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Manganese in PDB 8f4k: Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution, PDB code: 8f4k 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) 33.52 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.991, 221.755, 307.964, 90, 90, 90
R / Rfree (%) 18.5 / 24.1

Other elements in 8f4k:

The structure of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 4 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution (pdb code 8f4k). 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution, PDB code: 8f4k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 8f4k

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Manganese binding site 1 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:29.9
occ:0.65
 MN1 A:OEX601 0.0 29.9 0.7
MN1 A:OEY602 0.0 34.3 0.3
OE2 A:GLU189 1.8 30.2 0.7
O6 A:OEY602 1.8 38.9 0.3
O3 A:OEY602 1.9 38.9 0.3
O3 A:OEX601 1.9 36.5 0.7
O1 A:OEX601 1.9 31.5 0.7
O1 A:OEY602 2.0 32.5 0.3
NE2 A:HIS332 2.0 37.0 0.7
OE2 A:GLU189 2.0 37.6 0.3
OD2 A:ASP342 2.0 35.2 0.3
OD2 A:ASP342 2.0 35.8 0.7
NE2 A:HIS332 2.2 37.3 0.3
MN2 A:OEY602 2.8 36.1 0.3
O5 A:OEX601 2.8 32.1 0.7
MN2 A:OEX601 2.8 32.2 0.7
O5 A:OEY602 2.9 37.5 0.3
CE1 A:HIS332 2.9 33.5 0.7
CD A:GLU189 2.9 30.4 0.7
CG A:ASP342 3.0 37.3 0.7
CG A:ASP342 3.0 37.6 0.3
CD2 A:HIS332 3.0 31.7 0.7
CD A:GLU189 3.1 37.9 0.3
CD2 A:HIS332 3.1 36.1 0.3
CE1 A:HIS332 3.2 34.3 0.3
OD1 A:ASP342 3.2 34.1 0.7
OD1 A:ASP342 3.3 35.6 0.3
MN3 A:OEX601 3.3 31.1 0.7
MN3 A:OEY602 3.3 38.4 0.3
CA1 A:OEY602 3.4 40.0 0.3
CA1 A:OEX601 3.4 32.8 0.7
O2 A:OEX601 3.4 32.3 0.7
O2 A:OEY602 3.4 35.5 0.3
OE1 A:GLU189 3.5 35.2 0.3
OE1 A:GLU189 3.6 34.2 0.7
O A:HOH706 3.7 32.7 1.0
NE2 A:HIS337 4.0 33.9 0.7
OE1 A:GLU333 4.0 38.0 0.3
ND1 A:HIS332 4.0 26.4 0.7
NE2 A:HIS337 4.0 36.4 0.3
CG A:GLU189 4.1 30.1 0.7
CG A:HIS332 4.1 30.0 0.7
OE1 A:GLU333 4.1 33.1 0.7
OE1 C:GLU354 4.2 33.7 0.7
CG A:HIS332 4.3 37.5 0.3
ND1 A:HIS332 4.3 33.4 0.3
OE1 C:GLU354 4.3 35.4 0.3
OXT A:ALA344 4.3 34.0 0.7
CB A:ASP342 4.3 38.8 0.3
CG A:GLU189 4.4 38.2 0.3
CB A:ASP342 4.4 37.4 0.7
OXT A:ALA344 4.4 37.1 0.3
CG1 A:VAL185 4.5 35.0 0.3
OE2 C:GLU354 4.5 42.1 0.3
CG1 A:VAL185 4.6 26.5 0.7
CD A:GLU333 4.6 35.0 0.7
O A:HOH797 4.7 37.4 0.3
OE2 C:GLU354 4.7 35.0 0.7
O A:ALA344 4.7 36.2 0.7
O A:HOH806 4.7 37.8 0.6
CE1 A:HIS337 4.8 36.6 0.3
O A:HOH797 4.8 33.0 0.7
O A:ALA344 4.8 37.0 0.3
CE1 A:HIS337 4.8 32.7 0.7
CD A:GLU333 4.8 37.2 0.3
CD C:GLU354 4.8 39.1 0.3
CD C:GLU354 4.9 35.6 0.7
C A:ALA344 4.9 35.4 0.7
C A:ALA344 4.9 36.6 0.3
OE2 A:GLU333 4.9 30.9 0.7
CD2 A:HIS337 4.9 32.0 0.7

