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Manganese in PDB 6jll: Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1):
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1), PDB code: 6jll 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) 19.99 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.970, 228.720, 286.980, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 20.3

Other elements in 6jll:

The structure of Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1) also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 7 atoms
Calcium (Ca) 13 atoms
Chlorine (Cl) 10 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1) (pdb code 6jll). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1), PDB code: 6jll:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 6jll

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Manganese binding site 1 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:33.4
occ:0.49
 MN1 A:OEX418 0.0 33.4 0.5
MN1 A:OEY419 0.2 36.5 0.5
O6 A:OEY419 1.6 36.8 0.5
OE2 A:GLU189 1.8 37.1 0.5
O1 A:OEX418 1.9 36.0 0.5
O3 A:OEY419 1.9 47.2 0.5
OE2 A:GLU189 1.9 38.2 0.5
O3 A:OEX418 1.9 46.5 0.5
O1 A:OEY419 2.0 35.8 0.5
NE2 A:HIS332 2.0 30.0 0.5
NE2 A:HIS332 2.1 31.5 0.5
OD2 A:ASP342 2.1 41.0 0.5
OD2 A:ASP342 2.2 41.8 0.5
MN2 A:OEY419 2.6 37.1 0.5
MN2 A:OEX418 2.7 37.0 0.5
O5 A:OEX418 2.8 37.8 0.5
CD A:GLU189 3.0 36.0 0.5
CD2 A:HIS332 3.0 29.9 0.5
CE1 A:HIS332 3.0 28.4 0.5
O5 A:OEY419 3.0 33.9 0.5
CD A:GLU189 3.0 34.4 0.5
CG A:ASP342 3.0 38.6 0.5
CE1 A:HIS332 3.1 28.0 0.5
CG A:ASP342 3.1 37.5 0.5
CD2 A:HIS332 3.1 30.8 0.5
MN3 A:OEY419 3.2 38.0 0.5
MN3 A:OEX418 3.2 33.8 0.5
OD1 A:ASP342 3.3 33.4 0.5
OD1 A:ASP342 3.3 33.9 0.5
OE1 A:GLU189 3.5 37.5 0.5
CA1 A:OEX418 3.5 38.7 0.5
O2 A:OEY419 3.5 32.7 0.5
OE1 A:GLU189 3.5 41.1 0.5
CA1 A:OEY419 3.5 42.3 0.5
O2 A:OEX418 3.6 33.4 0.5
OE1 A:GLU333 3.9 29.1 0.5
NE2 A:HIS337 3.9 31.2 1.0
OE1 A:GLU333 3.9 29.9 0.5
ND1 A:HIS332 4.1 27.8 0.5
CG A:GLU189 4.1 32.0 0.5
ND1 A:HIS332 4.1 26.7 0.5
CG A:HIS332 4.1 30.4 0.5
OXT A:ALA344 4.2 32.1 0.5
OXT A:ALA344 4.2 33.6 0.5
O A:HOH529 4.2 48.4 1.0
OE2 C:GLU354 4.2 35.4 0.5
CG A:HIS332 4.2 30.1 0.5
CG A:GLU189 4.3 29.4 0.5
CB A:ASP342 4.4 31.1 0.5
OE1 C:GLU354 4.5 36.5 0.5
CB A:ASP342 4.5 28.9 0.5
OE1 C:GLU354 4.5 36.8 0.5
CG1 A:VAL185 4.6 32.5 1.0
CE1 A:HIS337 4.6 36.1 1.0
OE2 C:GLU354 4.6 33.3 0.5
CD A:GLU333 4.6 35.9 0.5
O A:ALA344 4.7 40.6 0.5
CD A:GLU333 4.7 36.4 0.5
C A:ALA344 4.8 38.2 0.5
O A:ALA344 4.8 38.8 0.5
CD C:GLU354 4.8 33.9 0.5
C A:ALA344 4.8 37.9 0.5
CD2 A:HIS337 4.9 30.1 1.0
OE2 A:GLU333 4.9 29.1 0.5
MN4 A:OEX418 4.9 35.7 0.5
CD C:GLU354 4.9 35.1 0.5
O A:HOH519 4.9 39.2 0.5
O A:HOH635 5.0 43.3 0.5

