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Manganese in PDB 8ir5: Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions:
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions, PDB code: 8ir5 was solved by H.Li, 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 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.75, 231.6, 288.28, 90, 90, 90
R / Rfree (%) 14.5 / 17.5

Other elements in 8ir5:

The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 72 atoms
Calcium (Ca) 9 atoms
Iron (Fe) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions (pdb code 8ir5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions, PDB code: 8ir5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8ir5

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Manganese binding site 1 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:44.7
occ:1.00
 MN1 A:OEX413 0.0 44.7 1.0
O1 A:OEX413 1.8 41.8 1.0
OE2 A:GLU189 1.8 47.2 1.0
O3 A:OEX413 1.9 46.4 1.0
NE2 A:HIS332 2.1 45.4 1.0
OD2 A:ASP342 2.2 41.1 1.0
O5 A:OEX413 2.6 46.6 1.0
MN2 A:OEX413 2.8 45.9 1.0
CD A:GLU189 2.9 45.5 1.0
CE1 A:HIS332 3.0 43.1 1.0
CG A:ASP342 3.1 47.1 1.0
CD2 A:HIS332 3.1 44.2 1.0
MN3 A:OEX413 3.2 44.6 1.0
OD1 A:ASP342 3.3 42.1 1.0
CA1 A:OEX413 3.5 50.7 1.0
OE1 A:GLU189 3.5 52.2 1.0
O2 A:OEX413 3.5 43.2 1.0
OE1 A:GLU333 3.9 42.9 1.0
NE2 A:HIS337 4.0 45.3 1.0
CG A:GLU189 4.1 44.4 1.0
O A:HOH590 4.1 59.8 1.0
ND1 A:HIS332 4.1 45.3 1.0
CG A:HIS332 4.2 47.5 1.0
OXT A:ALA344 4.4 46.2 1.0
CB A:ASP342 4.4 45.1 1.0
OE1 C:GLU354 4.5 51.2 1.0
OE2 C:GLU354 4.5 47.9 1.0
CG1 A:VAL185 4.6 42.1 1.0
CE1 A:HIS337 4.6 44.3 1.0
CD A:GLU333 4.7 45.6 1.0
O A:HOH621 4.7 48.5 1.0
O A:ALA344 4.7 51.2 1.0
MN4 A:OEX413 4.9 48.6 1.0
C A:ALA344 4.9 48.2 1.0
CD C:GLU354 4.9 55.5 1.0
O4 A:OEX413 5.0 42.6 1.0
OE2 A:GLU333 5.0 46.6 1.0

Manganese binding site 2 out of 8 in 8ir5

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Manganese binding site 2 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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Stereo pair view

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

b:45.9
occ:1.00
 MN2 A:OEX413 0.0 45.9 1.0
O1 A:OEX413 1.8 41.8 1.0
O2 A:OEX413 1.9 43.2 1.0
OXT A:ALA344 1.9 46.2 1.0
O3 A:OEX413 1.9 46.4 1.0
OD1 A:ASP342 2.1 42.1 1.0
OE1 C:GLU354 2.1 51.2 1.0
MN3 A:OEX413 2.8 44.6 1.0
MN1 A:OEX413 2.8 44.7 1.0
C A:ALA344 2.8 48.2 1.0
CD C:GLU354 2.9 55.5 1.0
CG A:ASP342 3.0 47.1 1.0
OE2 C:GLU354 3.1 47.9 1.0
O A:ALA344 3.1 51.2 1.0
OD2 A:ASP342 3.3 41.1 1.0
CA1 A:OEX413 3.4 50.7 1.0
O5 A:OEX413 3.5 46.6 1.0
NE2 A:HIS337 3.9 45.3 1.0
O C:HOH737 4.0 50.4 1.0
O A:HOH590 4.1 59.8 1.0
OE2 A:GLU189 4.2 47.2 1.0
CA A:ALA344 4.2 46.8 1.0
CG C:GLU354 4.2 51.5 1.0
N A:ALA344 4.3 52.0 1.0
O4 A:OEX413 4.3 42.6 1.0
OE1 A:GLU333 4.4 42.9 1.0
CD2 A:HIS337 4.4 42.2 1.0
CB A:ASP342 4.4 45.1 1.0
NH2 C:ARG357 4.6 45.1 1.0
NE2 A:HIS332 4.6 45.4 1.0
NH1 C:ARG357 4.8 44.2 1.0
CA A:ASP342 4.8 44.8 1.0
CB C:GLU354 4.9 45.8 1.0
OD1 A:ASP170 4.9 46.2 1.0
C A:ASP342 4.9 47.8 1.0
CD A:GLU189 4.9 45.5 1.0
CZ C:ARG357 4.9 51.7 1.0