Manganese binding site 2 out of 16 in 8f4k

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Manganese binding site 2 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:32.2
occ:0.65
 MN2 A:OEX601 0.0 32.2 0.7
MN2 A:OEY602 0.1 36.1 0.3
O1 A:OEX601 1.8 31.5 0.7
O1 A:OEY602 1.8 32.5 0.3
OE1 C:GLU354 1.9 35.4 0.3
OXT A:ALA344 1.9 34.0 0.7
O2 A:OEX601 1.9 32.3 0.7
O3 A:OEX601 1.9 36.5 0.7
O3 A:OEY602 1.9 38.9 0.3
OE1 C:GLU354 1.9 33.7 0.7
O2 A:OEY602 1.9 35.5 0.3
OD1 A:ASP342 2.0 35.6 0.3
OXT A:ALA344 2.0 37.1 0.3
OD1 A:ASP342 2.0 34.1 0.7
MN1 A:OEX601 2.8 29.9 0.7
MN1 A:OEY602 2.8 34.3 0.3
CG A:ASP342 2.8 37.6 0.3
CD C:GLU354 2.9 35.6 0.7
CD C:GLU354 2.9 39.1 0.3
C A:ALA344 2.9 35.4 0.7
MN3 A:OEX601 2.9 31.1 0.7
CG A:ASP342 2.9 37.3 0.7
C A:ALA344 2.9 36.6 0.3
MN3 A:OEY602 2.9 38.4 0.3
OD2 A:ASP342 3.0 35.2 0.3
OE2 C:GLU354 3.1 35.0 0.7
OD2 A:ASP342 3.2 35.8 0.7
OE2 C:GLU354 3.2 42.1 0.3
O A:ALA344 3.2 36.2 0.7
O A:ALA344 3.3 37.0 0.3
CA1 A:OEY602 3.4 40.0 0.3
CA1 A:OEX601 3.4 32.8 0.7
O A:HOH706 3.7 32.7 1.0
O5 A:OEX601 3.8 32.1 0.7
O5 A:OEY602 3.8 37.5 0.3
O A:HOH787 3.9 42.1 1.0
O6 A:OEY602 3.9 38.9 0.3
NE2 A:HIS337 4.0 33.9 0.7
NE2 A:HIS337 4.0 36.4 0.3
OE2 A:GLU189 4.1 37.6 0.3
OE2 A:GLU189 4.2 30.2 0.7
CA A:ALA344 4.2 38.4 0.3
CA A:ALA344 4.2 31.6 0.7
N A:ALA344 4.2 39.8 0.3
CG C:GLU354 4.2 41.4 0.3
CG C:GLU354 4.2 32.5 0.7
CB A:ASP342 4.3 38.8 0.3
N A:ALA344 4.3 36.3 0.7
OE1 A:GLU333 4.3 33.1 0.7
CD2 A:HIS337 4.3 32.0 0.7
CB A:ASP342 4.3 37.4 0.7
NE2 A:HIS332 4.4 37.0 0.7
CD2 A:HIS337 4.4 35.6 0.3
OE1 A:GLU333 4.4 38.0 0.3
O4 A:OEX601 4.5 31.1 0.7
O4 A:OEY602 4.5 33.6 0.3
CB C:GLU354 4.7 42.2 0.3
NH2 C:ARG357 4.7 38.7 0.3
CB C:GLU354 4.7 32.5 0.7
NE2 A:HIS332 4.7 37.3 0.3
CA A:ASP342 4.7 38.2 0.3
CA A:ASP342 4.7 32.0 0.7
C A:ASP342 4.7 39.1 0.3
NH1 C:ARG357 4.8 30.9 0.7
C A:ASP342 4.8 34.5 0.7
OD2 A:ASP170 4.9 36.9 0.3
O A:ASP342 4.9 36.3 0.3
NH1 C:ARG357 4.9 36.6 0.3
OD2 A:ASP170 4.9 35.1 0.7
NH2 C:ARG357 4.9 30.6 0.7
CD A:GLU189 5.0 30.4 0.7

