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Manganese in PDB 8f4d: Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution, PDB code: 8f4d was solved by A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.74 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.103, 222.196, 308.415, 90, 90, 90
R / Rfree (%) 18.8 / 24.3

Other elements in 8f4d:

The structure of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 4 atoms
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution (pdb code 8f4d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution, PDB code: 8f4d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 8f4d

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Manganese binding site 1 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:29.5
occ:0.65
 MN1 A:OEY601 0.0 29.5 0.7
MN1 A:OEX602 0.3 36.3 0.3
OE2 A:GLU189 1.6 36.5 0.3
O6 A:OEY601 1.7 32.9 0.7
O3 A:OEX602 1.8 38.7 0.3
O1 A:OEY601 1.9 30.1 0.7
OD2 A:ASP342 1.9 38.1 0.3
O1 A:OEX602 1.9 37.1 0.3
O3 A:OEY601 1.9 33.0 0.7
OE2 A:GLU189 1.9 34.4 0.7
OD2 A:ASP342 2.0 35.6 0.7
NE2 A:HIS332 2.1 41.0 0.3
NE2 A:HIS332 2.1 33.9 0.7
MN2 A:OEX602 2.8 31.9 0.3
CG A:ASP342 2.8 36.7 0.3
MN2 A:OEY601 2.8 33.6 0.7
CD A:GLU189 2.9 33.0 0.3
CG A:ASP342 2.9 34.2 0.7
CD A:GLU189 2.9 30.8 0.7
CE1 A:HIS332 3.0 30.6 0.7
CE1 A:HIS332 3.0 34.2 0.3
CD2 A:HIS332 3.1 35.2 0.3
O5 A:OEX602 3.1 39.5 0.3
OD1 A:ASP342 3.2 32.9 0.3
CD2 A:HIS332 3.2 32.3 0.7
O5 A:OEY601 3.2 33.1 0.7
OD1 A:ASP342 3.2 31.6 0.7
OE1 A:GLU189 3.4 31.9 0.7
MN3 A:OEY601 3.4 32.3 0.7
CA1 A:OEX602 3.5 37.1 0.3
CA1 A:OEY601 3.5 34.8 0.7
MN3 A:OEX602 3.5 34.6 0.3
O2 A:OEX602 3.5 26.7 0.3
O2 A:OEY601 3.6 32.4 0.7
OE1 A:GLU189 3.6 35.7 0.3
OE1 A:GLU333 4.0 34.3 0.7
CG A:GLU189 4.0 36.2 0.3
NE2 A:HIS337 4.0 35.0 0.7
O A:HOH778 4.0 33.1 1.0
NE2 A:HIS337 4.0 41.4 0.3
OXT A:ALA344 4.1 27.8 0.3
OE1 A:GLU333 4.2 31.2 0.3
ND1 A:HIS332 4.2 37.5 0.3
ND1 A:HIS332 4.2 29.8 0.7
CG A:GLU189 4.2 33.3 0.7
CB A:ASP342 4.2 43.4 0.3
CG A:HIS332 4.2 33.8 0.3
O A:HOH798 4.2 38.2 0.6
OXT A:ALA344 4.2 34.3 0.7
OE1 C:GLU354 4.2 37.0 0.3
CG A:HIS332 4.3 31.3 0.7
CB A:ASP342 4.3 32.9 0.7
OE1 C:GLU354 4.4 32.5 0.7
OE2 C:GLU354 4.4 32.2 0.3
CG1 A:VAL185 4.5 27.9 0.7
CG1 A:VAL185 4.7 37.6 0.3
OE2 C:GLU354 4.7 35.2 0.7
CD C:GLU354 4.7 38.5 0.3
O A:ALA344 4.7 39.6 0.3
C A:ALA344 4.8 31.7 0.3
O A:HOH715 4.8 32.4 0.7
O A:HOH781 4.8 29.5 0.3
O A:ALA344 4.8 36.2 0.7
CE1 A:HIS337 4.8 34.0 0.7
C A:ALA344 4.8 36.1 0.7
CD A:GLU333 4.9 31.9 0.3
CE1 A:HIS337 4.9 34.9 0.3
CD A:GLU333 4.9 33.3 0.7
CD2 A:HIS337 4.9 34.5 0.7
CD2 A:HIS337 4.9 30.3 0.3
CD C:GLU354 4.9 33.8 0.7