Manganese binding site 2 out of 16 in 6jll

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Manganese binding site 2 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:37.0
occ:0.49
 MN2 A:OEX418 0.0 37.0 0.5
MN2 A:OEY419 0.1 37.1 0.5
O2 A:OEY419 1.8 32.7 0.5
OXT A:ALA344 1.8 33.6 0.5
O1 A:OEX418 1.8 36.0 0.5
O1 A:OEY419 1.8 35.8 0.5
O2 A:OEX418 1.8 33.4 0.5
OXT A:ALA344 1.9 32.1 0.5
O3 A:OEY419 2.0 47.2 0.5
O3 A:OEX418 2.0 46.5 0.5
OE1 C:GLU354 2.1 36.5 0.5
OE1 C:GLU354 2.1 36.8 0.5
OD1 A:ASP342 2.1 33.4 0.5
OD1 A:ASP342 2.2 33.9 0.5
MN1 A:OEY419 2.6 36.5 0.5
MN1 A:OEX418 2.7 33.4 0.5
MN3 A:OEY419 2.7 38.0 0.5
MN3 A:OEX418 2.8 33.8 0.5
C A:ALA344 2.8 38.2 0.5
CD C:GLU354 2.9 33.9 0.5
C A:ALA344 2.9 37.9 0.5
OE2 C:GLU354 2.9 35.4 0.5
CD C:GLU354 2.9 35.1 0.5
CG A:ASP342 3.0 38.6 0.5
CG A:ASP342 3.1 37.5 0.5
O A:ALA344 3.2 40.6 0.5
OE2 C:GLU354 3.2 33.3 0.5
OD2 A:ASP342 3.2 41.0 0.5
OD2 A:ASP342 3.3 41.8 0.5
O A:ALA344 3.3 38.8 0.5
CA1 A:OEY419 3.4 42.3 0.5
CA1 A:OEX418 3.4 38.7 0.5
O6 A:OEY419 3.4 36.8 0.5
O5 A:OEY419 3.7 33.9 0.5
O5 A:OEX418 3.7 37.8 0.5
NE2 A:HIS337 3.9 31.2 1.0
O A:HOH529 4.0 48.4 1.0
OE2 A:GLU189 4.1 38.2 0.5
O C:HOH768 4.1 34.5 1.0
CA A:ALA344 4.1 38.0 0.5
OE2 A:GLU189 4.1 37.1 0.5
O4 A:OEY419 4.2 31.8 0.5
N A:ALA344 4.2 42.1 0.5
CA A:ALA344 4.2 37.9 0.5
OE1 A:GLU333 4.3 29.1 0.5
N A:ALA344 4.3 41.8 0.5
O4 A:OEX418 4.3 31.9 0.5
CD2 A:HIS337 4.3 30.1 1.0
OE1 A:GLU333 4.3 29.9 0.5
CG C:GLU354 4.3 35.0 0.5
CG C:GLU354 4.4 34.9 0.5
CB A:ASP342 4.4 31.1 0.5
NE2 A:HIS332 4.4 31.5 0.5
NE2 A:HIS332 4.5 30.0 0.5
CB A:ASP342 4.5 28.9 0.5
NH2 C:ARG357 4.7 28.1 1.0
OD1 A:ASP170 4.8 40.7 0.5
CA A:ASP342 4.8 30.5 0.5
CB C:GLU354 4.8 33.3 0.5
O A:HOH519 4.8 39.2 0.5
NH1 C:ARG357 4.8 29.1 1.0
CB C:GLU354 4.9 33.4 0.5
CD A:GLU189 4.9 34.4 0.5
CD A:GLU189 4.9 36.0 0.5
C A:ASP342 4.9 35.0 0.5
CA A:ASP342 4.9 28.9 0.5
OD1 A:ASP170 4.9 40.8 0.5
C A:ASP342 4.9 35.9 0.5
OE1 A:GLU189 4.9 41.1 0.5
OE1 A:GLU189 5.0 37.5 0.5