Manganese binding site 3 out of 16 in 8f4k

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Manganese binding site 3 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:31.1
occ:0.65
 MN3 A:OEX601 0.0 31.1 0.7
MN3 A:OEY602 0.1 38.4 0.3
O2 A:OEY602 1.8 35.5 0.3
O2 A:OEX601 1.9 32.3 0.7
O4 A:OEY602 1.9 33.6 0.3
OE1 A:GLU333 1.9 33.1 0.7
O5 A:OEY602 1.9 37.5 0.3
O3 A:OEX601 2.0 36.5 0.7
O4 A:OEX601 2.0 31.1 0.7
OE1 A:GLU333 2.0 38.0 0.3
OE2 C:GLU354 2.0 35.0 0.7
O3 A:OEY602 2.0 38.9 0.3
O5 A:OEX601 2.0 32.1 0.7
OE2 C:GLU354 2.2 42.1 0.3
MN4 A:OEY602 2.7 40.0 0.3
CD A:GLU333 2.8 35.0 0.7
MN4 A:OEX601 2.8 32.8 0.7
MN2 A:OEY602 2.8 36.1 0.3
MN2 A:OEX601 2.9 32.2 0.7
CD A:GLU333 2.9 37.2 0.3
OE2 A:GLU333 3.0 30.9 0.7
CD C:GLU354 3.0 35.6 0.7
CD C:GLU354 3.0 39.1 0.3
OE2 A:GLU333 3.2 37.1 0.3
OE1 C:GLU354 3.2 35.4 0.3
OE1 C:GLU354 3.2 33.7 0.7
MN1 A:OEX601 3.3 29.9 0.7
MN1 A:OEY602 3.4 34.3 0.3
CA1 A:OEY602 3.4 40.0 0.3
O1 A:OEY602 3.4 32.5 0.3
O C:HOH602 3.5 38.0 0.7
O1 A:OEX601 3.5 31.5 0.7
O6 A:OEY602 3.5 38.9 0.3
CA1 A:OEX601 3.5 32.8 0.7
NH2 C:ARG357 3.8 38.7 0.3
OD2 A:ASP170 3.9 36.9 0.3
OD1 A:ASP170 3.9 27.8 0.7
OD1 A:ASP170 4.0 40.3 0.3
NH2 C:ARG357 4.0 30.6 0.7
O A:HOH704 4.1 33.8 1.0
NE2 A:HIS332 4.1 37.0 0.7
OD2 A:ASP170 4.1 35.1 0.7
CG A:GLU333 4.2 32.0 0.7
NE2 A:HIS337 4.2 36.4 0.3
NE2 A:HIS337 4.3 33.9 0.7
O A:HOH722 4.3 29.3 0.7
CG A:GLU333 4.3 34.1 0.3
CG C:GLU354 4.3 32.5 0.7
O A:HOH722 4.4 39.8 0.3
OXT A:ALA344 4.4 34.0 0.7
O A:HOH733 4.4 40.8 0.3
CG A:ASP170 4.4 36.5 0.3
CD2 A:HIS332 4.4 31.7 0.7
OXT A:ALA344 4.4 37.1 0.3
CG C:GLU354 4.4 41.4 0.3
CG A:ASP170 4.4 32.1 0.7
NE2 A:HIS332 4.5 37.3 0.3
OD1 A:ASP342 4.6 35.6 0.3
OD1 A:ASP342 4.6 34.1 0.7
OD2 A:ASP342 4.6 35.2 0.3
O A:HOH733 4.6 29.1 0.7
CB A:GLU333 4.7 29.2 0.7
O A:HOH797 4.7 37.4 0.3
O A:ALA344 4.7 36.2 0.7
CD2 A:HIS332 4.7 36.1 0.3
OE2 A:GLU189 4.7 30.2 0.7
O A:ALA344 4.7 37.0 0.3
CB A:GLU333 4.7 33.0 0.3
O A:HOH797 4.8 33.0 0.7
OD2 A:ASP342 4.8 35.8 0.7
CZ C:ARG357 4.9 35.5 0.3
CZ C:ARG357 4.9 30.5 0.7
CE1 A:HIS337 4.9 32.7 0.7
CE1 A:HIS337 5.0 36.6 0.3

