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Manganese in PDB 8irc: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation):
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation), PDB code: 8irc 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) 19.99 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.77, 231.76, 288.58, 90, 90, 90
R / Rfree (%) 14.1 / 17.6

Other elements in 8irc:

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) (pdb code 8irc). 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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation), PDB code: 8irc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8irc

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Manganese binding site 1 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) 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
OE2 A:GLU189 1.7 49.6 1.0
O1 A:OEX413 1.9 42.3 1.0
O3 A:OEX413 1.9 46.8 1.0
NE2 A:HIS332 2.1 43.9 1.0
OD2 A:ASP342 2.1 41.3 1.0
O5 A:OEX413 2.8 49.8 1.0
MN2 A:OEX413 2.8 45.6 1.0
CD A:GLU189 2.9 45.3 1.0
CE1 A:HIS332 3.0 40.5 1.0
CG A:ASP342 3.0 49.4 1.0
CD2 A:HIS332 3.1 44.2 1.0
MN3 A:OEX413 3.2 45.8 1.0
OD1 A:ASP342 3.3 43.2 1.0
O2 A:OEX413 3.4 41.0 1.0
OE1 A:GLU189 3.5 48.6 1.0
CA1 A:OEX413 3.6 47.3 1.0
OE1 A:GLU333 3.9 44.9 1.0
NE2 A:HIS337 4.0 44.3 1.0
CG A:GLU189 4.1 44.7 1.0
ND1 A:HIS332 4.1 44.0 1.0
CG A:HIS332 4.2 46.2 1.0
OXT A:ALA344 4.3 43.4 1.0
O A:HOH606 4.4 69.9 1.0
CB A:ASP342 4.4 46.0 1.0
OE1 C:GLU354 4.5 49.8 1.0
OE2 C:GLU354 4.5 48.1 1.0
CE1 A:HIS337 4.6 46.0 1.0
CG1 A:VAL185 4.6 43.3 1.0
CD A:GLU333 4.6 45.5 1.0
O A:HOH605 4.7 46.2 1.0
O A:ALA344 4.7 49.3 1.0
C A:ALA344 4.9 48.1 1.0
O4 A:OEX413 4.9 45.8 1.0
OE2 A:GLU333 4.9 47.2 1.0
CD C:GLU354 5.0 54.1 1.0
MN4 A:OEX413 5.0 48.8 1.0

Manganese binding site 2 out of 8 in 8irc

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Manganese binding site 2 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:45.6
occ:1.00
 MN2 A:OEX413 0.0 45.6 1.0
O1 A:OEX413 1.8 42.3 1.0
O2 A:OEX413 1.8 41.0 1.0
OXT A:ALA344 1.9 43.4 1.0
O3 A:OEX413 2.0 46.8 1.0
OD1 A:ASP342 2.1 43.2 1.0
OE1 C:GLU354 2.1 49.8 1.0
MN3 A:OEX413 2.8 45.8 1.0
C A:ALA344 2.8 48.1 1.0
MN1 A:OEX413 2.8 44.7 1.0
CD C:GLU354 2.9 54.1 1.0
CG A:ASP342 3.0 49.4 1.0
OE2 C:GLU354 3.1 48.1 1.0
O A:ALA344 3.1 49.3 1.0
OD2 A:ASP342 3.2 41.3 1.0
CA1 A:OEX413 3.5 47.3 1.0
O5 A:OEX413 3.7 49.8 1.0
NE2 A:HIS337 3.8 44.3 1.0
O C:HOH737 4.0 51.5 1.0
OE2 A:GLU189 4.1 49.6 1.0
CA A:ALA344 4.2 46.2 1.0
O4 A:OEX413 4.2 45.8 1.0
CG C:GLU354 4.2 50.3 1.0
N A:ALA344 4.3 50.6 1.0
CD2 A:HIS337 4.4 46.0 1.0
OE1 A:GLU333 4.4 44.9 1.0
CB A:ASP342 4.4 46.0 1.0
O A:HOH606 4.4 69.9 1.0
NH2 C:ARG357 4.5 39.7 1.0
NE2 A:HIS332 4.6 43.9 1.0
CA A:ASP342 4.8 45.3 1.0
OD1 A:ASP170 4.8 47.1 1.0
NH1 C:ARG357 4.8 41.0 1.0
C A:ASP342 4.8 46.2 1.0
CB C:GLU354 4.8 45.9 1.0
CD A:GLU189 4.9 45.3 1.0
OE1 A:GLU189 5.0 48.6 1.0
CZ C:ARG357 5.0 49.2 1.0
CE1 A:HIS337 5.0 46.0 1.0