Manganese binding site 3 out of 16 in 6jll

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Manganese binding site 3 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:33.8
occ:0.49
 MN3 A:OEX418 0.0 33.8 0.5
MN3 A:OEY419 0.1 38.0 0.5
O5 A:OEY419 1.8 33.9 0.5
O2 A:OEY419 1.8 32.7 0.5
O2 A:OEX418 1.9 33.4 0.5
O4 A:OEY419 1.9 31.8 0.5
O4 A:OEX418 1.9 31.9 0.5
OE1 A:GLU333 2.0 29.1 0.5
O3 A:OEX418 2.1 46.5 0.5
O5 A:OEX418 2.1 37.8 0.5
OE2 C:GLU354 2.1 33.3 0.5
OE1 A:GLU333 2.1 29.9 0.5
O3 A:OEY419 2.2 47.2 0.5
OE2 C:GLU354 2.3 35.4 0.5
MN4 A:OEX418 2.8 35.7 0.5
MN2 A:OEX418 2.8 37.0 0.5
MN2 A:OEY419 2.8 37.1 0.5
MN4 A:OEY419 2.8 37.5 0.5
CD A:GLU333 2.9 36.4 0.5
CD A:GLU333 3.0 35.9 0.5
O6 A:OEY419 3.0 36.8 0.5
CD C:GLU354 3.0 35.1 0.5
OE2 A:GLU333 3.1 29.1 0.5
CD C:GLU354 3.2 33.9 0.5
OE2 A:GLU333 3.2 30.8 0.5
MN1 A:OEX418 3.2 33.4 0.5
OE1 C:GLU354 3.3 36.5 0.5
MN1 A:OEY419 3.3 36.5 0.5
CA1 A:OEY419 3.4 42.3 0.5
CA1 A:OEX418 3.4 38.7 0.5
O1 A:OEX418 3.5 36.0 0.5
OE1 C:GLU354 3.5 36.8 0.5
O1 A:OEY419 3.5 35.8 0.5
OD2 A:ASP170 3.9 38.8 0.5
NH2 C:ARG357 3.9 28.1 1.0
OD1 A:ASP170 3.9 40.7 0.5
OD1 A:ASP170 4.0 40.8 0.5
OD2 A:ASP170 4.0 38.5 0.5
OXT A:ALA344 4.1 33.6 0.5
NE2 A:HIS332 4.2 31.5 0.5
OXT A:ALA344 4.2 32.1 0.5
O A:HOH520 4.2 35.0 0.5
NE2 A:HIS337 4.3 31.2 1.0
O A:HOH520 4.3 40.5 0.5
O A:HOH523 4.3 33.0 0.5
CG A:GLU333 4.3 36.3 0.5
CG A:ASP170 4.4 38.6 0.5
NE2 A:HIS332 4.4 30.0 0.5
CG A:GLU333 4.4 34.7 0.5
CG C:GLU354 4.4 34.9 0.5
CG C:GLU354 4.4 35.0 0.5
O A:HOH512 4.5 35.1 0.5
O A:ALA344 4.5 40.6 0.5
CG A:ASP170 4.5 38.2 0.5
O A:HOH523 4.5 29.3 0.5
CD2 A:HIS332 4.5 30.8 0.5
O A:ALA344 4.6 38.8 0.5
CD2 A:HIS332 4.6 29.9 0.5
OD1 A:ASP342 4.7 33.4 0.5
OD1 A:ASP342 4.7 33.9 0.5
OE2 A:GLU189 4.7 37.1 0.5
C A:ALA344 4.8 38.2 0.5
O A:HOH512 4.8 32.1 0.5
OD2 A:ASP342 4.8 41.0 0.5
CB A:GLU333 4.8 31.7 0.5
CB A:GLU333 4.9 30.7 0.5
C A:ALA344 4.9 37.9 0.5
OD2 A:ASP342 4.9 41.8 0.5
CZ C:ARG357 4.9 48.1 1.0
O A:HOH635 5.0 43.3 0.5
OE2 A:GLU189 5.0 38.2 0.5

Manganese binding site 4 out of 16 in 6jll

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Manganese binding site 4 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn418

b:35.7
occ:0.49
 MN4 A:OEX418 0.0 35.7 0.5
MN4 A:OEY419 0.4 37.5 0.5
O A:HOH523 1.8 33.0 0.5
O5 A:OEY419 1.9 33.9 0.5
OD2 A:ASP170 1.9 38.8 0.5
OE2 A:GLU333 2.0 29.1 0.5
OE2 A:GLU333 2.0 30.8 0.5
OD2 A:ASP170 2.0 38.5 0.5
O A:HOH523 2.1 29.3 0.5
O4 A:OEX418 2.1 31.9 0.5
O5 A:OEX418 2.2 37.8 0.5
O A:HOH512 2.2 35.1 0.5
O4 A:OEY419 2.2 31.8 0.5
O A:HOH512 2.5 32.1 0.5
MN3 A:OEX418 2.8 33.8 0.5
MN3 A:OEY419 2.9 38.0 0.5
CD A:GLU333 2.9 36.4 0.5
CD A:GLU333 2.9 35.9 0.5
CG A:ASP170 3.1 38.6 0.5
CG A:ASP170 3.1 38.2 0.5
OE1 A:GLU333 3.2 29.1 0.5
OE1 A:GLU333 3.2 29.9 0.5
OD1 A:ASP170 3.5 40.8 0.5
OD1 A:ASP170 3.5 40.7 0.5
O6 A:OEY419 3.8 36.8 0.5
CA1 A:OEY419 3.8 42.3 0.5
O A:HOH635 3.8 43.3 0.5
CA1 A:OEX418 3.9 38.7 0.5
O2 A:OEX418 3.9 33.4 0.5
O2 A:OEY419 3.9 32.7 0.5
O A:HOH520 4.0 40.5 0.5
OD1 A:ASP61 4.0 34.9 0.5
O A:HOH615 4.0 29.9 0.5
O A:HOH520 4.0 35.0 0.5
O A:HOH561 4.1 32.3 1.0
O A:HOH615 4.1 31.3 0.5
O A:HOH635 4.2 41.1 0.5
CG A:GLU333 4.2 36.3 0.5
CG A:GLU333 4.3 34.7 0.5
O A:SER169 4.3 32.5 0.5
CB A:ASP170 4.3 32.6 0.5
OD1 A:ASP61 4.3 31.5 0.5
OE2 C:GLU354 4.4 33.3 0.5
CB A:ASP170 4.4 31.9 0.5
CA A:ASP170 4.5 29.5 0.5
O3 A:OEX418 4.5 46.5 0.5
O A:SER169 4.6 31.7 0.5
NH2 C:ARG357 4.6 28.1 1.0
CA A:ASP170 4.6 29.4 0.5
O3 A:OEY419 4.6 47.2 0.5
O D:HOH528 4.8 32.8 1.0
OE2 C:GLU354 4.8 35.4 0.5
C A:SER169 4.9 31.3 0.5
MN1 A:OEX418 4.9 33.4 0.5
CG A:ASP61 5.0 35.1 0.5
N A:ASP170 5.0 31.8 0.5