Manganese binding site 2 out of 16 in 8f4d

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Manganese binding site 2 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:33.6
occ:0.65
 MN2 A:OEY601 0.0 33.6 0.7
MN2 A:OEX602 0.1 31.9 0.3
OXT A:ALA344 1.8 34.3 0.7
O1 A:OEX602 1.8 37.1 0.3
OE1 C:GLU354 1.8 37.0 0.3
OXT A:ALA344 1.8 27.8 0.3
O1 A:OEY601 1.8 30.1 0.7
O2 A:OEX602 1.9 26.7 0.3
O3 A:OEY601 1.9 33.0 0.7
OE1 C:GLU354 1.9 32.5 0.7
O2 A:OEY601 2.0 32.4 0.7
OD1 A:ASP342 2.0 31.6 0.7
OD1 A:ASP342 2.0 32.9 0.3
O3 A:OEX602 2.1 38.7 0.3
CD C:GLU354 2.6 38.5 0.3
C A:ALA344 2.8 36.1 0.7
C A:ALA344 2.8 31.7 0.3
MN1 A:OEY601 2.8 29.5 0.7
OE2 C:GLU354 2.9 32.2 0.3
CD C:GLU354 2.9 33.8 0.7
CG A:ASP342 2.9 34.2 0.7
CG A:ASP342 2.9 36.7 0.3
MN1 A:OEX602 2.9 36.3 0.3
MN3 A:OEY601 2.9 32.3 0.7
MN3 A:OEX602 3.0 34.6 0.3
OD2 A:ASP342 3.1 35.6 0.7
OD2 A:ASP342 3.2 38.1 0.3
O A:ALA344 3.2 36.2 0.7
OE2 C:GLU354 3.2 35.2 0.7
O A:ALA344 3.2 39.6 0.3
CA1 A:OEY601 3.4 34.8 0.7
CA1 A:OEX602 3.4 37.1 0.3
O6 A:OEY601 3.8 32.9 0.7
O5 A:OEY601 3.8 33.1 0.7
O5 A:OEX602 3.8 39.5 0.3
O A:HOH787 3.8 40.5 1.0
NE2 A:HIS337 4.0 41.4 0.3
CG C:GLU354 4.1 37.1 0.3
OE2 A:GLU189 4.1 36.5 0.3
NE2 A:HIS337 4.1 35.0 0.7
CA A:ALA344 4.1 31.5 0.7
CA A:ALA344 4.1 33.2 0.3
O A:HOH778 4.1 33.1 1.0
N A:ALA344 4.1 40.2 0.3
N A:ALA344 4.2 34.1 0.7
OE2 A:GLU189 4.2 34.4 0.7
CG C:GLU354 4.3 31.0 0.7
CB A:ASP342 4.3 43.4 0.3
CD2 A:HIS337 4.3 30.3 0.3
CB A:ASP342 4.3 32.9 0.7
OE1 A:GLU333 4.3 34.3 0.7
CD2 A:HIS337 4.4 34.5 0.7
O4 A:OEY601 4.4 31.6 0.7
O4 A:OEX602 4.4 32.7 0.3
OE1 A:GLU333 4.5 31.2 0.3
CB C:GLU354 4.5 43.5 0.3
NE2 A:HIS332 4.6 33.9 0.7
NE2 A:HIS332 4.6 41.0 0.3
C A:ASP342 4.6 38.4 0.3
NH2 C:ARG357 4.7 30.1 0.7
CA A:ASP342 4.7 35.5 0.3
CB C:GLU354 4.7 31.1 0.7
C A:ASP342 4.7 34.9 0.7
NH2 C:ARG357 4.7 33.7 0.3
OD2 A:ASP170 4.7 38.7 0.7
CA A:ASP342 4.7 32.3 0.7
O A:ASP342 4.8 32.0 0.7
O A:ASP342 4.8 31.0 0.3
NH1 C:ARG357 4.9 33.7 0.3
OD2 A:ASP170 4.9 34.6 0.3
O A:HOH715 4.9 32.4 0.7
NH1 C:ARG357 4.9 28.0 0.7

