine 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
Iron (Fe) 6 atoms
Calcium (Ca) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus, PDB code: 5zzn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5zzn

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Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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
A:Cl402

b:31.6
occ:1.00
 O D:HOH550 3.1 33.1 1.0
NZ D:LYS317 3.3 32.4 1.0
ND2 A:ASN181 3.4 29.4 1.0
N A:GLU333 3.4 29.4 1.0
O A:HOH586 3.6 39.6 1.0
CB A:HIS332 3.7 28.7 1.0
CA A:HIS332 3.8 27.3 1.0
CE D:LYS317 3.8 30.9 1.0
CG A:GLU333 4.0 32.1 1.0
C A:HIS332 4.1 30.1 1.0
OD1 A:ASN181 4.1 30.1 1.0
CG A:ASN181 4.2 30.9 1.0
CD2 D:LEU321 4.3 25.0 1.0
CG2 A:VAL185 4.3 33.6 1.0
CB D:LYS317 4.4 27.3 1.0
CA A:GLU333 4.4 28.1 1.0
O A:HOH556 4.4 36.1 1.0
CD1 D:LEU321 4.5 31.5 1.0
O D:HOH527 4.6 31.2 1.0
CG D:LEU321 4.7 27.6 1.0
CG D:LYS317 4.7 27.5 1.0
CG A:HIS332 4.8 26.8 1.0
CB A:GLU333 4.8 27.9 1.0
O D:LYS317 4.8 25.3 1.0
CD D:LYS317 4.9 31.7 1.0
OE2 A:GLU333 4.9 32.1 1.0
CD A:GLU333 5.0 29.4 1.0
O D:HOH572 5.0 37.2 1.0

Chlorine binding site 2 out of 5 in 5zzn

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Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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
A:Cl403

b:29.8
occ:1.00
 O C:HOH731 2.8 29.6 1.0
O A:HOH591 3.2 32.5 1.0
N C:GLU354 3.2 31.2 1.0
N A:ASN338 3.3 27.9 1.0
CA C:GLY353 3.8 35.2 1.0
N A:PHE339 3.8 34.1 1.0
CD2 A:PHE339 3.8 28.5 1.0
CA A:HIS337 3.8 34.0 1.0
C C:GLY353 4.0 35.1 1.0
C A:HIS337 4.1 31.3 1.0
O A:ALA336 4.2 29.1 1.0
CB C:GLU354 4.2 32.6 1.0
CA A:ASN338 4.2 31.6 1.0
CA C:GLU354 4.3 33.7 1.0
CB A:ASN338 4.3 32.4 1.0
CB A:PHE339 4.3 29.9 1.0
O C:HOH678 4.4 28.5 1.0
CB A:HIS337 4.4 33.1 1.0
CG A:PHE339 4.4 31.8 1.0
O C:HOH759 4.5 31.4 1.0
CG C:GLU354 4.5 36.8 1.0
C A:ASN338 4.5 30.5 1.0
CE2 A:PHE339 4.5 30.0 1.0
CA A:PHE339 4.6 36.0 1.0
O A:PHE339 4.7 31.8 1.0
N C:THR355 4.8 29.0 1.0
O C:GLY352 4.9 30.8 1.0
CG A:ASN338 5.0 34.9 1.0
CD2 A:HIS337 5.0 29.9 1.0
N A:HIS337 5.0 32.6 1.0

Chlorine binding site 3 out of 5 in 5zzn

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Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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
a:Cl404

b:35.9
occ:1.00
 O d:HOH529 3.1 36.8 1.0
NZ d:LYS317 3.2 39.6 1.0
O a:HOH576 3.3 37.1 1.0
ND2 a:ASN181 3.3 32.4 1.0
N a:GLU333 3.4 31.5 1.0
CB a:HIS332 3.7 34.4 1.0
CA a:HIS332 3.8 31.7 1.0
CE d:LYS317 3.8 37.6 1.0
CG a:GLU333 4.1 40.3 1.0
OD1 a:ASN181 4.1 31.6 1.0
C a:HIS332 4.1 34.5 1.0
CG a:ASN181 4.2 34.7 1.0
CD2 d:LEU321 4.3 32.4 1.0
CG2 a:VAL185 4.3 27.7 1.0
CB d:LYS317 4.3 30.5 1.0
CA a:GLU333 4.4 33.8 1.0
O a:HOH507 4.5 29.2 1.0
O a:HOH577 4.5 35.0 1.0
CD1 d:LEU321 4.5 29.3 1.0
CG d:LYS317 4.7 30.9 1.0
CG d:LEU321 4.7 32.1 1.0
CG a:HIS332 4.8 31.1 1.0
CB a:GLU333 4.8 35.0 1.0
O d:LYS317 4.8 31.8 1.0
CD d:LYS317 4.8 33.0 1.0
OE2 a:GLU333 4.9 40.7 1.0
O d:HOH576 5.0 39.3 1.0
CD a:GLU333 5.0 38.0 1.0

Chlorine binding site 4 out of 5 in 5zzn

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Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl 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:Cl405

b:34.9
occ:1.00
 O a:HOH585 3.0 30.7 1.0
O c:HOH655 3.0 29.8 1.0
N a:ASN338 3.2 32.5 1.0
N c:GLU354 3.3 31.8 1.0
N a:PHE339 3.7 36.3 1.0
CD1 a:PHE339 3.7 35.3 1.0
CA c:GLY353 3.7 35.2 1.0
CA a:HIS337 3.8 34.6 1.0
C a:HIS337 4.0 38.5 1.0
C c:GLY353 4.0 32.2 1.0
CA a:ASN338 4.2 33.3 1.0
O a:ALA336 4.2 32.3 1.0
CB c:GLU354 4.3 32.7 1.0
CB a:ASN338 4.3 30.3 1.0
CB a:PHE339 4.3 34.5 1.0
CA c:GLU354 4.3 34.3 1.0
O c:HOH684 4.4 32.9 1.0
CG a:PHE339 4.4 32.0 1.0
CB a:HIS337 4.4 31.6 1.0
C a:ASN338 4.4 36.7 1.0
CE1 a:PHE339 4.5 38.6 1.0
CG c:GLU354 4.6 34.5 1.0
CA a:PHE339 4.6 32.6 1.0
O c:HOH745 4.6 37.3 1.0
O a:PHE339 4.7 36.9 1.0
N c:THR355 4.9 33.7 1.0
O c:GLY352 4.9 34.4 1.0
N a:HIS337 4.9 30.0 1.0
CG a:ASN338 4.9 33.7 1.0
CD2 a:HIS337 5.0 33.7 1.0
N c:GLY353 5.0 31.4 1.0

Chlorine binding site 5 out of 5 in 5zzn

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Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl 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
v:Cl201

b:93.8
occ:1.00
 O v:HOH302 2.9 43.3 1.0
O v:DMS207 3.6 78.3 1.0
C2 v:DMS207 4.0 83.2 1.0
S v:DMS207 4.0 99.9 1.0
NH1 v:ARG55 4.1 40.8 0.5
NZ u:LYS104 4.2 39.8 1.0
OD2 v:ASP53 4.5 47.5 1.0
O v:HOH341 4.6 46.7 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: Sat Dec 12 12:42:54 2020

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