Manganese binding site 5 out of 16 in 6jll

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Manganese binding site 5 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn419

b:36.5
occ:0.51
 MN1 A:OEY419 0.0 36.5 0.5
MN1 A:OEX418 0.2 33.4 0.5
O6 A:OEY419 1.7 36.8 0.5
O1 A:OEX418 1.7 36.0 0.5
OE2 A:GLU189 1.8 37.1 0.5
OE2 A:GLU189 1.8 38.2 0.5
O1 A:OEY419 1.8 35.8 0.5
O3 A:OEY419 1.9 47.2 0.5
O3 A:OEX418 2.0 46.5 0.5
OD2 A:ASP342 2.0 41.0 0.5
OD2 A:ASP342 2.1 41.8 0.5
NE2 A:HIS332 2.2 30.0 0.5
NE2 A:HIS332 2.2 31.5 0.5
MN2 A:OEY419 2.6 37.1 0.5
MN2 A:OEX418 2.6 37.0 0.5
CD A:GLU189 2.9 36.0 0.5
O5 A:OEX418 2.9 37.8 0.5
CD A:GLU189 2.9 34.4 0.5
CG A:ASP342 2.9 38.6 0.5
CG A:ASP342 3.0 37.5 0.5
CE1 A:HIS332 3.1 28.4 0.5
O5 A:OEY419 3.1 33.9 0.5
CE1 A:HIS332 3.1 28.0 0.5
CD2 A:HIS332 3.1 29.9 0.5
OD1 A:ASP342 3.2 33.4 0.5
OD1 A:ASP342 3.2 33.9 0.5
CD2 A:HIS332 3.3 30.8 0.5
MN3 A:OEY419 3.3 38.0 0.5
MN3 A:OEX418 3.3 33.8 0.5
OE1 A:GLU189 3.4 37.5 0.5
OE1 A:GLU189 3.5 41.1 0.5
CA1 A:OEX418 3.5 38.7 0.5
O2 A:OEY419 3.5 32.7 0.5
CA1 A:OEY419 3.5 42.3 0.5
O2 A:OEX418 3.5 33.4 0.5
NE2 A:HIS337 3.9 31.2 1.0
O A:HOH529 4.0 48.4 1.0
OE1 A:GLU333 4.0 29.1 0.5
OE1 A:GLU333 4.0 29.9 0.5
OXT A:ALA344 4.0 32.1 0.5
OXT A:ALA344 4.1 33.6 0.5
CG A:GLU189 4.1 32.0 0.5
CG A:GLU189 4.2 29.4 0.5
ND1 A:HIS332 4.2 27.8 0.5
ND1 A:HIS332 4.2 26.7 0.5
OE2 C:GLU354 4.2 35.4 0.5
CG A:HIS332 4.3 30.4 0.5
CB A:ASP342 4.3 31.1 0.5
CG A:HIS332 4.3 30.1 0.5
CB A:ASP342 4.4 28.9 0.5
OE1 C:GLU354 4.5 36.5 0.5
OE1 C:GLU354 4.5 36.8 0.5
O A:ALA344 4.6 40.6 0.5
CG1 A:VAL185 4.6 32.5 1.0
C A:ALA344 4.6 38.2 0.5
O A:ALA344 4.7 38.8 0.5
OE2 C:GLU354 4.7 33.3 0.5
C A:ALA344 4.7 37.9 0.5
CE1 A:HIS337 4.7 36.1 1.0
CD A:GLU333 4.8 35.9 0.5
CD C:GLU354 4.8 33.9 0.5
O A:HOH519 4.8 39.2 0.5
CD2 A:HIS337 4.9 30.1 1.0
CD A:GLU333 4.9 36.4 0.5
CD C:GLU354 5.0 35.1 0.5