Manganese binding site 3 out of 16 in 8f4d

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Manganese binding site 3 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:32.3
occ:0.65
 MN3 A:OEY601 0.0 32.3 0.7
MN3 A:OEX602 0.1 34.6 0.3
O4 A:OEY601 1.8 31.6 0.7
OE2 C:GLU354 1.8 32.2 0.3
O5 A:OEY601 1.8 33.1 0.7
OE1 A:GLU333 1.9 34.3 0.7
O4 A:OEX602 1.9 32.7 0.3
O2 A:OEY601 1.9 32.4 0.7
O2 A:OEX602 1.9 26.7 0.3
O5 A:OEX602 1.9 39.5 0.3
O3 A:OEX602 2.0 38.7 0.3
OE1 A:GLU333 2.0 31.2 0.3
OE2 C:GLU354 2.0 35.2 0.7
O3 A:OEY601 2.1 33.0 0.7
MN4 A:OEX602 2.7 38.1 0.3
CD A:GLU333 2.8 33.3 0.7
MN4 A:OEY601 2.8 34.1 0.7
CD A:GLU333 2.8 31.9 0.3
MN2 A:OEX602 2.8 31.9 0.3
CD C:GLU354 2.9 38.5 0.3
OE2 A:GLU333 2.9 36.5 0.3
MN2 A:OEY601 2.9 33.6 0.7
CD C:GLU354 3.0 33.8 0.7
OE2 A:GLU333 3.0 36.8 0.7
O6 A:OEY601 3.2 32.9 0.7
OE1 C:GLU354 3.2 32.5 0.7
MN1 A:OEX602 3.3 36.3 0.3
OE1 C:GLU354 3.4 37.0 0.3
MN1 A:OEY601 3.4 29.5 0.7
O1 A:OEY601 3.5 30.1 0.7
O1 A:OEX602 3.5 37.1 0.3
CA1 A:OEY601 3.5 34.8 0.7
CA1 A:OEX602 3.6 37.1 0.3
O A:HOH703 3.8 32.8 1.0
OD2 A:ASP170 3.8 38.7 0.7
OD1 A:ASP170 3.9 34.2 0.7
OD1 A:ASP170 3.9 31.9 0.3
NH2 C:ARG357 3.9 30.1 0.7
NH2 C:ARG357 4.0 33.7 0.3
OD2 A:ASP170 4.1 34.6 0.3
CG A:GLU333 4.1 30.9 0.7
NE2 A:HIS337 4.2 35.0 0.7
CG C:GLU354 4.2 37.1 0.3
NE2 A:HIS332 4.2 33.9 0.7
NE2 A:HIS337 4.2 41.4 0.3
CG A:GLU333 4.2 30.7 0.3
O A:HOH724 4.3 36.5 0.3
CG A:ASP170 4.3 33.1 0.7
OXT A:ALA344 4.3 34.3 0.7
NE2 A:HIS332 4.3 41.0 0.3
CG C:GLU354 4.4 31.0 0.7
OXT A:ALA344 4.4 27.8 0.3
O A:HOH755 4.4 34.9 0.7
CG A:ASP170 4.4 35.9 0.3
O A:HOH724 4.5 34.4 0.7
CD2 A:HIS332 4.5 35.2 0.3
CD2 A:HIS332 4.5 32.3 0.7
O A:HOH755 4.5 32.5 0.3
CB A:GLU333 4.6 29.8 0.7
OD1 A:ASP342 4.6 31.6 0.7
OD1 A:ASP342 4.6 32.9 0.3
OD2 A:ASP342 4.6 38.1 0.3
O A:ALA344 4.7 36.2 0.7
O A:HOH781 4.7 29.5 0.3
OE2 A:GLU189 4.7 36.5 0.3
OD2 A:ASP342 4.7 35.6 0.7
CB A:GLU333 4.7 28.6 0.3
O A:ALA344 4.7 39.6 0.3
O A:HOH781 4.9 31.7 0.7
OD1 A:ASP61 4.9 28.7 0.7
C A:ALA344 5.0 36.1 0.7
CZ C:ARG357 5.0 29.5 0.7
CE1 A:HIS337 5.0 34.0 0.7
CZ C:ARG357 5.0 30.6 0.3

Manganese binding site 4 out of 16 in 8f4d

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Manganese binding site 4 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:34.1
occ:0.65
 MN4 A:OEY601 0.0 34.1 0.7
MN4 A:OEX602 0.2 38.1 0.3
O4 A:OEX602 1.7 32.7 0.3
O4 A:OEY601 1.8 31.6 0.7
OE2 A:GLU333 1.8 36.5 0.3
OD1 A:ASP170 1.8 34.2 0.7
OE2 A:GLU333 1.9 36.8 0.7
O A:HOH724 1.9 36.5 0.3
OD1 A:ASP170 1.9 31.9 0.3
O A:HOH755 2.1 34.9 0.7
O5 A:OEY601 2.1 33.1 0.7
O A:HOH724 2.1 34.4 0.7
O A:HOH755 2.2 32.5 0.3
O5 A:OEX602 2.2 39.5 0.3
MN3 A:OEX602 2.7 34.6 0.3
MN3 A:OEY601 2.8 32.3 0.7
CD A:GLU333 2.8 33.3 0.7
CD A:GLU333 2.9 31.9 0.3
CG A:ASP170 2.9 33.1 0.7
CG A:ASP170 3.1 35.9 0.3
OE1 A:GLU333 3.2 34.3 0.7
OE1 A:GLU333 3.3 31.2 0.3
OD2 A:ASP170 3.4 38.7 0.7
O A:HOH703 3.4 32.8 1.0
OD2 A:ASP170 3.6 34.6 0.3
O A:HOH781 3.7 29.5 0.3
O2 A:OEY601 3.8 32.4 0.7
O2 A:OEX602 3.9 26.7 0.3
O A:HOH781 3.9 31.7 0.7
OD1 A:ASP61 3.9 32.8 0.3
OD1 A:ASP61 4.0 28.7 0.7
O6 A:OEY601 4.1 32.9 0.7
O A:SER169 4.1 28.0 0.3
CA1 A:OEY601 4.1 34.8 0.7
O A:HOH727 4.2 30.1 1.0
CG A:GLU333 4.2 30.9 0.7
CB A:ASP170 4.2 28.3 0.7
CA1 A:OEX602 4.2 37.1 0.3
CG A:GLU333 4.2 30.7 0.3
O A:SER169 4.3 31.9 0.7
OE2 C:GLU354 4.3 32.2 0.3
CB A:ASP170 4.3 30.2 0.3
O A:HOH790 4.3 40.7 1.0
OE2 C:GLU354 4.3 35.2 0.7
CA A:ASP170 4.4 27.1 0.3
CA A:ASP170 4.4 29.3 0.7
NH2 C:ARG357 4.5 33.7 0.3
O3 A:OEX602 4.5 38.7 0.3
NH2 C:ARG357 4.5 30.1 0.7
O3 A:OEY601 4.6 33.0 0.7
C A:SER169 4.7 29.5 0.3
C A:SER169 4.7 29.0 0.7
N A:ASP170 4.7 30.2 0.7
OG A:SER169 4.7 36.3 0.3
N A:ASP170 4.7 31.1 0.3
CG A:ASP61 4.7 31.7 0.3
O A:HOH714 4.7 33.3 1.0
OD2 A:ASP61 4.9 35.1 0.3

