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Manganese in PDB 5gth: Native Xfel Structure of Photosystem II (Dark Dataset)

Enzymatic activity of Native Xfel Structure of Photosystem II (Dark Dataset)

All present enzymatic activity of Native Xfel Structure of Photosystem II (Dark Dataset):
1.10.3.9;

Protein crystallography data

The structure of Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth was solved by M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.520, 231.230, 287.460, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 18.6

Other elements in 5gth:

The structure of Native Xfel Structure of Photosystem II (Dark Dataset) also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 8 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Native Xfel Structure of Photosystem II (Dark Dataset) (pdb code 5gth). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5gth

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Manganese binding site 1 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:27.9
occ:1.00
 MN1 A:OEX413 0.0 27.9 1.0
OE2 A:GLU189 1.8 36.3 1.0
O1 A:OEX413 1.8 43.3 1.0
O3 A:OEX413 1.9 37.4 1.0
NE2 A:HIS332 2.1 33.1 1.0
OD2 A:ASP342 2.2 24.6 1.0
MN2 A:OEX413 2.6 30.7 1.0
O5 A:OEX413 2.7 31.5 1.0
CD A:GLU189 2.9 29.5 1.0
CE1 A:HIS332 3.0 24.1 1.0
CD2 A:HIS332 3.1 25.1 1.0
CG A:ASP342 3.1 24.8 1.0
MN3 A:OEX413 3.2 28.0 1.0
OD1 A:ASP342 3.4 29.6 1.0
OE1 A:GLU189 3.4 36.9 1.0
O2 A:OEX413 3.5 26.4 1.0
CA1 A:OEX413 3.6 45.8 1.0
NE2 A:HIS337 3.9 26.2 1.0
OE1 A:GLU333 4.0 25.1 1.0
ND1 A:HIS332 4.1 21.8 1.0
CG A:GLU189 4.1 22.6 1.0
OXT A:ALA344 4.2 31.1 1.0
CG A:HIS332 4.2 24.8 1.0
O A:HOH560 4.2 35.0 1.0
CE1 A:HIS337 4.4 36.7 1.0
O A:ALA344 4.5 34.1 1.0
CB A:ASP342 4.5 24.5 1.0
OE1 C:GLU354 4.5 57.1 1.0
OE2 C:GLU354 4.5 35.0 1.0
CG1 A:VAL185 4.7 21.5 1.0
C A:ALA344 4.7 42.4 1.0
CD A:GLU333 4.7 30.9 1.0
O A:HOH614 4.9 45.2 1.0
CD C:GLU354 4.9 23.2 1.0
O4 A:OEX413 4.9 22.4 1.0

Manganese binding site 2 out of 8 in 5gth

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Manganese binding site 2 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:30.7
occ:1.00
 MN2 A:OEX413 0.0 30.7 1.0
O1 A:OEX413 1.8 43.3 1.0
OXT A:ALA344 1.9 31.1 1.0
O2 A:OEX413 1.9 26.4 1.0
O3 A:OEX413 1.9 37.4 1.0
OE1 C:GLU354 2.1 57.1 1.0
OD1 A:ASP342 2.2 29.6 1.0
MN1 A:OEX413 2.6 27.9 1.0
MN3 A:OEX413 2.8 28.0 1.0
C A:ALA344 2.9 42.4 1.0
CD C:GLU354 2.9 23.2 1.0
CG A:ASP342 3.0 24.8 1.0
OE2 C:GLU354 3.0 35.0 1.0
OD2 A:ASP342 3.1 24.6 1.0
O A:ALA344 3.2 34.1 1.0
CA1 A:OEX413 3.5 45.8 1.0
NE2 A:HIS337 3.6 26.2 1.0
O5 A:OEX413 3.6 31.5 1.0
OE2 A:GLU189 4.0 36.3 1.0
O A:HOH560 4.2 35.0 1.0
CA A:ALA344 4.2 51.4 1.0
CD2 A:HIS337 4.2 38.9 1.0
CG C:GLU354 4.3 28.6 1.0
O4 A:OEX413 4.3 22.4 1.0
NE2 A:HIS332 4.3 33.1 1.0
OE1 A:GLU333 4.4 25.1 1.0
N A:ALA344 4.4 57.5 1.0
CB A:ASP342 4.4 24.5 1.0
O A:HOH611 4.5 31.7 1.0
CE1 A:HIS337 4.7 36.7 1.0
CD A:GLU189 4.8 29.5 1.0
CB C:GLU354 4.8 23.9 1.0
OE1 A:GLU189 4.8 36.9 1.0
NH2 C:ARG357 4.8 24.8 1.0
CA A:ASP342 4.8 24.1 1.0
C A:ASP342 4.9 34.6 1.0
NH1 C:ARG357 5.0 23.8 1.0