Manganese binding site 6 out of 16 in 6jll

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Manganese binding site 6 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn419

b:37.1
occ:0.51
 MN2 A:OEY419 0.0 37.1 0.5
MN2 A:OEX418 0.1 37.0 0.5
O1 A:OEX418 1.8 36.0 0.5
O1 A:OEY419 1.8 35.8 0.5
O2 A:OEY419 1.9 32.7 0.5
OXT A:ALA344 1.9 33.6 0.5
O3 A:OEY419 1.9 47.2 0.5
O3 A:OEX418 1.9 46.5 0.5
O2 A:OEX418 1.9 33.4 0.5
OXT A:ALA344 1.9 32.1 0.5
OD1 A:ASP342 2.1 33.4 0.5
OE1 C:GLU354 2.1 36.5 0.5
OD1 A:ASP342 2.1 33.9 0.5
OE1 C:GLU354 2.1 36.8 0.5
MN1 A:OEY419 2.6 36.5 0.5
MN1 A:OEX418 2.6 33.4 0.5
MN3 A:OEY419 2.7 38.0 0.5
MN3 A:OEX418 2.8 33.8 0.5
CD C:GLU354 2.8 33.9 0.5
C A:ALA344 2.9 38.2 0.5
OE2 C:GLU354 2.9 35.4 0.5
CG A:ASP342 2.9 38.6 0.5
CD C:GLU354 3.0 35.1 0.5
CG A:ASP342 3.0 37.5 0.5
C A:ALA344 3.0 37.9 0.5
OD2 A:ASP342 3.1 41.0 0.5
OD2 A:ASP342 3.2 41.8 0.5
OE2 C:GLU354 3.2 33.3 0.5
O A:ALA344 3.3 40.6 0.5
O A:ALA344 3.4 38.8 0.5
O6 A:OEY419 3.4 36.8 0.5
CA1 A:OEY419 3.5 42.3 0.5
CA1 A:OEX418 3.5 38.7 0.5
O5 A:OEY419 3.7 33.9 0.5
O5 A:OEX418 3.7 37.8 0.5
NE2 A:HIS337 3.8 31.2 1.0
O A:HOH529 4.0 48.4 1.0
OE2 A:GLU189 4.0 38.2 0.5
O C:HOH768 4.1 34.5 1.0
OE2 A:GLU189 4.1 37.1 0.5
CA A:ALA344 4.2 38.0 0.5
CD2 A:HIS337 4.2 30.1 1.0
N A:ALA344 4.2 42.1 0.5
O4 A:OEY419 4.2 31.8 0.5
OE1 A:GLU333 4.2 29.1 0.5
CA A:ALA344 4.3 37.9 0.5
OE1 A:GLU333 4.3 29.9 0.5
CG C:GLU354 4.3 35.0 0.5
N A:ALA344 4.3 41.8 0.5
CB A:ASP342 4.3 31.1 0.5
O4 A:OEX418 4.3 31.9 0.5
CG C:GLU354 4.3 34.9 0.5
NE2 A:HIS332 4.4 31.5 0.5
NE2 A:HIS332 4.4 30.0 0.5
CB A:ASP342 4.4 28.9 0.5
CA A:ASP342 4.8 30.5 0.5
NH2 C:ARG357 4.8 28.1 1.0
CA A:ASP342 4.8 28.9 0.5
C A:ASP342 4.8 35.0 0.5
CB C:GLU354 4.8 33.3 0.5
OD1 A:ASP170 4.8 40.7 0.5
CD A:GLU189 4.8 34.4 0.5
CD A:GLU189 4.9 36.0 0.5
CB C:GLU354 4.9 33.4 0.5
C A:ASP342 4.9 35.9 0.5
O A:HOH519 4.9 39.2 0.5
NH1 C:ARG357 4.9 29.1 1.0
OE1 A:GLU189 5.0 41.1 0.5
OD1 A:ASP170 5.0 40.8 0.5
OE1 A:GLU189 5.0 37.5 0.5

Manganese binding site 7 out of 16 in 6jll

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Manganese binding site 7 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn419