Manganese binding site 4 out of 16 in 8f4k

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Manganese binding site 4 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:32.8
occ:0.65
 MN4 A:OEX601 0.0 32.8 0.7
MN4 A:OEY602 0.2 40.0 0.3
O4 A:OEX601 1.8 31.1 0.7
OE2 A:GLU333 1.8 30.9 0.7
O4 A:OEY602 1.9 33.6 0.3
O A:HOH733 1.9 40.8 0.3
OE2 A:GLU333 2.0 37.1 0.3
OD1 A:ASP170 2.0 40.3 0.3
OD1 A:ASP170 2.0 27.8 0.7
O A:HOH722 2.0 29.3 0.7
O A:HOH722 2.1 39.8 0.3
O5 A:OEY602 2.2 37.5 0.3
O A:HOH733 2.2 29.1 0.7
O5 A:OEX601 2.3 32.1 0.7
MN3 A:OEX601 2.8 31.1 0.7
MN3 A:OEY602 2.8 38.4 0.3
CD A:GLU333 2.8 35.0 0.7
CD A:GLU333 2.9 37.2 0.3
CG A:ASP170 3.0 36.5 0.3
CG A:ASP170 3.1 32.1 0.7
OE1 A:GLU333 3.2 38.0 0.3
OE1 A:GLU333 3.2 33.1 0.7
OD2 A:ASP170 3.4 36.9 0.3
OD2 A:ASP170 3.5 35.1 0.7
O A:HOH797 3.6 37.4 0.3
O A:HOH797 3.7 33.0 0.7
O A:HOH704 3.7 33.8 1.0
O2 A:OEY602 3.8 35.5 0.3
O2 A:OEX601 3.8 32.3 0.7
O A:HOH762 3.9 27.8 1.0
CA1 A:OEY602 4.0 40.0 0.3
CA1 A:OEX601 4.1 32.8 0.7
O6 A:OEY602 4.1 38.9 0.3
OD1 A:ASP61 4.1 32.2 0.7
OD1 A:ASP61 4.1 32.5 0.3
CG A:GLU333 4.2 32.0 0.7
O A:SER169 4.2 31.0 0.7
CG A:GLU333 4.3 34.1 0.3
CB A:ASP170 4.3 35.3 0.3
O A:HOH780 4.3 35.9 1.0
CB A:ASP170 4.3 29.8 0.7
O A:SER169 4.3 36.4 0.3
OE2 C:GLU354 4.4 35.0 0.7
O3 A:OEX601 4.4 36.5 0.7
CA A:ASP170 4.5 29.5 0.7
CA A:ASP170 4.5 36.3 0.3
O3 A:OEY602 4.5 38.9 0.3
NH2 C:ARG357 4.5 38.7 0.3
NH2 C:ARG357 4.6 30.6 0.7
OE2 C:GLU354 4.6 42.1 0.3
O C:HOH602 4.6 38.0 0.7
C A:SER169 4.8 29.6 0.7
OG A:SER169 4.8 32.1 0.7
N A:ASP170 4.9 30.5 0.7
C A:SER169 4.9 37.6 0.3
N A:ASP170 4.9 39.1 0.3

Manganese binding site 5 out of 16 in 8f4k

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Manganese binding site 5 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:34.3
occ:0.35
 MN1 A:OEY602 0.0 34.3 0.3
MN1 A:OEX601 0.0 29.9 0.7
OE2 A:GLU189 1.7 30.2 0.7
O6 A:OEY602 1.8 38.9 0.3
O3 A:OEY602 1.9 38.9 0.3
O3 A:OEX601 1.9 36.5 0.7
O1 A:OEX601 1.9 31.5 0.7
O1 A:OEY602 1.9 32.5 0.3
NE2 A:HIS332 2.0 37.0 0.7
OE2 A:GLU189 2.0 37.6 0.3
OD2 A:ASP342 2.0 35.2 0.3
OD2 A:ASP342 2.0 35.8 0.7
NE2 A:HIS332 2.2 37.3 0.3
MN2 A:OEY602 2.8 36.1 0.3
MN2 A:OEX601 2.8 32.2 0.7
O5 A:OEX601 2.8 32.1 0.7
O5 A:OEY602 2.9 37.5 0.3
CD A:GLU189 2.9 30.4 0.7
CE1 A:HIS332 2.9 33.5 0.7
CG A:ASP342 3.0 37.3 0.7
CG A:ASP342 3.0 37.6 0.3
CD2 A:HIS332 3.0 31.7 0.7
CD A:GLU189 3.1 37.9 0.3
CD2 A:HIS332 3.1 36.1 0.3
CE1 A:HIS332 3.2 34.3 0.3
OD1 A:ASP342 3.2 34.1 0.7
OD1 A:ASP342 3.3 35.6 0.3
CA1 A:OEY602 3.4 40.0 0.3
MN3 A:OEX601 3.4 31.1 0.7
MN3 A:OEY602 3.4 38.4 0.3
CA1 A:OEX601 3.4 32.8 0.7
O2 A:OEX601 3.4 32.3 0.7
O2 A:OEY602 3.5 35.5 0.3
OE1 A:GLU189 3.5 35.2 0.3
OE1 A:GLU189 3.5 34.2 0.7
O A:HOH706 3.7 32.7 1.0
NE2 A:HIS337 4.0 33.9 0.7
OE1 A:GLU333 4.0 38.0 0.3
ND1 A:HIS332 4.0 26.4 0.7
CG A:GLU189 4.0 30.1 0.7
NE2 A:HIS337 4.1 36.4 0.3
CG A:HIS332 4.1 30.0 0.7
OE1 A:GLU333 4.1 33.1 0.7
OE1 C:GLU354 4.2 33.7 0.7
CG A:HIS332 4.3 37.5 0.3
CG A:GLU189 4.3 38.2 0.3
ND1 A:HIS332 4.3 33.4 0.3
CB A:ASP342 4.3 38.8 0.3
OXT A:ALA344 4.3 34.0 0.7
OE1 C:GLU354 4.3 35.4 0.3
CB A:ASP342 4.4 37.4 0.7
OXT A:ALA344 4.4 37.1 0.3
CG1 A:VAL185 4.5 35.0 0.3
OE2 C:GLU354 4.6 42.1 0.3
CG1 A:VAL185 4.6 26.5 0.7
O A:HOH797 4.7 37.4 0.3
CD A:GLU333 4.7 35.0 0.7
O A:HOH806 4.7 37.8 0.6
O A:ALA344 4.7 36.2 0.7
OE2 C:GLU354 4.7 35.0 0.7
O A:HOH797 4.8 33.0 0.7
CE1 A:HIS337 4.8 36.6 0.3
O A:ALA344 4.8 37.0 0.3
CE1 A:HIS337 4.8 32.7 0.7
CD C:GLU354 4.9 39.1 0.3
C A:ALA344 4.9 35.4 0.7
CD A:GLU333 4.9 37.2 0.3
C A:ALA344 4.9 36.6 0.3
CD C:GLU354 4.9 35.6 0.7
CD2 A:HIS337 4.9 32.0 0.7
OE2 A:GLU333 5.0 30.9 0.7