Manganese binding site 5 out of 16 in 8f4d

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Manganese binding site 5 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:36.3
occ:0.35
 MN1 A:OEX602 0.0 36.3 0.3
MN1 A:OEY601 0.3 29.5 0.7
O6 A:OEY601 1.5 32.9 0.7
OE2 A:GLU189 1.7 36.5 0.3
O3 A:OEX602 1.8 38.7 0.3
O3 A:OEY601 1.9 33.0 0.7
O1 A:OEY601 1.9 30.1 0.7
O1 A:OEX602 2.0 37.1 0.3
NE2 A:HIS332 2.0 41.0 0.3
OE2 A:GLU189 2.1 34.4 0.7
NE2 A:HIS332 2.1 33.9 0.7
OD2 A:ASP342 2.1 38.1 0.3
OD2 A:ASP342 2.2 35.6 0.7
MN2 A:OEX602 2.8 31.9 0.3
O5 A:OEX602 2.9 39.5 0.3
CD2 A:HIS332 2.9 35.2 0.3
MN2 A:OEY601 2.9 33.6 0.7
CD A:GLU189 2.9 33.0 0.3
O5 A:OEY601 3.0 33.1 0.7
CD A:GLU189 3.0 30.8 0.7
CD2 A:HIS332 3.0 32.3 0.7
CE1 A:HIS332 3.1 30.6 0.7
CE1 A:HIS332 3.1 34.2 0.3
CG A:ASP342 3.1 36.7 0.3
CG A:ASP342 3.2 34.2 0.7
MN3 A:OEY601 3.3 32.3 0.7
MN3 A:OEX602 3.3 34.6 0.3
OD1 A:ASP342 3.4 32.9 0.3
CA1 A:OEX602 3.4 37.1 0.3
CA1 A:OEY601 3.4 34.8 0.7
OE1 A:GLU189 3.4 31.9 0.7
OD1 A:ASP342 3.4 31.6 0.7
O2 A:OEX602 3.5 26.7 0.3
O2 A:OEY601 3.5 32.4 0.7
OE1 A:GLU189 3.6 35.7 0.3
OE1 A:GLU333 3.8 34.3 0.7
OE1 A:GLU333 4.0 31.2 0.3
NE2 A:HIS337 4.0 35.0 0.7
CG A:GLU189 4.1 36.2 0.3
NE2 A:HIS337 4.1 41.4 0.3
CG A:HIS332 4.1 33.8 0.3
ND1 A:HIS332 4.1 37.5 0.3
ND1 A:HIS332 4.1 29.8 0.7
CG A:HIS332 4.1 31.3 0.7
O A:HOH778 4.2 33.1 1.0
OXT A:ALA344 4.2 27.8 0.3
CG A:GLU189 4.2 33.3 0.7
OE1 C:GLU354 4.3 37.0 0.3
OE2 C:GLU354 4.3 32.2 0.3
OXT A:ALA344 4.3 34.3 0.7
CG1 A:VAL185 4.3 27.9 0.7
OE1 C:GLU354 4.4 32.5 0.7
O A:HOH798 4.4 38.2 0.6
CB A:ASP342 4.4 43.4 0.3
CG1 A:VAL185 4.5 37.6 0.3
CB A:ASP342 4.5 32.9 0.7
O A:HOH781 4.6 29.5 0.3
OE2 C:GLU354 4.6 35.2 0.7
CD A:GLU333 4.6 31.9 0.3
CD A:GLU333 4.7 33.3 0.7
CD C:GLU354 4.7 38.5 0.3
O A:HOH715 4.7 32.4 0.7
O A:ALA344 4.8 39.6 0.3
O A:ALA344 4.8 36.2 0.7
CE1 A:HIS337 4.8 34.0 0.7
O A:HOH781 4.8 31.7 0.7
C A:ALA344 4.8 31.7 0.3
MN4 A:OEX602 4.8 38.1 0.3
OE2 A:GLU333 4.9 36.5 0.3
CE1 A:HIS337 4.9 34.9 0.3
O4 A:OEY601 4.9 31.6 0.7
C A:ALA344 4.9 36.1 0.7
CD C:GLU354 4.9 33.8 0.7
O4 A:OEX602 4.9 32.7 0.3
CD2 A:HIS337 5.0 34.5 0.7