b:38.0
occ:0.51
 MN3 A:OEY419 0.0 38.0 0.5
MN3 A:OEX418 0.1 33.8 0.5
O2 A:OEY419 1.8 32.7 0.5
O2 A:OEX418 1.8 33.4 0.5
O5 A:OEY419 1.9 33.9 0.5
O4 A:OEY419 1.9 31.8 0.5
O4 A:OEX418 2.0 31.9 0.5
O3 A:OEX418 2.0 46.5 0.5
OE2 C:GLU354 2.0 33.3 0.5
OE1 A:GLU333 2.0 29.1 0.5
OE1 A:GLU333 2.1 29.9 0.5
O3 A:OEY419 2.1 47.2 0.5
O5 A:OEX418 2.2 37.8 0.5
OE2 C:GLU354 2.2 35.4 0.5
MN2 A:OEX418 2.7 37.0 0.5
MN2 A:OEY419 2.7 37.1 0.5
MN4 A:OEX418 2.9 35.7 0.5
MN4 A:OEY419 2.9 37.5 0.5
CD C:GLU354 2.9 35.1 0.5
CD A:GLU333 2.9 36.4 0.5
CD A:GLU333 3.0 35.9 0.5
CD C:GLU354 3.0 33.9 0.5
O6 A:OEY419 3.1 36.8 0.5
OE1 C:GLU354 3.2 36.5 0.5
OE2 A:GLU333 3.2 29.1 0.5
MN1 A:OEX418 3.2 33.4 0.5
OE2 A:GLU333 3.2 30.8 0.5
MN1 A:OEY419 3.3 36.5 0.5
OE1 C:GLU354 3.4 36.8 0.5
CA1 A:OEY419 3.4 42.3 0.5
O1 A:OEX418 3.4 36.0 0.5
CA1 A:OEX418 3.5 38.7 0.5
O1 A:OEY419 3.5 35.8 0.5
NH2 C:ARG357 3.9 28.1 1.0
OD2 A:ASP170 4.0 38.8 0.5
OD1 A:ASP170 4.0 40.7 0.5
OXT A:ALA344 4.0 33.6 0.5
OD1 A:ASP170 4.1 40.8 0.5
OD2 A:ASP170 4.1 38.5 0.5
NE2 A:HIS337 4.2 31.2 1.0
OXT A:ALA344 4.2 32.1 0.5
NE2 A:HIS332 4.2 31.5 0.5
O A:HOH520 4.3 35.0 0.5
CG C:GLU354 4.3 34.9 0.5
CG C:GLU354 4.3 35.0 0.5
O A:HOH520 4.3 40.5 0.5
CG A:GLU333 4.3 36.3 0.5
NE2 A:HIS332 4.4 30.0 0.5
CG A:GLU333 4.4 34.7 0.5
O A:HOH523 4.4 33.0 0.5
CG A:ASP170 4.5 38.6 0.5
O A:ALA344 4.5 40.6 0.5
CD2 A:HIS332 4.5 30.8 0.5
O A:HOH512 4.6 35.1 0.5
CG A:ASP170 4.6 38.2 0.5
OD1 A:ASP342 4.6 33.4 0.5
O A:HOH523 4.6 29.3 0.5
OD1 A:ASP342 4.6 33.9 0.5
O A:ALA344 4.6 38.8 0.5
CD2 A:HIS332 4.6 29.9 0.5
OE2 A:GLU189 4.7 37.1 0.5
C A:ALA344 4.7 38.2 0.5
OD2 A:ASP342 4.7 41.0 0.5
CB A:GLU333 4.8 31.7 0.5
CB A:GLU333 4.8 30.7 0.5
O A:HOH512 4.9 32.1 0.5
C A:ALA344 4.9 37.9 0.5
OD2 A:ASP342 4.9 41.8 0.5
CZ C:ARG357 4.9 48.1 1.0
CE1 A:HIS337 4.9 36.1 1.0
OE2 A:GLU189 5.0 38.2 0.5

Manganese binding site 8 out of 16 in 6jll

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Manganese binding site 8 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


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 (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn419

b:37.5
occ:0.51
 MN4 A:OEY419 0.0 37.5 0.5
MN4 A:OEX418 0.4 35.7 0.5
O4 A:OEX418 1.9 31.9 0.5
OD2 A:ASP170 1.9 38.8 0.5
OD2 A:ASP170 2.0 38.5 0.5
O A:HOH512 2.0 35.1 0.5
OE2 A:GLU333 2.0 30.8 0.5
O4 A:OEY419 2.0 31.8 0.5
O A:HOH523 2.1 33.0 0.5
OE2 A:GLU333 2.1 29.1 0.5
O5 A:OEY419 2.2 33.9 0.5
O A:HOH512 2.2 32.1 0.5
O A:HOH523 2.3 29.3 0.5
O5 A:OEX418 2.5 37.8 0.5
MN3 A:OEX418 2.8 33.8 0.5
MN3 A:OEY419 2.9 38.0 0.5
CD A:GLU333 3.0 36.4 0.5
CG A:ASP170 3.0 38.6 0.5
CD A:GLU333 3.0 35.9 0.5
CG A:ASP170 3.0 38.2 0.5
OE1 A:GLU333 3.2 29.1 0.5
OE1 A:GLU333 3.3 29.9 0.5
OD1 A:ASP170 3.5 40.8 0.5
OD1 A:ASP170 3.5 40.7 0.5
O A:HOH520 3.6 40.5 0.5
O A:HOH520 3.7 35.0 0.5
OD1 A:ASP61 3.7 34.9 0.5
O2 A:OEX418 3.9 33.4 0.5
O2 A:OEY419 3.9 32.7 0.5
CA1 A:OEY419 4.0 42.3 0.5
OD1 A:ASP61 4.1 31.5 0.5
CA1 A:OEX418 4.1 38.7 0.5
O6 A:OEY419 4.1 36.8 0.5
O A:SER169 4.1 32.5 0.5
O A:HOH635 4.1 43.3 0.5
O A:HOH615 4.2 29.9 0.5
CB A:ASP170 4.3 32.6 0.5
O A:HOH561 4.3 32.3 1.0
O A:HOH615 4.3 31.3 0.5
OE2 C:GLU354 4.3 33.3 0.5
CB A:ASP170 4.3 31.9 0.5
O A:SER169 4.3 31.7 0.5
CG A:GLU333 4.3 36.3 0.5
CA A:ASP170 4.4 29.5 0.5
CG A:GLU333 4.4 34.7 0.5
NH2 C:ARG357 4.4 28.1 1.0
O A:HOH635 4.5 41.1 0.5
CA A:ASP170 4.5 29.4 0.5
C A:SER169 4.6 31.3 0.5
O3 A:OEX418 4.7 46.5 0.5
CG A:ASP61 4.7 35.1 0.5
O D:HOH528 4.7 32.8 1.0
O3 A:OEY419 4.7 47.2 0.5
N A:ASP170 4.8 31.8 0.5
OE2 C:GLU354 4.8 35.4 0.5
OG A:SER169 4.8 34.5 0.5
CG A:ASP61 4.8 34.3 0.5
C A:SER169 4.8 30.6 0.5
OG A:SER169 4.9 35.2 0.5
N A:ASP170 4.9 31.6 0.5