Manganese binding site 3 out of 8 in 8ir5

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Manganese binding site 3 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:44.6
occ:1.00
 MN3 A:OEX413 0.0 44.6 1.0
O2 A:OEX413 1.8 43.2 1.0
O4 A:OEX413 1.9 42.6 1.0
O5 A:OEX413 2.0 46.6 1.0
OE1 A:GLU333 2.0 42.9 1.0
OE2 C:GLU354 2.0 47.9 1.0
O3 A:OEX413 2.1 46.4 1.0
MN4 A:OEX413 2.8 48.6 1.0
MN2 A:OEX413 2.8 45.9 1.0
CD A:GLU333 2.9 45.6 1.0
CD C:GLU354 3.0 55.5 1.0
OE2 A:GLU333 3.1 46.6 1.0
MN1 A:OEX413 3.2 44.7 1.0
OE1 C:GLU354 3.3 51.2 1.0
O1 A:OEX413 3.4 41.8 1.0
CA1 A:OEX413 3.5 50.7 1.0
NH2 C:ARG357 3.9 45.1 1.0
NE2 A:HIS337 4.1 45.3 1.0
OD2 A:ASP170 4.1 42.4 1.0
O C:HOH684 4.1 60.2 1.0
NE2 A:HIS332 4.2 45.4 1.0
OD1 A:ASP170 4.2 46.2 1.0
CG C:GLU354 4.2 51.5 1.0
O A:HOH514 4.3 44.7 1.0
CG A:GLU333 4.3 40.4 1.0
OXT A:ALA344 4.4 46.2 1.0
O A:HOH542 4.4 42.0 1.0
CD2 A:HIS332 4.5 44.2 1.0
OD1 A:ASP342 4.5 42.1 1.0
O A:HOH546 4.6 45.4 1.0
CG A:ASP170 4.6 43.5 1.0
O A:ALA344 4.6 51.2 1.0
OE2 A:GLU189 4.6 47.2 1.0
CB A:GLU333 4.7 43.9 1.0
OD2 A:ASP342 4.8 41.1 1.0
CE1 A:HIS337 4.8 44.3 1.0
O A:HOH621 4.8 48.5 1.0
CZ C:ARG357 4.9 51.7 1.0
C A:ALA344 5.0 48.2 1.0

Manganese binding site 4 out of 8 in 8ir5

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Manganese binding site 4 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:48.6
occ:1.00
 MN4 A:OEX413 0.0 48.6 1.0
O4 A:OEX413 1.9 42.6 1.0
OD2 A:ASP170 2.0 42.4 1.0
OE2 A:GLU333 2.1 46.6 1.0
O A:HOH542 2.1 42.0 1.0
O A:HOH546 2.3 45.4 1.0
O5 A:OEX413 2.3 46.6 1.0
MN3 A:OEX413 2.8 44.6 1.0
CD A:GLU333 3.0 45.6 1.0
CG A:ASP170 3.1 43.5 1.0
OE1 A:GLU333 3.2 42.9 1.0
OD1 A:ASP170 3.5 46.2 1.0
O A:HOH621 3.7 48.5 1.0
O2 A:OEX413 3.7 43.2 1.0
O A:HOH514 3.8 44.7 1.0
CA1 A:OEX413 3.8 50.7 1.0
O A:HOH567 4.1 48.4 1.0
O A:HOH628 4.2 49.0 1.0
OD1 A:ASP61 4.2 45.8 1.0
CG A:GLU333 4.4 40.4 1.0
CB A:ASP170 4.4 42.4 1.0
OE2 C:GLU354 4.4 47.9 1.0
NH2 C:ARG357 4.4 45.1 1.0
O A:SER169 4.5 44.2 1.0
CA A:ASP170 4.6 44.2 1.0
O3 A:OEX413 4.6 46.4 1.0
MN1 A:OEX413 4.9 44.7 1.0
O D:HOH513 4.9 44.6 1.0
C A:SER169 5.0 49.6 1.0