Manganese binding site 6 out of 16 in 8f4d

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Manganese binding site 6 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:31.9
occ:0.35
 MN2 A:OEX602 0.0 31.9 0.3
MN2 A:OEY601 0.1 33.6 0.7
O1 A:OEX602 1.8 37.1 0.3
O3 A:OEY601 1.8 33.0 0.7
OE1 C:GLU354 1.8 37.0 0.3
O1 A:OEY601 1.8 30.1 0.7
O2 A:OEX602 1.8 26.7 0.3
OXT A:ALA344 1.9 34.3 0.7
O2 A:OEY601 1.9 32.4 0.7
OXT A:ALA344 1.9 27.8 0.3
OE1 C:GLU354 1.9 32.5 0.7
O3 A:OEX602 1.9 38.7 0.3
OD1 A:ASP342 2.1 31.6 0.7
OD1 A:ASP342 2.1 32.9 0.3
CD C:GLU354 2.6 38.5 0.3
OE2 C:GLU354 2.8 32.2 0.3
MN1 A:OEY601 2.8 29.5 0.7
MN3 A:OEY601 2.8 32.3 0.7
MN1 A:OEX602 2.8 36.3 0.3
CD C:GLU354 2.8 33.8 0.7
MN3 A:OEX602 2.8 34.6 0.3
C A:ALA344 2.9 36.1 0.7
C A:ALA344 2.9 31.7 0.3
CG A:ASP342 2.9 34.2 0.7
CG A:ASP342 2.9 36.7 0.3
OE2 C:GLU354 3.1 35.2 0.7
OD2 A:ASP342 3.1 35.6 0.7
OD2 A:ASP342 3.1 38.1 0.3
O A:ALA344 3.2 36.2 0.7
O A:ALA344 3.3 39.6 0.3
CA1 A:OEY601 3.4 34.8 0.7
CA1 A:OEX602 3.4 37.1 0.3
O5 A:OEY601 3.7 33.1 0.7
O6 A:OEY601 3.7 32.9 0.7
O5 A:OEX602 3.7 39.5 0.3
O A:HOH787 3.9 40.5 1.0
NE2 A:HIS337 4.0 41.4 0.3
NE2 A:HIS337 4.0 35.0 0.7
OE2 A:GLU189 4.0 36.5 0.3
CG C:GLU354 4.0 37.1 0.3
OE2 A:GLU189 4.1 34.4 0.7
O A:HOH778 4.2 33.1 1.0
OE1 A:GLU333 4.2 34.3 0.7
CA A:ALA344 4.2 31.5 0.7
CA A:ALA344 4.2 33.2 0.3
CG C:GLU354 4.2 31.0 0.7
O4 A:OEY601 4.2 31.6 0.7
N A:ALA344 4.3 40.2 0.3
CD2 A:HIS337 4.3 30.3 0.3
N A:ALA344 4.3 34.1 0.7
OE1 A:GLU333 4.3 31.2 0.3
CD2 A:HIS337 4.3 34.5 0.7
O4 A:OEX602 4.3 32.7 0.3
CB A:ASP342 4.4 43.4 0.3
CB A:ASP342 4.4 32.9 0.7
NE2 A:HIS332 4.5 33.9 0.7
NE2 A:HIS332 4.5 41.0 0.3
CB C:GLU354 4.6 43.5 0.3
NH2 C:ARG357 4.6 30.1 0.7
OD2 A:ASP170 4.7 38.7 0.7
NH2 C:ARG357 4.7 33.7 0.3
CB C:GLU354 4.7 31.1 0.7
C A:ASP342 4.8 38.4 0.3
CA A:ASP342 4.8 35.5 0.3
C A:ASP342 4.8 34.9 0.7
CA A:ASP342 4.8 32.3 0.7
OD2 A:ASP170 4.8 34.6 0.3
O A:ASP342 4.9 32.0 0.7
NH1 C:ARG357 4.9 33.7 0.3
O A:ASP342 4.9 31.0 0.3
O A:HOH715 4.9 32.4 0.7
NH1 C:ARG357 4.9 28.0 0.7
CD A:GLU189 5.0 33.0 0.3