Manganese binding site 9 out of 16 in 6jll

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Manganese binding site 9 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn417

b:35.7
occ:0.49
 MN1 a:OEX417 0.0 35.7 0.5
MN1 a:OEY418 0.1 40.2 0.5
O6 a:OEY418 1.7 57.9 0.5
OE2 a:GLU189 1.8 44.3 0.5
OE2 a:GLU189 1.8 43.5 0.5
O3 a:OEX417 1.9 32.1 0.5
O1 a:OEX417 1.9 39.3 0.5
O3 a:OEY418 1.9 33.6 0.5
O1 a:OEY418 2.0 39.1 0.5
NE2 a:HIS332 2.0 35.7 0.5
NE2 a:HIS332 2.1 36.0 0.5
OD2 a:ASP342 2.2 35.2 0.5
OD2 a:ASP342 2.2 35.7 0.5
MN2 a:OEX417 2.7 37.2 0.5
MN2 a:OEY418 2.7 37.9 0.5
O5 a:OEX417 2.7 31.9 0.5
CD a:GLU189 2.8 43.5 0.5
CD a:GLU189 2.9 43.7 0.5
CE1 a:HIS332 2.9 32.2 0.5
O5 a:OEY418 2.9 36.5 0.5
CE1 a:HIS332 3.0 32.7 0.5
CD2 a:HIS332 3.0 34.1 0.5
CD2 a:HIS332 3.1 34.0 0.5
CG a:ASP342 3.1 40.6 0.5
MN3 a:OEX417 3.2 39.6 0.5
CG a:ASP342 3.2 40.5 0.5
MN3 a:OEY418 3.3 35.2 0.5
OE1 a:GLU189 3.3 45.3 0.5
OE1 a:GLU189 3.4 46.2 0.5
OD1 a:ASP342 3.5 44.0 0.5
O2 a:OEX417 3.5 37.2 0.5
OD1 a:ASP342 3.5 44.5 0.5
O2 a:OEY418 3.5 37.7 0.5
CA1 a:OEX417 3.5 45.1 0.5
CA1 a:OEY418 3.6 44.8 0.5
OE1 a:GLU333 3.7 38.4 0.5
OE1 a:GLU333 4.0 40.1 0.5
NE2 a:HIS337 4.0 40.7 1.0
O a:HOH516 4.0 50.6 1.0
ND1 a:HIS332 4.1 34.3 0.5
CG a:GLU189 4.1 40.4 0.5
CG a:GLU189 4.1 39.1 0.5
ND1 a:HIS332 4.1 34.6 0.5
CG a:HIS332 4.1 35.9 0.5
CG a:HIS332 4.2 35.4 0.5
OXT a:ALA344 4.2 38.9 0.5
OXT a:ALA344 4.3 38.2 0.5
OE1 c:GLU354 4.4 44.7 0.5
CB a:ASP342 4.5 39.2 0.5
CB a:ASP342 4.5 39.3 0.5
CG1 a:VAL185 4.5 28.4 1.0
OE2 c:GLU354 4.5 44.4 0.5
OE1 c:GLU354 4.5 44.5 0.5
O a:ALA344 4.6 45.6 0.5
O a:ALA344 4.6 45.9 0.5
OE2 c:GLU354 4.6 42.7 0.5
CE1 a:HIS337 4.6 40.5 1.0
CD a:GLU333 4.7 42.2 0.5
CD a:GLU333 4.8 42.1 0.5
C a:ALA344 4.8 45.3 0.5
C a:ALA344 4.8 45.5 0.5
MN4 a:OEX417 4.9 38.6 0.5
CD c:GLU354 4.9 42.8 0.5
O a:HOH625 5.0 40.8 0.5
CD c:GLU354 5.0 43.8 0.5
OE2 a:GLU333 5.0 39.3 0.5
O4 a:OEX417 5.0 33.6 0.5