Manganese binding site 6 out of 16 in 8f4k

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Manganese binding site 6 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:36.1
occ:0.35
 MN2 A:OEY602 0.0 36.1 0.3
MN2 A:OEX601 0.1 32.2 0.7
O1 A:OEX601 1.8 31.5 0.7
O1 A:OEY602 1.8 32.5 0.3
O3 A:OEX601 1.9 36.5 0.7
O3 A:OEY602 1.9 38.9 0.3
O2 A:OEX601 1.9 32.3 0.7
OE1 C:GLU354 1.9 35.4 0.3
O2 A:OEY602 1.9 35.5 0.3
OE1 C:GLU354 1.9 33.7 0.7
OXT A:ALA344 2.0 34.0 0.7
OD1 A:ASP342 2.0 35.6 0.3
OXT A:ALA344 2.0 37.1 0.3
OD1 A:ASP342 2.1 34.1 0.7
MN1 A:OEX601 2.8 29.9 0.7
MN1 A:OEY602 2.8 34.3 0.3
CD C:GLU354 2.8 35.6 0.7
MN3 A:OEX601 2.8 31.1 0.7
CD C:GLU354 2.8 39.1 0.3
MN3 A:OEY602 2.9 38.4 0.3
CG A:ASP342 2.9 37.6 0.3
C A:ALA344 2.9 35.4 0.7
CG A:ASP342 2.9 37.3 0.7
C A:ALA344 3.0 36.6 0.3
OD2 A:ASP342 3.0 35.2 0.3
OE2 C:GLU354 3.1 35.0 0.7
OE2 C:GLU354 3.1 42.1 0.3
OD2 A:ASP342 3.2 35.8 0.7
O A:ALA344 3.2 36.2 0.7
O A:ALA344 3.3 37.0 0.3
CA1 A:OEY602 3.3 40.0 0.3
CA1 A:OEX601 3.4 32.8 0.7
O5 A:OEX601 3.7 32.1 0.7
O5 A:OEY602 3.7 37.5 0.3
O A:HOH706 3.7 32.7 1.0
O6 A:OEY602 3.8 38.9 0.3
O A:HOH787 3.9 42.1 1.0
NE2 A:HIS337 3.9 33.9 0.7
NE2 A:HIS337 3.9 36.4 0.3
OE2 A:GLU189 4.1 30.2 0.7
OE2 A:GLU189 4.2 37.6 0.3
CG C:GLU354 4.2 41.4 0.3
CG C:GLU354 4.2 32.5 0.7
CA A:ALA344 4.2 38.4 0.3
CA A:ALA344 4.3 31.6 0.7
OE1 A:GLU333 4.3 33.1 0.7
N A:ALA344 4.3 39.8 0.3
CB A:ASP342 4.3 38.8 0.3
CD2 A:HIS337 4.3 32.0 0.7
NE2 A:HIS332 4.3 37.0 0.7
OE1 A:GLU333 4.4 38.0 0.3
N A:ALA344 4.4 36.3 0.7
CD2 A:HIS337 4.4 35.6 0.3
CB A:ASP342 4.4 37.4 0.7
O4 A:OEX601 4.4 31.1 0.7
O4 A:OEY602 4.4 33.6 0.3
NH2 C:ARG357 4.6 38.7 0.3
CB C:GLU354 4.7 42.2 0.3
NE2 A:HIS332 4.7 37.3 0.3
CB C:GLU354 4.7 32.5 0.7
CA A:ASP342 4.8 38.2 0.3
CA A:ASP342 4.8 32.0 0.7
C A:ASP342 4.8 39.1 0.3
NH1 C:ARG357 4.8 30.9 0.7
OD2 A:ASP170 4.8 36.9 0.3
C A:ASP342 4.9 34.5 0.7
OD2 A:ASP170 4.9 35.1 0.7
NH1 C:ARG357 4.9 36.6 0.3
NH2 C:ARG357 4.9 30.6 0.7
O A:ASP342 5.0 36.3 0.3
CD A:GLU189 5.0 30.4 0.7