Manganese binding site 7 out of 16 in 8f4d

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Manganese binding site 7 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:34.6
occ:0.35
 MN3 A:OEX602 0.0 34.6 0.3
MN3 A:OEY601 0.1 32.3 0.7
O4 A:OEY601 1.7 31.6 0.7
O4 A:OEX602 1.8 32.7 0.3
O5 A:OEY601 1.8 33.1 0.7
OE2 C:GLU354 1.8 32.2 0.3
OE1 A:GLU333 1.9 34.3 0.7
O2 A:OEY601 1.9 32.4 0.7
O2 A:OEX602 1.9 26.7 0.3
O5 A:OEX602 1.9 39.5 0.3
OE1 A:GLU333 2.0 31.2 0.3
OE2 C:GLU354 2.0 35.2 0.7
O3 A:OEX602 2.1 38.7 0.3
O3 A:OEY601 2.1 33.0 0.7
MN4 A:OEX602 2.6 38.1 0.3
MN4 A:OEY601 2.7 34.1 0.7
CD A:GLU333 2.8 33.3 0.7
CD A:GLU333 2.8 31.9 0.3
MN2 A:OEX602 2.8 31.9 0.3
OE2 A:GLU333 2.9 36.5 0.3
CD C:GLU354 2.9 38.5 0.3
CD C:GLU354 3.0 33.8 0.7
MN2 A:OEY601 3.0 33.6 0.7
OE2 A:GLU333 3.0 36.8 0.7
O6 A:OEY601 3.2 32.9 0.7
OE1 C:GLU354 3.3 32.5 0.7
MN1 A:OEX602 3.3 36.3 0.3
OE1 C:GLU354 3.4 37.0 0.3
MN1 A:OEY601 3.5 29.5 0.7
O1 A:OEY601 3.5 30.1 0.7
CA1 A:OEY601 3.5 34.8 0.7
O1 A:OEX602 3.5 37.1 0.3
CA1 A:OEX602 3.6 37.1 0.3
O A:HOH703 3.8 32.8 1.0
OD2 A:ASP170 3.8 38.7 0.7
OD1 A:ASP170 3.8 34.2 0.7
OD1 A:ASP170 3.8 31.9 0.3
NH2 C:ARG357 3.9 30.1 0.7
NH2 C:ARG357 3.9 33.7 0.3
OD2 A:ASP170 4.1 34.6 0.3
CG A:GLU333 4.1 30.9 0.7
CG C:GLU354 4.2 37.1 0.3
NE2 A:HIS337 4.2 35.0 0.7
O A:HOH724 4.2 36.5 0.3
CG A:ASP170 4.2 33.1 0.7
CG A:GLU333 4.2 30.7 0.3
NE2 A:HIS332 4.3 33.9 0.7
NE2 A:HIS337 4.3 41.4 0.3
OXT A:ALA344 4.3 34.3 0.7
NE2 A:HIS332 4.4 41.0 0.3
O A:HOH755 4.4 34.9 0.7
CG C:GLU354 4.4 31.0 0.7
CG A:ASP170 4.4 35.9 0.3
OXT A:ALA344 4.4 27.8 0.3
O A:HOH724 4.4 34.4 0.7
O A:HOH755 4.5 32.5 0.3
CD2 A:HIS332 4.5 35.2 0.3
CD2 A:HIS332 4.5 32.3 0.7
CB A:GLU333 4.6 29.8 0.7
OD1 A:ASP342 4.6 31.6 0.7
O A:HOH781 4.7 29.5 0.3
O A:ALA344 4.7 36.2 0.7
OD1 A:ASP342 4.7 32.9 0.3
OD2 A:ASP342 4.7 38.1 0.3
CB A:GLU333 4.7 28.6 0.3
O A:ALA344 4.7 39.6 0.3
OE2 A:GLU189 4.8 36.5 0.3
OD2 A:ASP342 4.8 35.6 0.7
O A:HOH781 4.8 31.7 0.7
OD1 A:ASP61 4.9 28.7 0.7
CZ C:ARG357 4.9 29.5 0.7
CZ C:ARG357 4.9 30.6 0.3
C A:ALA344 5.0 36.1 0.7

Manganese binding site 8 out of 16 in 8f4d

Go back to Manganese Binding Sites List in 8f4d
Manganese binding site 8 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:38.1
occ:0.35
 MN4 A:OEX602 0.0 38.1 0.3
MN4 A:OEY601 0.2 34.1 0.7
O4 A:OEX602 1.7 32.7 0.3
O4 A:OEY601 1.8 31.6 0.7
OD1 A:ASP170 1.8 34.2 0.7
OE2 A:GLU333 1.9 36.5 0.3
O5 A:OEY601 1.9 33.1 0.7
OD1 A:ASP170 1.9 31.9 0.3
OE2 A:GLU333 2.0 36.8 0.7
O5 A:OEX602 2.0 39.5 0.3
O A:HOH755 2.0 34.9 0.7
O A:HOH724 2.1 36.5 0.3
O A:HOH755 2.2 32.5 0.3
O A:HOH724 2.4 34.4 0.7
MN3 A:OEX602 2.6 34.6 0.3
MN3 A:OEY601 2.7 32.3 0.7
CD A:GLU333 2.9 33.3 0.7
CG A:ASP170 2.9 33.1 0.7
CD A:GLU333 2.9 31.9 0.3
CG A:ASP170 3.0 35.9 0.3
OE1 A:GLU333 3.1 34.3 0.7
OE1 A:GLU333 3.2 31.2 0.3
OD2 A:ASP170 3.2 38.7 0.7
OD2 A:ASP170 3.5 34.6 0.3
O A:HOH781 3.6 29.5 0.3
O A:HOH703 3.6 32.8 1.0
O2 A:OEY601 3.7 32.4 0.7
O A:HOH781 3.7 31.7 0.7
O2 A:OEX602 3.7 26.7 0.3
O6 A:OEY601 3.9 32.9 0.7
CA1 A:OEY601 3.9 34.8 0.7
CA1 A:OEX602 4.0 37.1 0.3
OD1 A:ASP61 4.1 32.8 0.3
CB A:ASP170 4.2 28.3 0.7
O A:HOH727 4.2 30.1 1.0
OD1 A:ASP61 4.2 28.7 0.7
O A:HOH790 4.2 40.7 1.0
CG A:GLU333 4.2 30.9 0.7
OE2 C:GLU354 4.2 32.2 0.3
CB A:ASP170 4.2 30.2 0.3
CG A:GLU333 4.2 30.7 0.3
O A:SER169 4.3 28.0 0.3
OE2 C:GLU354 4.3 35.2 0.7
O3 A:OEX602 4.3 38.7 0.3
CA A:ASP170 4.4 27.1 0.3
O A:SER169 4.4 31.9 0.7
CA A:ASP170 4.4 29.3 0.7
NH2 C:ARG357 4.5 33.7 0.3
O3 A:OEY601 4.5 33.0 0.7
NH2 C:ARG357 4.5 30.1 0.7
N A:ASP170 4.8 30.2 0.7
C A:SER169 4.8 29.5 0.3
N A:ASP170 4.8 31.1 0.3
C A:SER169 4.8 29.0 0.7
MN1 A:OEX602 4.8 36.3 0.3
OG A:SER169 4.9 36.3 0.3
O A:HOH714 4.9 33.3 1.0
CG A:ASP61 4.9 31.7 0.3

