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Manganese 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
Iron (Fe) 6 atoms
Calcium (Ca) 9 atoms
Chlorine (Cl) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus, PDB code: 5zzn:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5zzn

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Manganese binding site 1 out of 8 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 Manganese with other atoms in the Mn 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:Mn401

b:30.2
occ:1.00
 MN1 A:OEX401 0.0 30.2 1.0
O3 A:OEX401 1.9 28.2 1.0
O1 A:OEX401 2.0 30.1 1.0
OE2 A:GLU189 2.0 34.1 1.0
NE2 A:HIS332 2.2 26.3 1.0
OD2 A:ASP342 2.2 30.2 1.0
O5 A:OEX401 2.5 33.0 1.0
MN2 A:OEX401 2.7 30.0 1.0
CD A:GLU189 2.9 33.7 1.0
CG A:ASP342 3.1 30.7 1.0
CD2 A:HIS332 3.2 29.0 1.0
MN3 A:OEX401 3.2 34.2 1.0
CE1 A:HIS332 3.2 31.3 1.0
OE1 A:GLU189 3.3 37.7 1.0
OD1 A:ASP342 3.4 32.6 1.0
O2 A:OEX401 3.4 31.3 1.0
CA1 A:OEX401 3.4 39.7 1.0
OE1 A:GLU333 3.9 30.7 1.0
NE2 A:HIS337 4.0 29.6 1.0
CG A:GLU189 4.1 33.2 1.0
O A:HOH569 4.2 53.5 1.0
ND1 A:HIS332 4.3 25.3 1.0
CG A:HIS332 4.3 26.8 1.0
OXT A:ALA344 4.4 35.3 1.0
OE1 C:GLU354 4.4 31.7 1.0
CG1 A:VAL185 4.5 28.7 1.0
CB A:ASP342 4.5 29.8 1.0
O A:HOH593 4.6 42.8 1.0
OE2 C:GLU354 4.7 35.2 1.0
CE1 A:HIS337 4.7 29.2 1.0
CD A:GLU333 4.7 29.4 1.0
O A:ALA344 4.7 35.3 1.0
O4 A:OEX401 4.8 34.5 1.0
O A:HOH535 4.8 34.5 1.0
C A:ALA344 4.8 32.0 1.0
MN4 A:OEX401 5.0 40.7 1.0
CD C:GLU354 5.0 33.9 1.0

Manganese binding site 2 out of 8 in 5zzn

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Manganese binding site 2 out of 8 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn401

b:30.0
occ:1.00
 MN2 A:OEX401 0.0 30.0 1.0
O1 A:OEX401 1.9 30.1 1.0
O2 A:OEX401 1.9 31.3 1.0
OXT A:ALA344 2.0 35.3 1.0
OD1 A:ASP342 2.1 32.6 1.0
O3 A:OEX401 2.1 28.2 1.0
OE1 C:GLU354 2.1 31.7 1.0
MN1 A:OEX401 2.7 30.2 1.0
MN3 A:OEX401 2.8 34.2 1.0
C A:ALA344 2.9 32.0 1.0
CG A:ASP342 3.0 30.7 1.0
CD C:GLU354 3.0 33.9 1.0
OD2 A:ASP342 3.1 30.2 1.0
O A:ALA344 3.2 35.3 1.0
OE2 C:GLU354 3.3 35.2 1.0
CA1 A:OEX401 3.3 39.7 1.0
O5 A:OEX401 3.7 33.0 1.0
NE2 A:HIS337 3.9 29.6 1.0
O C:HOH759 4.1 31.4 1.0
CA A:ALA344 4.1 38.5 1.0
O A:HOH569 4.2 53.5 1.0
N A:ALA344 4.3 39.1 1.0
O4 A:OEX401 4.3 34.5 1.0
OE1 A:GLU333 4.4 30.7 1.0
CB A:ASP342 4.4 29.8 1.0
OE2 A:GLU189 4.4 34.1 1.0
CD2 A:HIS337 4.4 29.9 1.0
CG C:GLU354 4.5 36.8 1.0
NE2 A:HIS332 4.5 26.3 1.0
NH2 C:ARG357 4.7 46.0 1.0
CA A:ASP342 4.8 32.2 1.0
O A:HOH535 4.8 34.5 1.0
CB C:GLU354 4.9 32.6 1.0
C A:ASP342 4.9 29.4 1.0
OE1 A:GLU189 4.9 37.7 1.0
CD A:GLU189 4.9 33.7 1.0
NH1 C:ARG357 5.0 37.8 1.0
OD2 A:ASP170 5.0 36.6 1.0