Manganese binding site 5 out of 8 in 8ir5

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Manganese binding site 5 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:49.4
occ:1.00
 MN1 a:OEX413 0.0 49.4 1.0
OE2 a:GLU189 1.8 54.0 1.0
O1 a:OEX413 1.8 49.7 1.0
O3 a:OEX413 1.9 48.0 1.0
NE2 a:HIS332 2.1 50.2 1.0
OD2 a:ASP342 2.1 54.8 1.0
O5 a:OEX413 2.6 50.1 1.0
MN2 a:OEX413 2.8 51.6 1.0
CD a:GLU189 2.9 49.9 1.0
CE1 a:HIS332 2.9 49.0 1.0
CG a:ASP342 3.1 51.5 1.0
CD2 a:HIS332 3.2 50.3 1.0
OD1 a:ASP342 3.3 50.0 1.0
MN3 a:OEX413 3.3 50.7 1.0
OE1 a:GLU189 3.4 51.2 1.0
CA1 a:OEX413 3.5 55.0 1.0
O2 a:OEX413 3.6 50.2 1.0
OE1 a:GLU333 3.9 51.4 1.0
NE2 a:HIS337 4.0 49.5 1.0
ND1 a:HIS332 4.1 50.3 1.0
CG a:GLU189 4.1 52.4 1.0
O a:HOH590 4.1 62.5 1.0
CG a:HIS332 4.2 49.4 1.0
OXT a:ALA344 4.3 53.5 1.0
CB a:ASP342 4.4 46.3 1.0
OE1 c:GLU354 4.5 52.3 1.0
CG1 a:VAL185 4.6 45.5 1.0
OE2 c:GLU354 4.6 51.0 1.0
CD a:GLU333 4.7 52.3 1.0
CE1 a:HIS337 4.7 50.9 1.0
O a:ALA344 4.7 53.0 1.0
O a:HOH622 4.8 54.3 1.0
MN4 a:OEX413 4.8 49.7 1.0
C a:ALA344 4.9 55.9 1.0
CD c:GLU354 5.0 48.4 1.0

Manganese binding site 6 out of 8 in 8ir5

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Manganese binding site 6 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:51.6
occ:1.00
 MN2 a:OEX413 0.0 51.6 1.0
O1 a:OEX413 1.8 49.7 1.0
O2 a:OEX413 1.8 50.2 1.0
O3 a:OEX413 1.9 48.0 1.0
OXT a:ALA344 2.0 53.5 1.0
OD1 a:ASP342 2.0 50.0 1.0
OE1 c:GLU354 2.1 52.3 1.0
MN1 a:OEX413 2.8 49.4 1.0
MN3 a:OEX413 2.8 50.7 1.0
C a:ALA344 2.9 55.9 1.0
CD c:GLU354 3.0 48.4 1.0
CG a:ASP342 3.0 51.5 1.0
OE2 c:GLU354 3.2 51.0 1.0
OD2 a:ASP342 3.2 54.8 1.0
O a:ALA344 3.2 53.0 1.0
CA1 a:OEX413 3.4 55.0 1.0
O5 a:OEX413 3.6 50.1 1.0
NE2 a:HIS337 3.9 49.5 1.0
O a:HOH623 4.1 52.6 1.0
O a:HOH590 4.1 62.5 1.0
OE2 a:GLU189 4.2 54.0 1.0
CA a:ALA344 4.2 55.9 1.0
OE1 a:GLU333 4.3 51.4 1.0
N a:ALA344 4.3 62.3 1.0
O4 a:OEX413 4.3 50.6 1.0
CG c:GLU354 4.4 53.9 1.0
CB a:ASP342 4.4 46.3 1.0
CD2 a:HIS337 4.4 48.2 1.0
NE2 a:HIS332 4.5 50.2 1.0
NH2 c:ARG357 4.6 46.1 1.0
NH1 c:ARG357 4.8 52.9 1.0
CA a:ASP342 4.8 53.0 1.0
CB c:GLU354 4.8 50.6 1.0
OD1 a:ASP170 4.9 49.7 1.0
OE1 a:GLU189 4.9 51.2 1.0
CD a:GLU189 4.9 49.9 1.0
C a:ASP342 4.9 56.3 1.0