Manganese binding site 7 out of 16 in 8f4k

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Manganese binding site 7 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:38.4
occ:0.35
 MN3 A:OEY602 0.0 38.4 0.3
MN3 A:OEX601 0.1 31.1 0.7
OE1 A:GLU333 1.8 33.1 0.7
O2 A:OEY602 1.9 35.5 0.3
OE1 A:GLU333 1.9 38.0 0.3
O4 A:OEY602 1.9 33.6 0.3
O3 A:OEX601 1.9 36.5 0.7
O2 A:OEX601 2.0 32.3 0.7
O5 A:OEY602 2.0 37.5 0.3
OE2 C:GLU354 2.0 35.0 0.7
O3 A:OEY602 2.0 38.9 0.3
O4 A:OEX601 2.0 31.1 0.7
OE2 C:GLU354 2.1 42.1 0.3
O5 A:OEX601 2.1 32.1 0.7
CD A:GLU333 2.7 35.0 0.7
MN4 A:OEY602 2.7 40.0 0.3
MN4 A:OEX601 2.8 32.8 0.7
MN2 A:OEY602 2.9 36.1 0.3
CD A:GLU333 2.9 37.2 0.3
OE2 A:GLU333 2.9 30.9 0.7
MN2 A:OEX601 2.9 32.2 0.7
CD C:GLU354 2.9 35.6 0.7
CD C:GLU354 3.0 39.1 0.3
OE2 A:GLU333 3.1 37.1 0.3
OE1 C:GLU354 3.2 33.7 0.7
OE1 C:GLU354 3.2 35.4 0.3
MN1 A:OEX601 3.3 29.9 0.7
MN1 A:OEY602 3.4 34.3 0.3
O C:HOH602 3.4 38.0 0.7
O1 A:OEY602 3.5 32.5 0.3
CA1 A:OEY602 3.5 40.0 0.3
O6 A:OEY602 3.5 38.9 0.3
O1 A:OEX601 3.5 31.5 0.7
CA1 A:OEX601 3.6 32.8 0.7
NH2 C:ARG357 3.9 38.7 0.3
OD1 A:ASP170 4.0 27.8 0.7
OD2 A:ASP170 4.0 36.9 0.3
NE2 A:HIS332 4.0 37.0 0.7
CG A:GLU333 4.1 32.0 0.7
O A:HOH704 4.1 33.8 1.0
OD1 A:ASP170 4.1 40.3 0.3
NH2 C:ARG357 4.1 30.6 0.7
NE2 A:HIS337 4.2 36.4 0.3
NE2 A:HIS337 4.2 33.9 0.7
OD2 A:ASP170 4.2 35.1 0.7
CG A:GLU333 4.2 34.1 0.3
CG C:GLU354 4.3 32.5 0.7
O A:HOH722 4.3 29.3 0.7
CD2 A:HIS332 4.4 31.7 0.7
O A:HOH722 4.4 39.8 0.3
CG C:GLU354 4.4 41.4 0.3
O A:HOH733 4.4 40.8 0.3
OXT A:ALA344 4.4 34.0 0.7
NE2 A:HIS332 4.5 37.3 0.3
OXT A:ALA344 4.5 37.1 0.3
CG A:ASP170 4.5 36.5 0.3
CB A:GLU333 4.5 29.2 0.7
CG A:ASP170 4.6 32.1 0.7
OD2 A:ASP342 4.6 35.2 0.3
OD1 A:ASP342 4.6 35.6 0.3
CB A:GLU333 4.6 33.0 0.3
OD1 A:ASP342 4.6 34.1 0.7
O A:HOH733 4.7 29.1 0.7
CD2 A:HIS332 4.7 36.1 0.3
OE2 A:GLU189 4.7 30.2 0.7
O A:HOH797 4.8 37.4 0.3
O A:ALA344 4.8 36.2 0.7
OD2 A:ASP342 4.8 35.8 0.7
O A:ALA344 4.8 37.0 0.3
CE1 A:HIS337 4.8 32.7 0.7
O A:HOH797 4.9 33.0 0.7
CE1 A:HIS337 4.9 36.6 0.3
CZ C:ARG357 4.9 35.5 0.3