Manganese binding site 3 out of 8 in 8irc

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Manganese binding site 3 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:45.8
occ:1.00
 MN3 A:OEX413 0.0 45.8 1.0
O2 A:OEX413 1.8 41.0 1.0
O4 A:OEX413 1.9 45.8 1.0
OE2 C:GLU354 2.0 48.1 1.0
OE1 A:GLU333 2.0 44.9 1.0
O5 A:OEX413 2.0 49.8 1.0
O3 A:OEX413 2.0 46.8 1.0
MN2 A:OEX413 2.8 45.6 1.0
MN4 A:OEX413 2.8 48.8 1.0
CD A:GLU333 2.9 45.5 1.0
CD C:GLU354 3.0 54.1 1.0
OE2 A:GLU333 3.1 47.2 1.0
MN1 A:OEX413 3.2 44.7 1.0
OE1 C:GLU354 3.3 49.8 1.0
O1 A:OEX413 3.4 42.3 1.0
CA1 A:OEX413 3.6 47.3 1.0
NH2 C:ARG357 3.9 39.7 1.0
OD2 A:ASP170 4.0 44.1 1.0
OD1 A:ASP170 4.0 47.1 1.0
NE2 A:HIS332 4.1 43.9 1.0
NE2 A:HIS337 4.1 44.3 1.0
O A:HOH518 4.2 51.4 1.0
CG C:GLU354 4.3 50.3 1.0
CG A:GLU333 4.3 42.9 1.0
OXT A:ALA344 4.4 43.4 1.0
CD2 A:HIS332 4.4 44.2 1.0
O A:HOH517 4.4 42.1 1.0
CG A:ASP170 4.5 41.9 1.0
OD1 A:ASP342 4.5 43.2 1.0
O A:HOH515 4.6 48.1 1.0
OE2 A:GLU189 4.6 49.6 1.0
O A:ALA344 4.6 49.3 1.0
CB A:GLU333 4.7 42.7 1.0
OD2 A:ASP342 4.7 41.3 1.0
O A:HOH605 4.8 46.2 1.0
CE1 A:HIS337 4.8 46.0 1.0
C A:ALA344 5.0 48.1 1.0

Manganese binding site 4 out of 8 in 8irc

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Manganese binding site 4 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:48.8
occ:1.00
 MN4 A:OEX413 0.0 48.8 1.0
OE2 A:GLU333 1.9 47.2 1.0
OD2 A:ASP170 1.9 44.1 1.0
O4 A:OEX413 2.0 45.8 1.0
O A:HOH517 2.1 42.1 1.0
O5 A:OEX413 2.2 49.8 1.0
O A:HOH515 2.2 48.1 1.0
MN3 A:OEX413 2.8 45.8 1.0
CD A:GLU333 2.9 45.5 1.0
CG A:ASP170 3.0 41.9 1.0
OE1 A:GLU333 3.2 44.9 1.0
OD1 A:ASP170 3.4 47.1 1.0
O A:HOH605 3.7 46.2 1.0
O2 A:OEX413 3.7 41.0 1.0
O A:HOH518 3.8 51.4 1.0
OD1 A:ASP61 4.0 44.3 1.0
CA1 A:OEX413 4.1 47.3 1.0
O A:HOH534 4.1 44.9 1.0
O A:HOH620 4.2 49.3 1.0
CG A:GLU333 4.2 42.9 1.0
CB A:ASP170 4.3 43.3 1.0
O A:SER169 4.3 43.7 1.0
OE2 C:GLU354 4.3 48.1 1.0
CA A:ASP170 4.5 49.2 1.0
NH2 C:ARG357 4.6 39.7 1.0
O3 A:OEX413 4.6 46.8 1.0
O D:HOH512 4.8 42.0 1.0
C A:SER169 4.8 48.5 1.0
N A:ASP170 4.9 43.7 1.0
CG A:ASP61 4.9 47.7 1.0
MN1 A:OEX413 5.0 44.7 1.0