Manganese binding site 7 out of 8 in 8ir5

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Manganese binding site 7 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:50.7
occ:1.00
 MN3 a:OEX413 0.0 50.7 1.0
O2 a:OEX413 1.8 50.2 1.0
O4 a:OEX413 1.9 50.6 1.0
O3 a:OEX413 2.0 48.0 1.0
OE1 a:GLU333 2.0 51.4 1.0
OE2 c:GLU354 2.1 51.0 1.0
O5 a:OEX413 2.1 50.1 1.0
MN4 a:OEX413 2.7 49.7 1.0
MN2 a:OEX413 2.8 51.6 1.0
CD a:GLU333 2.9 52.3 1.0
CD c:GLU354 3.0 48.4 1.0
OE2 a:GLU333 3.1 50.1 1.0
OE1 c:GLU354 3.3 52.3 1.0
MN1 a:OEX413 3.3 49.4 1.0
CA1 a:OEX413 3.4 55.0 1.0
O1 a:OEX413 3.4 49.7 1.0
NH2 c:ARG357 3.9 46.1 1.0
O c:HOH620 3.9 64.0 1.0
OD2 a:ASP170 4.1 49.0 1.0
OD1 a:ASP170 4.1 49.7 1.0
NE2 a:HIS332 4.1 50.2 1.0
O a:HOH505 4.2 45.0 1.0
CG a:GLU333 4.3 47.5 1.0
NE2 a:HIS337 4.3 49.5 1.0
OXT a:ALA344 4.4 53.5 1.0
CG c:GLU354 4.4 53.9 1.0
O a:HOH538 4.5 45.0 1.0
CD2 a:HIS332 4.5 50.3 1.0
CG a:ASP170 4.5 48.6 1.0
O a:HOH569 4.5 48.7 1.0
OD1 a:ASP342 4.5 50.0 1.0
O a:ALA344 4.7 53.0 1.0
CB a:GLU333 4.7 47.1 1.0
OD2 a:ASP342 4.8 54.8 1.0
OE2 a:GLU189 4.8 54.0 1.0
CZ c:ARG357 4.9 53.5 1.0
O a:HOH622 4.9 54.3 1.0
C a:ALA344 5.0 55.9 1.0
CE1 a:HIS337 5.0 50.9 1.0

Manganese binding site 8 out of 8 in 8ir5

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Manganese binding site 8 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

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

b:49.7
occ:1.00
 MN4 a:OEX413 0.0 49.7 1.0
OE2 a:GLU333 2.0 50.1 1.0
OD2 a:ASP170 2.0 49.0 1.0
O4 a:OEX413 2.1 50.6 1.0
O a:HOH569 2.2 48.7 1.0
O a:HOH538 2.2 45.0 1.0
O5 a:OEX413 2.3 50.1 1.0
MN3 a:OEX413 2.7 50.7 1.0
CD a:GLU333 2.9 52.3 1.0
CG a:ASP170 3.0 48.6 1.0
OE1 a:GLU333 3.2 51.4 1.0
OD1 a:ASP170 3.4 49.7 1.0
O a:HOH622 3.7 54.3 1.0
CA1 a:OEX413 3.8 55.0 1.0
O2 a:OEX413 3.8 50.2 1.0
O a:HOH505 3.8 45.0 1.0
O a:HOH574 4.0 48.5 1.0
OD1 a:ASP61 4.2 44.7 1.0
O a:HOH629 4.3 61.1 1.0
CG a:GLU333 4.3 47.5 1.0
O3 a:OEX413 4.3 48.0 1.0
CB a:ASP170 4.4 47.6 1.0
OE2 c:GLU354 4.4 51.0 1.0
O a:SER169 4.4 46.0 1.0
NH2 c:ARG357 4.5 46.1 1.0
CA a:ASP170 4.6 50.0 1.0
O a:HOH539 4.7 48.8 1.0
MN1 a:OEX413 4.8 49.4 1.0
C a:SER169 5.0 48.8 1.0

Reference:

H.Li, Y.Nakajima, E.Nango, S.Owada, D.Yamada, K.Hashimoto, F.Luo, R.Tanaka, F.Akita, K.Kato, J.M.Kang, Y.Saitoh, S.Kishi, H.Yu, N.Matsubara, H.Fujii, M.Sugahara, M.Suzuki, T.Masuda, T.Kimura, T.N.Thao, S.Yonekura, L.J.Yu, T.Tosha, K.Tono, Y.Joti, T.Hatsui, M.Yabashi, M.Kubo, S.Iwata, H.Isobe, K.Yamaguchi, M.Suga, J.R.Shen. Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Sun Oct 6 12:34:44 2024

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