Manganese binding site 9 out of 16 in 8f4d

Go back to Manganese Binding Sites List in 8f4d
Manganese binding site 9 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:35.4
occ:0.65
 MN1 a:OEY601 0.0 35.4 0.7
MN1 a:OEX602 0.2 33.8 0.3
OE2 a:GLU189 1.8 33.3 0.3
O6 a:OEY601 1.8 33.6 0.7
OE2 a:GLU189 1.8 30.9 0.7
O3 a:OEY601 1.9 32.0 0.7
O1 a:OEY601 1.9 29.4 0.7
O1 a:OEX602 1.9 36.9 0.3
O3 a:OEX602 1.9 31.1 0.3
OD2 a:ASP342 2.0 39.2 0.3
NE2 a:HIS332 2.3 29.8 0.7
OD2 a:ASP342 2.3 29.9 0.7
NE2 a:HIS332 2.4 35.7 0.3
MN2 a:OEX602 2.6 38.8 0.3
MN2 a:OEY601 2.8 28.8 0.7
CD a:GLU189 2.8 33.3 0.7
CG a:ASP342 2.9 38.4 0.3
CD a:GLU189 2.9 32.9 0.3
O5 a:OEX602 3.0 43.8 0.3
CG a:ASP342 3.0 33.5 0.7
O2 a:OEX602 3.1 29.1 0.3
CE1 a:HIS332 3.1 31.1 0.7
OD1 a:ASP342 3.2 34.1 0.3
OD1 a:ASP342 3.2 31.3 0.7
OE1 a:GLU189 3.2 32.4 0.7
O5 a:OEY601 3.3 30.1 0.7
CA1 a:OEX602 3.3 36.1 0.3
CD2 a:HIS332 3.3 32.4 0.7
CE1 a:HIS332 3.3 36.2 0.3
MN3 a:OEX602 3.4 35.0 0.3
CD2 a:HIS332 3.4 33.2 0.3
CA1 a:OEY601 3.4 34.3 0.7
MN3 a:OEY601 3.4 33.5 0.7
O2 a:OEY601 3.4 28.0 0.7
OE1 a:GLU189 3.6 36.5 0.3
NE2 a:HIS337 3.9 32.0 0.7
OE1 a:GLU333 4.0 31.6 0.7
CG a:GLU189 4.0 35.9 0.3
OE1 a:GLU333 4.1 31.7 0.3
NE2 a:HIS337 4.1 35.5 0.3
CG a:GLU189 4.1 34.5 0.7
O a:HOH710 4.2 36.5 1.0
OXT a:ALA344 4.2 35.8 0.3
CB a:ASP342 4.3 35.4 0.3
OXT a:ALA344 4.3 31.4 0.7
ND1 a:HIS332 4.3 32.9 0.7
OE1 c:GLU354 4.3 37.5 0.3
CG a:HIS332 4.4 29.6 0.7
OE1 c:GLU354 4.4 30.1 0.7
OE2 c:GLU354 4.4 35.5 0.7
CB a:ASP342 4.4 36.2 0.7
ND1 a:HIS332 4.4 38.5 0.3
CG a:HIS332 4.5 32.9 0.3
OE2 c:GLU354 4.5 37.8 0.3
O a:ALA344 4.6 30.0 0.7
CE1 a:HIS337 4.6 33.1 0.7
CG1 a:VAL185 4.6 36.9 0.3
CG1 a:VAL185 4.7 32.4 0.7
O a:ALA344 4.7 32.8 0.3
CD a:GLU333 4.7 33.5 0.7
C a:ALA344 4.8 34.0 0.7
CD c:GLU354 4.8 39.4 0.3
C a:ALA344 4.8 35.1 0.3
O a:HOH782 4.8 33.7 0.7
CD c:GLU354 4.9 31.7 0.7
CD a:GLU333 4.9 33.6 0.3
O a:HOH782 4.9 37.2 0.3
CE1 a:HIS337 4.9 40.5 0.3
CD2 a:HIS337 5.0 36.4 0.3