Manganese binding site 5 out of 8 in 8irc

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Manganese binding site 5 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:50.2
occ:1.00
 MN1 a:OEX413 0.0 50.2 1.0
OE2 a:GLU189 1.7 52.5 1.0
O1 a:OEX413 1.8 53.1 1.0
O3 a:OEX413 1.9 50.1 1.0
NE2 a:HIS332 2.1 50.7 1.0
OD2 a:ASP342 2.1 51.0 1.0
O5 a:OEX413 2.7 52.2 1.0
MN2 a:OEX413 2.7 50.2 1.0
CD a:GLU189 2.9 51.1 1.0
CE1 a:HIS332 3.0 48.0 1.0
CG a:ASP342 3.0 49.5 1.0
CD2 a:HIS332 3.2 47.2 1.0
MN3 a:OEX413 3.2 48.8 1.0
OD1 a:ASP342 3.2 48.2 1.0
OE1 a:GLU189 3.4 50.3 1.0
CA1 a:OEX413 3.5 55.4 1.0
O2 a:OEX413 3.5 47.1 1.0
OE1 a:GLU333 3.8 48.6 1.0
NE2 a:HIS337 4.0 51.5 1.0
ND1 a:HIS332 4.1 49.3 1.0
CG a:GLU189 4.1 51.4 1.0
CG a:HIS332 4.2 50.1 1.0
OXT a:ALA344 4.3 54.7 1.0
O a:HOH607 4.4 79.3 1.0
CB a:ASP342 4.4 46.4 1.0
OE1 c:GLU354 4.5 49.3 1.0
CG1 a:VAL185 4.6 45.2 1.0
CD a:GLU333 4.7 48.1 1.0
OE2 c:GLU354 4.7 52.1 1.0
O a:ALA344 4.7 54.3 1.0
CE1 a:HIS337 4.7 51.1 1.0
O a:HOH611 4.8 54.7 1.0
C a:ALA344 4.9 53.2 1.0
MN4 a:OEX413 4.9 48.3 1.0
CD c:GLU354 5.0 47.1 1.0

Manganese binding site 6 out of 8 in 8irc

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Manganese binding site 6 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:50.2
occ:1.00
 MN2 a:OEX413 0.0 50.2 1.0
O1 a:OEX413 1.7 53.1 1.0
O2 a:OEX413 1.8 47.1 1.0
OXT a:ALA344 1.9 54.7 1.0
O3 a:OEX413 1.9 50.1 1.0
OD1 a:ASP342 2.1 48.2 1.0
OE1 c:GLU354 2.1 49.3 1.0
MN1 a:OEX413 2.7 50.2 1.0
MN3 a:OEX413 2.8 48.8 1.0
C a:ALA344 2.9 53.2 1.0
CD c:GLU354 3.0 47.1 1.0
CG a:ASP342 3.0 49.5 1.0
OE2 c:GLU354 3.2 52.1 1.0
O a:ALA344 3.2 54.3 1.0
OD2 a:ASP342 3.2 51.0 1.0
CA1 a:OEX413 3.4 55.4 1.0
O5 a:OEX413 3.7 52.2 1.0
NE2 a:HIS337 4.0 51.5 1.0
O c:HOH739 4.1 58.4 1.0
OE2 a:GLU189 4.1 52.5 1.0
CA a:ALA344 4.2 54.5 1.0
OE1 a:GLU333 4.3 48.6 1.0
O a:HOH607 4.3 79.3 1.0
O4 a:OEX413 4.3 48.6 1.0
N a:ALA344 4.3 59.6 1.0
CG c:GLU354 4.4 49.9 1.0
CB a:ASP342 4.4 46.4 1.0
CD2 a:HIS337 4.5 48.5 1.0
NE2 a:HIS332 4.5 50.7 1.0
NH2 c:ARG357 4.6 43.1 1.0
OD1 a:ASP170 4.7 50.9 1.0
NH1 c:ARG357 4.8 46.1 1.0
CA a:ASP342 4.8 50.8 1.0
CB c:GLU354 4.8 49.5 1.0
CD a:GLU189 4.8 51.1 1.0
C a:ASP342 4.9 53.8 1.0
OE1 a:GLU189 4.9 50.3 1.0