Manganese binding site 3 out of 8 in 5zzn

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Manganese binding site 3 out of 8 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn401

b:34.2
occ:1.00
 MN3 A:OEX401 0.0 34.2 1.0
O2 A:OEX401 1.8 31.3 1.0
O4 A:OEX401 1.9 34.5 1.0
OE1 A:GLU333 1.9 30.7 1.0
O3 A:OEX401 2.2 28.2 1.0
OE2 C:GLU354 2.3 35.2 1.0
O5 A:OEX401 2.3 33.0 1.0
MN2 A:OEX401 2.8 30.0 1.0
CD A:GLU333 2.9 29.4 1.0
MN4 A:OEX401 3.0 40.7 1.0
CD C:GLU354 3.2 33.9 1.0
MN1 A:OEX401 3.2 30.2 1.0
OE2 A:GLU333 3.3 32.1 1.0
OE1 C:GLU354 3.4 31.7 1.0
CA1 A:OEX401 3.4 39.7 1.0
O1 A:OEX401 3.6 30.1 1.0
NH2 C:ARG357 4.1 46.0 1.0
NE2 A:HIS337 4.2 29.6 1.0
NE2 A:HIS332 4.2 26.3 1.0
O C:HOH720 4.2 39.4 1.0
O A:HOH524 4.2 36.8 1.0
OD1 A:ASP170 4.3 32.5 1.0
CG A:GLU333 4.3 32.1 1.0
OD2 A:ASP170 4.4 36.6 1.0
OXT A:ALA344 4.4 35.3 1.0
CD2 A:HIS332 4.4 29.0 1.0
CG C:GLU354 4.6 36.8 1.0
OD1 A:ASP342 4.6 32.6 1.0
CB A:GLU333 4.7 27.9 1.0
OD2 A:ASP342 4.7 30.2 1.0
O A:ALA344 4.7 35.3 1.0
O A:HOH579 4.8 36.1 1.0
CG A:ASP170 4.8 32.4 1.0
O A:HOH553 4.8 30.5 1.0
CE1 A:HIS337 4.8 29.2 1.0
O A:HOH593 4.9 42.8 1.0
OE2 A:GLU189 4.9 34.1 1.0
C A:ALA344 5.0 32.0 1.0

Manganese binding site 4 out of 8 in 5zzn

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Manganese binding site 4 out of 8 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 Manganese with other atoms in the Mn 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:Mn401

b:40.7
occ:1.00
 MN4 A:OEX401 0.0 40.7 1.0
O4 A:OEX401 2.0 34.5 1.0
OD1 A:ASP170 2.1 32.5 1.0
OE2 A:GLU333 2.2 32.1 1.0
O A:HOH579 2.2 36.1 1.0
O A:HOH553 2.3 30.5 1.0
O5 A:OEX401 2.5 33.0 1.0
MN3 A:OEX401 3.0 34.2 1.0
CD A:GLU333 3.1 29.4 1.0
CG A:ASP170 3.2 32.4 1.0
OE1 A:GLU333 3.3 30.7 1.0
OD2 A:ASP170 3.7 36.6 1.0
O A:HOH524 3.8 36.8 1.0
O2 A:OEX401 3.8 31.3 1.0
O A:HOH593 3.8 42.8 1.0
O A:HOH586 3.9 39.6 1.0
CA1 A:OEX401 3.9 39.7 1.0
O A:HOH617 4.1 44.6 1.0
OD1 A:ASP61 4.2 31.6 1.0
O A:SER169 4.4 30.1 1.0
CG A:GLU333 4.5 32.1 1.0
CB A:ASP170 4.5 32.1 1.0
CA A:ASP170 4.6 31.5 1.0
O D:HOH527 4.7 31.2 1.0
NH2 C:ARG357 4.8 46.0 1.0
O3 A:OEX401 4.9 28.2 1.0
OE2 C:GLU354 4.9 35.2 1.0
C A:SER169 4.9 32.9 1.0
MN1 A:OEX401 5.0 30.2 1.0
N A:ASP170 5.0 29.0 1.0