Manganese binding site 10 out of 16 in 8f4d

Go back to Manganese Binding Sites List in 8f4d
Manganese binding site 10 out of 16 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:28.8
occ:0.65
 MN2 a:OEY601 0.0 28.8 0.7
MN2 a:OEX602 0.2 38.8 0.3
O2 a:OEX602 1.7 29.1 0.3
OE1 c:GLU354 1.8 37.5 0.3
O1 a:OEX602 1.8 36.9 0.3
OXT a:ALA344 1.9 35.8 0.3
O1 a:OEY601 1.9 29.4 0.7
OXT a:ALA344 1.9 31.4 0.7
O2 a:OEY601 1.9 28.0 0.7
O3 a:OEX602 2.0 31.1 0.3
O3 a:OEY601 2.0 32.0 0.7
OE1 c:GLU354 2.0 30.1 0.7
OD1 a:ASP342 2.1 34.1 0.3
OD1 a:ASP342 2.2 31.3 0.7
CD c:GLU354 2.7 39.4 0.3
MN1 a:OEY601 2.8 35.4 0.7
CD c:GLU354 2.8 31.7 0.7
MN1 a:OEX602 2.9 33.8 0.3
MN3 a:OEY601 2.9 33.5 0.7
C a:ALA344 2.9 34.0 0.7
C a:ALA344 2.9 35.1 0.3
MN3 a:OEX602 2.9 35.0 0.3
OE2 c:GLU354 3.0 37.8 0.3
CG a:ASP342 3.0 38.4 0.3
OE2 c:GLU354 3.0 35.5 0.7
CG a:ASP342 3.1 33.5 0.7
OD2 a:ASP342 3.2 39.2 0.3
O a:ALA344 3.2 30.0 0.7
O a:ALA344 3.3 32.8 0.3
OD2 a:ASP342 3.4 29.9 0.7
CA1 a:OEX602 3.4 36.1 0.3
CA1 a:OEY601 3.6 34.3 0.7
O5 a:OEY601 3.8 30.1 0.7
O6 a:OEY601 3.8 33.6 0.7
NE2 a:HIS337 3.8 32.0 0.7
O a:HOH762 3.9 32.6 1.0
O5 a:OEX602 3.9 43.8 0.3
CG c:GLU354 4.1 30.1 0.3
NE2 a:HIS337 4.1 35.5 0.3
OE2 a:GLU189 4.2 30.9 0.7
CG c:GLU354 4.2 31.3 0.7
OE2 a:GLU189 4.2 33.3 0.3
CA a:ALA344 4.2 39.5 0.3
CA a:ALA344 4.2 34.0 0.7
N a:ALA344 4.3 32.9 0.7
CD2 a:HIS337 4.3 33.9 0.7
N a:ALA344 4.3 38.8 0.3
OE1 a:GLU333 4.4 31.6 0.7
CB a:ASP342 4.4 35.4 0.3
O a:HOH710 4.4 36.5 1.0
NH2 c:ARG357 4.4 27.5 0.7
CD2 a:HIS337 4.4 36.4 0.3
O4 a:OEX602 4.5 29.7 0.3
CB a:ASP342 4.5 36.2 0.7
OE1 a:GLU333 4.5 31.7 0.3
CB c:GLU354 4.6 38.5 0.3
NE2 a:HIS332 4.7 29.8 0.7
NH1 c:ARG357 4.7 27.5 0.3
C a:ASP342 4.7 35.2 0.7
OD2 a:ASP170 4.7 33.9 0.7
OD2 a:ASP170 4.7 37.5 0.3
NH2 c:ARG357 4.7 36.1 0.3
O4 a:OEY601 4.7 33.5 0.7
C a:ASP342 4.7 37.1 0.3
CA a:ASP342 4.7 26.3 0.3
CB c:GLU354 4.7 29.8 0.7
O a:ASP342 4.7 29.6 0.7
NE2 a:HIS332 4.8 35.7 0.3
CA a:ASP342 4.8 34.2 0.7
NH1 c:ARG357 4.9 29.2 0.7
CZ c:ARG357 4.9 28.8 0.7
CD a:GLU189 4.9 32.9 0.3
OE1 a:GLU189 4.9 32.4 0.7
CD a:GLU189 5.0 33.3 0.7
O a:ASP342 5.0 31.1 0.3
OE1 a:GLU189 5.0 36.5 0.3

Reference:

A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra. Structural Evidence For Intermediates During O2 Formation in Photosystem II To Be Published.
Page generated: Sun Oct 6 11:50:23 2024

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