Manganese binding site 3 out of 8 in 5gth

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Manganese binding site 3 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:28.0
occ:1.00
 MN3 A:OEX413 0.0 28.0 1.0
O2 A:OEX413 1.8 26.4 1.0
O4 A:OEX413 1.9 22.4 1.0
O5 A:OEX413 2.0 31.5 1.0
OE1 A:GLU333 2.0 25.1 1.0
O3 A:OEX413 2.1 37.4 1.0
OE2 C:GLU354 2.1 35.0 1.0
MN2 A:OEX413 2.8 30.7 1.0
CD A:GLU333 2.9 30.9 1.0
MN4 A:OEX413 3.0 36.6 1.0
CD C:GLU354 3.1 23.2 1.0
OE2 A:GLU333 3.1 21.5 1.0
MN1 A:OEX413 3.2 27.9 1.0
OE1 C:GLU354 3.4 57.1 1.0
O1 A:OEX413 3.5 43.3 1.0
CA1 A:OEX413 3.5 45.8 1.0
O C:HOH670 4.0 41.6 1.0
NE2 A:HIS337 4.0 26.2 1.0
NH2 C:ARG357 4.1 24.8 1.0
NE2 A:HIS332 4.1 33.1 1.0
OD2 A:ASP170 4.2 38.6 1.0
OXT A:ALA344 4.2 31.1 1.0
CG A:GLU333 4.3 32.7 1.0
OD1 A:ASP170 4.4 46.3 1.0
CD2 A:HIS332 4.4 25.1 1.0
CG C:GLU354 4.4 28.6 1.0
O A:HOH530 4.5 22.9 1.0
O A:HOH534 4.6 37.0 1.0
CB A:GLU333 4.7 21.5 1.0
CE1 A:HIS337 4.7 36.7 1.0
OE2 A:GLU189 4.7 36.3 1.0
OD1 A:ASP342 4.7 29.6 1.0
O A:ALA344 4.7 34.1 1.0
CG A:ASP170 4.7 30.7 1.0
O A:HOH573 4.8 42.2 1.0
OD2 A:ASP342 4.8 24.6 1.0
O A:HOH614 4.9 45.2 1.0
C A:ALA344 4.9 42.4 1.0

Manganese binding site 4 out of 8 in 5gth

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Manganese binding site 4 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:36.6
occ:1.00
 MN4 A:OEX413 0.0 36.6 1.0
O4 A:OEX413 2.0 22.4 1.0
OD2 A:ASP170 2.1 38.6 1.0
O A:HOH573 2.1 42.2 1.0
OE2 A:GLU333 2.1 21.5 1.0
O A:HOH534 2.2 37.0 1.0
O5 A:OEX413 2.3 31.5 1.0
MN3 A:OEX413 3.0 28.0 1.0
CD A:GLU333 3.1 30.9 1.0
CG A:ASP170 3.2 30.7 1.0
OE1 A:GLU333 3.5 25.1 1.0
O A:HOH614 3.6 45.2 1.0
OD1 A:ASP170 3.7 46.3 1.0
CA1 A:OEX413 3.8 45.8 1.0
O A:HOH580 3.9 27.1 1.0
O2 A:OEX413 4.0 26.4 1.0
O A:HOH530 4.0 22.9 1.0
O A:HOH574 4.2 32.1 1.0
OD1 A:ASP61 4.2 26.9 1.0
CB A:ASP170 4.4 23.0 1.0
CG A:GLU333 4.4 32.7 1.0
O A:SER169 4.5 24.3 1.0
CA A:ASP170 4.5 32.1 1.0
NH2 C:ARG357 4.7 24.8 1.0
OE2 C:GLU354 4.7 35.0 1.0
O3 A:OEX413 4.8 37.4 1.0
O D:HOH512 5.0 30.9 1.0
C A:SER169 5.0 33.5 1.0