Manganese binding site 7 out of 8 in 8irc

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Manganese binding site 7 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:48.8
occ:1.00
 MN3 a:OEX413 0.0 48.8 1.0
O2 a:OEX413 1.8 47.1 1.0
O4 a:OEX413 1.9 48.6 1.0
O3 a:OEX413 2.0 50.1 1.0
OE1 a:GLU333 2.0 48.6 1.0
O5 a:OEX413 2.0 52.2 1.0
OE2 c:GLU354 2.1 52.1 1.0
MN2 a:OEX413 2.8 50.2 1.0
MN4 a:OEX413 2.8 48.3 1.0
CD a:GLU333 2.9 48.1 1.0
CD c:GLU354 3.0 47.1 1.0
OE2 a:GLU333 3.2 48.6 1.0
MN1 a:OEX413 3.2 50.2 1.0
OE1 c:GLU354 3.3 49.3 1.0
O1 a:OEX413 3.4 53.1 1.0
CA1 a:OEX413 3.5 55.4 1.0
NH2 c:ARG357 3.9 43.1 1.0
OD1 a:ASP170 4.0 50.9 1.0
OD2 a:ASP170 4.0 53.4 1.0
NE2 a:HIS332 4.1 50.7 1.0
O a:HOH515 4.3 51.2 1.0
OXT a:ALA344 4.3 54.7 1.0
CG a:GLU333 4.3 48.2 1.0
NE2 a:HIS337 4.3 51.5 1.0
CG c:GLU354 4.4 49.9 1.0
CG a:ASP170 4.4 48.5 1.0
O a:HOH522 4.5 45.2 1.0
CD2 a:HIS332 4.5 47.2 1.0
O a:HOH548 4.5 47.5 1.0
OD1 a:ASP342 4.5 48.2 1.0
O a:ALA344 4.7 54.3 1.0
CB a:GLU333 4.7 46.8 1.0
OE2 a:GLU189 4.7 52.5 1.0
OD2 a:ASP342 4.8 51.0 1.0
O a:HOH611 4.9 54.7 1.0
CZ c:ARG357 4.9 51.7 1.0
C a:ALA344 5.0 53.2 1.0

Manganese binding site 8 out of 8 in 8irc

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Manganese binding site 8 out of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn413

b:48.3
occ:1.00
 MN4 a:OEX413 0.0 48.3 1.0
OE2 a:GLU333 1.9 48.6 1.0
OD2 a:ASP170 2.0 53.4 1.0
O4 a:OEX413 2.1 48.6 1.0
O a:HOH548 2.1 47.5 1.0
O a:HOH522 2.2 45.2 1.0
O5 a:OEX413 2.2 52.2 1.0
MN3 a:OEX413 2.8 48.8 1.0
CD a:GLU333 2.9 48.1 1.0
CG a:ASP170 3.0 48.5 1.0
OE1 a:GLU333 3.2 48.6 1.0
OD1 a:ASP170 3.4 50.9 1.0
O a:HOH611 3.7 54.7 1.0
O2 a:OEX413 3.8 47.1 1.0
CA1 a:OEX413 4.0 55.4 1.0
O a:HOH558 4.0 48.6 1.0
O a:HOH515 4.0 51.2 1.0
OD1 a:ASP61 4.1 45.6 1.0
O a:HOH621 4.2 55.0 1.0
CG a:GLU333 4.2 48.2 1.0
CB a:ASP170 4.3 46.1 1.0
O a:SER169 4.3 46.7 1.0
OE2 c:GLU354 4.4 52.1 1.0
O3 a:OEX413 4.4 50.1 1.0
CA a:ASP170 4.5 49.9 1.0
NH2 c:ARG357 4.6 43.1 1.0
O d:HOH527 4.7 49.2 1.0
MN1 a:OEX413 4.9 50.2 1.0
C a:SER169 4.9 47.5 1.0
N a:ASP170 5.0 45.1 1.0
CG a:ASP61 5.0 50.2 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 12:40:11 2024

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