Manganese binding site 5 out of 8 in 5zzn

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Manganese binding site 5 out of 8 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 Manganese with other atoms in the Mn 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
a:Mn402

b:31.9
occ:1.00
 MN1 a:OEX402 0.0 31.9 1.0
O1 a:OEX402 1.8 30.8 1.0
OE2 a:GLU189 2.0 31.0 1.0
O3 a:OEX402 2.1 28.6 1.0
NE2 a:HIS332 2.2 34.7 1.0
OD2 a:ASP342 2.2 33.1 1.0
O5 a:OEX402 2.5 34.6 1.0
MN2 a:OEX402 2.7 33.1 1.0
CD a:GLU189 2.9 39.7 1.0
CG a:ASP342 3.1 35.9 1.0
CD2 a:HIS332 3.1 35.8 1.0
CE1 a:HIS332 3.1 33.3 1.0
MN3 a:OEX402 3.2 34.2 1.0
OE1 a:GLU189 3.3 38.2 1.0
OD1 a:ASP342 3.3 30.8 1.0
CA1 a:OEX402 3.4 39.8 1.0
O2 a:OEX402 3.5 33.8 1.0
OE1 a:GLU333 3.9 37.3 1.0
NE2 a:HIS337 4.0 35.9 1.0
O a:HOH518 4.1 53.0 1.0
CG a:GLU189 4.2 43.4 1.0
ND1 a:HIS332 4.3 34.8 1.0
CG a:HIS332 4.3 31.1 1.0
OXT a:ALA344 4.4 42.9 1.0
CB a:ASP342 4.4 33.7 1.0
OE1 c:GLU354 4.5 29.6 1.0
CG1 a:VAL185 4.5 30.5 1.0
CE1 a:HIS337 4.7 42.7 1.0
CD a:GLU333 4.7 38.0 1.0
O a:HOH592 4.7 35.7 1.0
OE2 c:GLU354 4.8 29.4 1.0
O a:HOH559 4.8 38.0 1.0
O a:ALA344 4.8 43.0 1.0
C a:ALA344 4.8 47.0 1.0
MN4 a:OEX402 4.9 41.4 1.0
OE2 a:GLU333 5.0 40.7 1.0
CD c:GLU354 5.0 33.4 1.0
O4 a:OEX402 5.0 36.0 1.0

Manganese binding site 6 out of 8 in 5zzn

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Manganese binding site 6 out of 8 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 Manganese with other atoms in the Mn 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
a:Mn402

b:33.1
occ:1.00
 MN2 a:OEX402 0.0 33.1 1.0
O3 a:OEX402 1.9 28.6 1.0
OXT a:ALA344 1.9 42.9 1.0
O2 a:OEX402 2.0 33.8 1.0
O1 a:OEX402 2.0 30.8 1.0
OD1 a:ASP342 2.0 30.8 1.0
OE1 c:GLU354 2.1 29.6 1.0
MN1 a:OEX402 2.7 31.9 1.0
MN3 a:OEX402 2.8 34.2 1.0
C a:ALA344 2.8 47.0 1.0
CG a:ASP342 2.9 35.9 1.0
CD c:GLU354 3.0 33.4 1.0
OD2 a:ASP342 3.2 33.1 1.0
O a:ALA344 3.2 43.0 1.0
CA1 a:OEX402 3.3 39.8 1.0
OE2 c:GLU354 3.3 29.4 1.0
O5 a:OEX402 3.6 34.6 1.0
O c:HOH745 3.9 37.3 1.0
NE2 a:HIS337 3.9 35.9 1.0
O a:HOH518 4.1 53.0 1.0
CA a:ALA344 4.2 42.9 1.0
N a:ALA344 4.3 45.2 1.0
CB a:ASP342 4.3 33.7 1.0
O4 a:OEX402 4.4 36.0 1.0
OE1 a:GLU333 4.4 37.3 1.0
OE2 a:GLU189 4.4 31.0 1.0
CD2 a:HIS337 4.5 33.7 1.0
CG c:GLU354 4.5 34.5 1.0
NE2 a:HIS332 4.5 34.7 1.0
O a:HOH559 4.8 38.0 1.0
CA a:ASP342 4.8 36.4 1.0
NH2 c:ARG357 4.8 37.5 1.0
OE1 a:GLU189 4.8 38.2 1.0
CB c:GLU354 4.9 32.7 1.0
CD a:GLU189 4.9 39.7 1.0
C a:ASP342 4.9 37.4 1.0
OD2 a:ASP170 5.0 41.7 1.0