Manganese binding site 5 out of 8 in 5gth

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Manganese binding site 5 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:37.2
occ:1.00
 MN1 a:OEX413 0.0 37.2 1.0
OE2 a:GLU189 1.8 28.1 1.0
O1 a:OEX413 1.8 42.9 1.0
O3 a:OEX413 1.9 45.3 1.0
NE2 a:HIS332 2.1 35.0 1.0
OD2 a:ASP342 2.2 31.2 1.0
MN2 a:OEX413 2.6 33.6 1.0
O5 a:OEX413 2.7 37.9 1.0
CD a:GLU189 2.9 41.0 1.0
CE1 a:HIS332 3.0 27.7 1.0
CG a:ASP342 3.1 32.0 1.0
CD2 a:HIS332 3.1 26.9 1.0
MN3 a:OEX413 3.2 28.9 1.0
OD1 a:ASP342 3.3 35.4 1.0
O2 a:OEX413 3.5 28.3 1.0
OE1 a:GLU189 3.5 41.7 1.0
CA1 a:OEX413 3.7 53.4 1.0
NE2 a:HIS337 3.9 28.3 1.0
OE1 a:GLU333 3.9 27.1 1.0
O a:HOH509 4.0 61.8 1.0
ND1 a:HIS332 4.1 27.3 1.0
OXT a:ALA344 4.1 29.4 1.0
CG a:GLU189 4.2 28.3 1.0
CG a:HIS332 4.2 27.8 1.0
OE1 c:GLU354 4.4 32.2 1.0
CB a:ASP342 4.5 29.9 1.0
OE2 c:GLU354 4.5 28.1 1.0
CE1 a:HIS337 4.6 35.3 1.0
O a:ALA344 4.6 35.0 1.0
O a:HOH594 4.7 62.3 1.0
CD a:GLU333 4.7 28.5 1.0
C a:ALA344 4.8 47.0 1.0
CG1 a:VAL185 4.8 26.6 1.0
CD c:GLU354 4.9 39.8 1.0
CD2 a:HIS337 5.0 39.0 1.0
O4 a:OEX413 5.0 27.2 1.0
MN4 a:OEX413 5.0 34.9 1.0

Manganese binding site 6 out of 8 in 5gth

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Manganese binding site 6 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:33.6
occ:1.00
 MN2 a:OEX413 0.0 33.6 1.0
O1 a:OEX413 1.8 42.9 1.0
O2 a:OEX413 1.9 28.3 1.0
OXT a:ALA344 1.9 29.4 1.0
O3 a:OEX413 1.9 45.3 1.0
OE1 c:GLU354 2.1 32.2 1.0
OD1 a:ASP342 2.2 35.4 1.0
MN1 a:OEX413 2.6 37.2 1.0
MN3 a:OEX413 2.7 28.9 1.0
C a:ALA344 2.9 47.0 1.0
CD c:GLU354 2.9 39.8 1.0
CG a:ASP342 3.0 32.0 1.0
OE2 c:GLU354 3.1 28.1 1.0
OD2 a:ASP342 3.2 31.2 1.0
O a:ALA344 3.3 35.0 1.0
CA1 a:OEX413 3.5 53.4 1.0
O5 a:OEX413 3.5 37.9 1.0
NE2 a:HIS337 3.7 28.3 1.0
O a:HOH509 3.9 61.8 1.0
OE2 a:GLU189 3.9 28.1 1.0
O c:HOH698 4.0 30.4 1.0
CA a:ALA344 4.2 54.7 1.0
CD2 a:HIS337 4.3 39.0 1.0
NE2 a:HIS332 4.3 35.0 1.0
OE1 a:GLU333 4.3 27.1 1.0
CG c:GLU354 4.3 28.9 1.0
N a:ALA344 4.4 60.2 1.0
O4 a:OEX413 4.4 27.2 1.0
CB a:ASP342 4.4 29.9 1.0
CD a:GLU189 4.7 41.0 1.0
OE1 a:GLU189 4.7 41.7 1.0
CA a:ASP342 4.8 30.5 1.0
C a:ASP342 4.9 33.5 1.0
CB c:GLU354 4.9 35.5 1.0
CE1 a:HIS337 4.9 35.3 1.0
NH2 c:ARG357 4.9 28.3 1.0
NH1 c:ARG357 5.0 29.1 1.0
CB a:ALA344 5.0 60.6 1.0