Manganese binding site 8 out of 16 in 8f4k

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Manganese binding site 8 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:40.0
occ:0.35
 MN4 A:OEY602 0.0 40.0 0.3
MN4 A:OEX601 0.2 32.8 0.7
O4 A:OEX601 1.6 31.1 0.7
O4 A:OEY602 1.8 33.6 0.3
OD1 A:ASP170 1.9 40.3 0.3
OD1 A:ASP170 1.9 27.8 0.7
OE2 A:GLU333 2.0 30.9 0.7
OE2 A:GLU333 2.1 37.1 0.3
O A:HOH722 2.1 29.3 0.7
O A:HOH733 2.1 40.8 0.3
O A:HOH722 2.1 39.8 0.3
O5 A:OEY602 2.2 37.5 0.3
O5 A:OEX601 2.3 32.1 0.7
O A:HOH733 2.4 29.1 0.7
MN3 A:OEX601 2.7 31.1 0.7
MN3 A:OEY602 2.7 38.4 0.3
CG A:ASP170 2.9 36.5 0.3
CD A:GLU333 2.9 35.0 0.7
CD A:GLU333 3.0 37.2 0.3
CG A:ASP170 3.0 32.1 0.7
OE1 A:GLU333 3.2 38.0 0.3
OE1 A:GLU333 3.2 33.1 0.7
OD2 A:ASP170 3.2 36.9 0.3
OD2 A:ASP170 3.4 35.1 0.7
O A:HOH704 3.6 33.8 1.0
O A:HOH797 3.6 37.4 0.3
O2 A:OEY602 3.6 35.5 0.3
O2 A:OEX601 3.7 32.3 0.7
O A:HOH797 3.7 33.0 0.7
CA1 A:OEY602 3.9 40.0 0.3
CA1 A:OEX601 4.0 32.8 0.7
OD1 A:ASP61 4.1 32.5 0.3
OD1 A:ASP61 4.1 32.2 0.7
O6 A:OEY602 4.1 38.9 0.3
O A:HOH762 4.1 27.8 1.0
O A:SER169 4.2 31.0 0.7
CB A:ASP170 4.2 35.3 0.3
OE2 C:GLU354 4.3 35.0 0.7
CB A:ASP170 4.3 29.8 0.7
CG A:GLU333 4.3 32.0 0.7
O A:SER169 4.3 36.4 0.3
NH2 C:ARG357 4.3 38.7 0.3
CG A:GLU333 4.4 34.1 0.3
NH2 C:ARG357 4.4 30.6 0.7
O A:HOH780 4.4 35.9 1.0
O3 A:OEX601 4.4 36.5 0.7
CA A:ASP170 4.4 29.5 0.7
CA A:ASP170 4.4 36.3 0.3
O3 A:OEY602 4.5 38.9 0.3
OE2 C:GLU354 4.5 42.1 0.3
O C:HOH602 4.5 38.0 0.7
OG A:SER169 4.7 32.1 0.7
C A:SER169 4.7 29.6 0.7
N A:ASP170 4.8 30.5 0.7
C A:SER169 4.8 37.6 0.3
N A:ASP170 4.9 39.1 0.3