Manganese binding site 7 out of 8 in 5zzn

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Manganese binding site 7 out of 8 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 Manganese with other atoms in the Mn binding site number 7 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:Mn402

b:34.2
occ:1.00
 MN3 a:OEX402 0.0 34.2 1.0
O2 a:OEX402 1.8 33.8 1.0
O3 a:OEX402 1.8 28.6 1.0
O4 a:OEX402 1.9 36.0 1.0
OE1 a:GLU333 1.9 37.3 1.0
O5 a:OEX402 2.2 34.6 1.0
OE2 c:GLU354 2.3 29.4 1.0
MN2 a:OEX402 2.8 33.1 1.0
MN4 a:OEX402 2.9 41.4 1.0
CD a:GLU333 2.9 38.0 1.0
CD c:GLU354 3.2 33.4 1.0
MN1 a:OEX402 3.2 31.9 1.0
OE2 a:GLU333 3.2 40.7 1.0
OE1 c:GLU354 3.4 29.6 1.0
CA1 a:OEX402 3.4 39.8 1.0
O1 a:OEX402 3.6 30.8 1.0
O c:HOH627 4.0 43.7 1.0
NH2 c:ARG357 4.2 37.5 1.0
NE2 a:HIS337 4.2 35.9 1.0
OD1 a:ASP170 4.2 43.8 1.0
NE2 a:HIS332 4.2 34.7 1.0
O a:HOH501 4.2 35.9 1.0
OXT a:ALA344 4.3 42.9 1.0
CG a:GLU333 4.4 40.3 1.0
OD2 a:ASP170 4.4 41.7 1.0
CD2 a:HIS332 4.5 35.8 1.0
OD1 a:ASP342 4.6 30.8 1.0
CG c:GLU354 4.6 34.5 1.0
O a:HOH547 4.6 36.7 1.0
O a:ALA344 4.7 43.0 1.0
CG a:ASP170 4.8 38.8 1.0
O a:HOH590 4.8 36.2 1.0
CB a:GLU333 4.8 35.0 1.0
OD2 a:ASP342 4.8 33.1 1.0
CE1 a:HIS337 4.9 42.7 1.0
C a:ALA344 5.0 47.0 1.0
OE2 a:GLU189 5.0 31.0 1.0
O a:HOH592 5.0 35.7 1.0

Manganese binding site 8 out of 8 in 5zzn

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Manganese binding site 8 out of 8 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 Manganese with other atoms in the Mn binding site number 8 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:Mn402

b:41.4
occ:1.00
 MN4 a:OEX402 0.0 41.4 1.0
OE2 a:GLU333 2.1 40.7 1.0
O4 a:OEX402 2.2 36.0 1.0
O a:HOH547 2.2 36.7 1.0
OD1 a:ASP170 2.2 43.8 1.0
O a:HOH590 2.2 36.2 1.0
O5 a:OEX402 2.5 34.6 1.0
MN3 a:OEX402 2.9 34.2 1.0
CD a:GLU333 3.0 38.0 1.0
OE1 a:GLU333 3.3 37.3 1.0
CG a:ASP170 3.3 38.8 1.0
OD2 a:ASP170 3.7 41.7 1.0
O2 a:OEX402 3.8 33.8 1.0
O a:HOH501 3.9 35.9 1.0
CA1 a:OEX402 3.9 39.8 1.0
O a:HOH592 3.9 35.7 1.0
O a:HOH576 4.0 37.1 1.0
OD1 a:ASP61 4.2 36.3 1.0
O a:HOH604 4.3 39.9 1.0
CG a:GLU333 4.4 40.3 1.0
O a:SER169 4.4 29.8 1.0
O3 a:OEX402 4.5 28.6 1.0
CB a:ASP170 4.5 38.2 1.0
CA a:ASP170 4.6 29.7 1.0
O a:HOH507 4.7 29.2 1.0
OE2 c:GLU354 4.8 29.4 1.0
NH2 c:ARG357 4.9 37.5 1.0
MN1 a:OEX402 4.9 31.9 1.0
C a:SER169 4.9 33.1 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 Oct 6 03:46:38 2024

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