Manganese binding site 7 out of 8 in 5gth

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Manganese binding site 7 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:28.9
occ:1.00
 MN3 a:OEX413 0.0 28.9 1.0
O2 a:OEX413 1.8 28.3 1.0
O4 a:OEX413 1.9 27.2 1.0
O5 a:OEX413 2.0 37.9 1.0
OE1 a:GLU333 2.0 27.1 1.0
O3 a:OEX413 2.1 45.3 1.0
OE2 c:GLU354 2.1 28.1 1.0
MN2 a:OEX413 2.7 33.6 1.0
MN4 a:OEX413 2.9 34.9 1.0
CD a:GLU333 2.9 28.5 1.0
CD c:GLU354 3.1 39.8 1.0
OE2 a:GLU333 3.2 26.3 1.0
MN1 a:OEX413 3.2 37.2 1.0
OE1 c:GLU354 3.4 32.2 1.0
O1 a:OEX413 3.4 42.9 1.0
CA1 a:OEX413 3.5 53.4 1.0
O c:HOH616 3.8 50.6 1.0
NH2 c:ARG357 4.0 28.3 1.0
NE2 a:HIS332 4.1 35.0 1.0
OXT a:ALA344 4.1 29.4 1.0
NE2 a:HIS337 4.2 28.3 1.0
OD2 a:ASP170 4.3 47.9 1.0
O a:HOH512 4.3 27.2 1.0
CG a:GLU333 4.3 31.8 1.0
CD2 a:HIS332 4.4 26.9 1.0
OD1 a:ASP170 4.4 47.0 1.0
CG c:GLU354 4.5 28.9 1.0
O a:HOH535 4.6 26.2 1.0
OE2 a:GLU189 4.6 28.1 1.0
O a:HOH565 4.7 26.1 1.0
OD1 a:ASP342 4.7 35.4 1.0
CB a:GLU333 4.7 26.4 1.0
O a:HOH594 4.8 62.3 1.0
CG a:ASP170 4.8 27.4 1.0
O a:ALA344 4.8 35.0 1.0
CE1 a:HIS337 4.9 35.3 1.0
C a:ALA344 4.9 47.0 1.0
OD2 a:ASP342 4.9 31.2 1.0

Manganese binding site 8 out of 8 in 5gth

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Manganese binding site 8 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:34.9
occ:1.00
 MN4 a:OEX413 0.0 34.9 1.0
O4 a:OEX413 2.0 27.2 1.0
OD2 a:ASP170 2.1 47.9 1.0
O a:HOH565 2.1 26.1 1.0
OE2 a:GLU333 2.1 26.3 1.0
O a:HOH535 2.2 26.2 1.0
O5 a:OEX413 2.3 37.9 1.0
MN3 a:OEX413 2.9 28.9 1.0
CD a:GLU333 3.0 28.5 1.0
CG a:ASP170 3.2 27.4 1.0
OE1 a:GLU333 3.4 27.1 1.0
OD1 a:ASP170 3.6 47.0 1.0
O a:HOH594 3.6 62.3 1.0
O a:HOH512 3.9 27.2 1.0
O a:HOH570 3.9 25.3 1.0
CA1 a:OEX413 3.9 53.4 1.0
O2 a:OEX413 4.0 28.3 1.0
O a:HOH621 4.0 46.2 1.0
OD1 a:ASP61 4.2 38.1 1.0
CG a:GLU333 4.4 31.8 1.0
O a:SER169 4.4 26.1 1.0
CB a:ASP170 4.4 27.4 1.0
CA a:ASP170 4.6 31.1 1.0
NH2 c:ARG357 4.6 28.3 1.0
OE2 c:GLU354 4.7 28.1 1.0
O3 a:OEX413 4.7 45.3 1.0
O a:HOH519 4.8 33.3 1.0
O c:HOH616 4.9 50.6 1.0
MN1 a:OEX413 5.0 37.2 1.0
C a:SER169 5.0 35.1 1.0

Reference:

M.Suga, F.Akita, M.Sugahara, M.Kubo, Y.Nakajima, T.Nakane, K.Yamashita, Y.Umena, M.Nakabayashi, T.Yamane, T.Nakano, M.Suzuki, T.Masuda, S.Inoue, T.Kimura, T.Nomura, S.Yonekura, L.J.Yu, T.Sakamoto, T.Motomura, J.H.Chen, Y.Kato, T.Noguchi, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, E.Nango, R.Tanaka, H.Naitow, Y.Matsuura, A.Yamashita, M.Yamamoto, O.Nureki, M.Yabashi, T.Ishikawa, S.Iwata, J.R.Shen. Light-Induced Structural Changes and the Site of O=O Bond Formation in Psii Caught By Xfel. Nature V. 543 131 2017.
ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400
Page generated: Sat Aug 16 17:33:27 2025

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