Manganese binding site 10 out of 16 in 6jll

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Manganese binding site 10 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Xfel Structure of Cyanobacterial Photosystem II (2F State, DATASET1) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn417

b:37.2
occ:0.49
 MN2 a:OEX417 0.0 37.2 0.5
MN2 a:OEY418 0.1 37.9 0.5
O1 a:OEY418 1.7 39.1 0.5
O1 a:OEX417 1.8 39.3 0.5
OXT a:ALA344 1.8 38.2 0.5
O2 a:OEY418 1.8 37.7 0.5
OXT a:ALA344 1.9 38.9 0.5
O2 a:OEX417 1.9 37.2 0.5
O3 a:OEY418 2.0 33.6 0.5
O3 a:OEX417 2.0 32.1 0.5
OE1 c:GLU354 2.1 44.7 0.5
OD1 a:ASP342 2.1 44.5 0.5
OD1 a:ASP342 2.1 44.0 0.5
OE1 c:GLU354 2.2 44.5 0.5
MN1 a:OEY418 2.6 40.2 0.5
MN1 a:OEX417 2.7 35.7 0.5
MN3 a:OEX417 2.7 39.6 0.5
MN3 a:OEY418 2.7 35.2 0.5
C a:ALA344 2.8 45.5 0.5
C a:ALA344 2.8 45.3 0.5
CG a:ASP342 2.8 40.5 0.5
OD2 a:ASP342 2.9 35.7 0.5
CG a:ASP342 2.9 40.6 0.5
CD c:GLU354 2.9 42.8 0.5
OD2 a:ASP342 3.0 35.2 0.5
CD c:GLU354 3.0 43.8 0.5
OE2 c:GLU354 3.1 44.4 0.5
O a:ALA344 3.1 45.9 0.5
O a:ALA344 3.1 45.6 0.5
OE2 c:GLU354 3.1 42.7 0.5
CA1 a:OEY418 3.4 44.8 0.5
CA1 a:OEX417 3.4 45.1 0.5
O6 a:OEY418 3.5 57.9 0.5
O5 a:OEY418 3.5 36.5 0.5
O5 a:OEX417 3.6 31.9 0.5
NE2 a:HIS337 3.8 40.7 1.0
O a:HOH516 3.9 50.6 1.0
OE2 a:GLU189 4.0 43.5 0.5
OE2 a:GLU189 4.1 44.3 0.5
CA a:ALA344 4.1 48.7 0.5
CA a:ALA344 4.2 48.8 0.5
O4 a:OEY418 4.2 32.3 0.5
O a:HOH634 4.2 42.6 1.0
O4 a:OEX417 4.3 33.6 0.5
CB a:ASP342 4.3 39.3 0.5
OE1 a:GLU333 4.3 38.4 0.5
N a:ALA344 4.3 48.0 0.5
NE2 a:HIS332 4.3 35.7 0.5
CD2 a:HIS337 4.3 35.9 1.0
N a:ALA344 4.3 47.6 0.5
OE1 a:GLU333 4.3 40.1 0.5
CB a:ASP342 4.4 39.2 0.5
CG c:GLU354 4.4 38.9 0.5
NE2 a:HIS332 4.4 36.0 0.5
CG c:GLU354 4.4 39.4 0.5
NH2 c:ARG357 4.7 37.4 0.5
CD a:GLU189 4.7 43.5 0.5
OE1 a:GLU189 4.8 45.3 0.5
CD a:GLU189 4.8 43.7 0.5
NH1 c:ARG357 4.8 34.8 0.5
OE1 a:GLU189 4.8 46.2 0.5
NH2 c:ARG357 4.8 37.2 0.5
CA a:ASP342 4.8 39.5 0.5
OD1 a:ASP170 4.9 37.6 0.5
CA a:ASP342 4.9 39.1 0.5
O a:HOH514 4.9 42.1 0.5
CB c:GLU354 4.9 39.3 0.5
C a:ASP342 4.9 43.6 0.5
NH1 c:ARG357 4.9 36.0 0.5
CB c:GLU354 4.9 38.4 0.5
C a:ASP342 5.0 43.3 0.5
OD1 a:ASP170 5.0 37.6 0.5
CE1 a:HIS337 5.0 40.5 1.0

Reference:

M.Suga, F.Akita, K.Yamashita, Y.Nakajima, G.Ueno, H.Li, T.Yamane, K.Hirata, Y.Umena, S.Yonekura, L.J.Yu, H.Murakami, T.Nomura, T.Kimura, M.Kubo, S.Baba, T.Kumasaka, K.Tono, M.Yabashi, H.Isobe, K.Yamaguchi, M.Yamamoto, H.Ago, J.R.Shen. An Oxyl/Oxo Mechanism For Oxygen-Oxygen Coupling in Psii Revealed By An X-Ray Free-Electron Laser. Science V. 366 334 2019.
ISSN: ESSN 1095-9203
PubMed: 31624207
DOI: 10.1126/SCIENCE.AAX6998
Page generated: Tue Dec 15 04:55:16 2020

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