Manganese binding site 9 out of 16 in 8f4k

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Manganese binding site 9 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:31.4
occ:0.65
 MN1 a:OEX601 0.0 31.4 0.7
MN1 a:OEY602 0.0 37.7 0.3
OE2 a:GLU189 1.7 32.4 0.7
O6 a:OEY602 1.8 43.5 0.3
O3 a:OEY602 1.9 38.1 0.3
O3 a:OEX601 1.9 33.5 0.7
O1 a:OEY602 1.9 36.9 0.3
O1 a:OEX601 2.0 34.3 0.7
OD2 a:ASP342 2.0 37.5 0.3
OE2 a:GLU189 2.1 38.6 0.3
NE2 a:HIS332 2.2 33.5 0.7
NE2 a:HIS332 2.3 39.2 0.3
OD2 a:ASP342 2.3 35.4 0.7
O5 a:OEX601 2.7 36.8 0.7
MN2 a:OEY602 2.8 35.3 0.3
CD a:GLU189 2.8 29.4 0.7
MN2 a:OEX601 2.8 32.3 0.7
O5 a:OEY602 2.9 39.4 0.3
CG a:ASP342 3.0 41.7 0.3
CD a:GLU189 3.0 39.6 0.3
CE1 a:HIS332 3.1 31.7 0.7
CD2 a:HIS332 3.1 38.9 0.3
CG a:ASP342 3.2 36.8 0.7
CD2 a:HIS332 3.2 31.5 0.7
OD1 a:ASP342 3.3 37.6 0.3
MN3 a:OEX601 3.3 31.7 0.7
OE1 a:GLU189 3.3 29.5 0.7
CE1 a:HIS332 3.3 39.4 0.3
MN3 a:OEY602 3.3 38.7 0.3
CA1 a:OEY602 3.3 40.5 0.3
OD1 a:ASP342 3.4 33.8 0.7
OE1 a:GLU189 3.4 40.8 0.3
CA1 a:OEX601 3.4 36.5 0.7
O2 a:OEX601 3.4 29.9 0.7
O2 a:OEY602 3.4 36.2 0.3
NE2 a:HIS337 3.9 37.0 0.3
CG a:GLU189 3.9 34.1 0.7
OE1 a:GLU333 4.0 32.3 0.7
NE2 a:HIS337 4.0 32.1 0.7
O a:HOH703 4.0 38.0 1.0
OE1 a:GLU333 4.2 35.9 0.3
ND1 a:HIS332 4.2 34.3 0.7
OXT a:ALA344 4.3 34.2 0.3
CG a:GLU189 4.3 41.1 0.3
CB a:ASP342 4.3 40.2 0.3
OE1 c:GLU354 4.3 37.1 0.3
CG a:HIS332 4.3 29.6 0.7
CG a:HIS332 4.3 38.1 0.3
OXT a:ALA344 4.3 33.1 0.7
ND1 a:HIS332 4.4 40.2 0.3
CG1 a:VAL185 4.4 31.8 0.7
CE1 a:HIS337 4.5 39.2 0.3
CB a:ASP342 4.5 37.1 0.7
OE1 c:GLU354 4.5 33.8 0.7
CG1 a:VAL185 4.6 36.0 0.3
CD a:GLU333 4.6 33.4 0.7
OE2 c:GLU354 4.6 34.9 0.7
OE2 c:GLU354 4.7 38.1 0.3
O a:HOH786 4.7 37.6 0.3
O a:ALA344 4.7 40.6 0.3
O a:HOH786 4.8 33.2 0.7
O a:ALA344 4.8 33.7 0.7
CE1 a:HIS337 4.8 33.6 0.7
C a:ALA344 4.8 39.0 0.3
CD2 a:HIS337 4.9 34.7 0.7
CD c:GLU354 4.9 39.4 0.3
OE2 a:GLU333 4.9 32.9 0.7
CD a:GLU333 4.9 36.8 0.3
CD2 a:HIS337 4.9 35.7 0.3
CD c:GLU354 4.9 34.4 0.7
C a:ALA344 5.0 36.5 0.7
MN4 a:OEX601 5.0 31.0 0.7

Manganese binding site 10 out of 16 in 8f4k

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Manganese binding site 10 out of 16 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:32.3
occ:0.65
 MN2 a:OEX601 0.0 32.3 0.7
MN2 a:OEY602 0.1 35.3 0.3
O1 a:OEY602 1.8 36.9 0.3
O1 a:OEX601 1.8 34.3 0.7
OXT a:ALA344 1.9 34.2 0.3
O2 a:OEX601 1.9 29.9 0.7
O3 a:OEX601 1.9 33.5 0.7
O2 a:OEY602 1.9 36.2 0.3
O3 a:OEY602 1.9 38.1 0.3
OE1 c:GLU354 2.0 37.1 0.3
OE1 c:GLU354 2.0 33.8 0.7
OD1 a:ASP342 2.0 37.6 0.3
OXT a:ALA344 2.0 33.1 0.7
OD1 a:ASP342 2.2 33.8 0.7
MN1 a:OEX601 2.8 31.4 0.7
MN1 a:OEY602 2.8 37.7 0.3
CD c:GLU354 2.8 34.4 0.7
MN3 a:OEX601 2.8 31.7 0.7
CG a:ASP342 2.9 41.7 0.3
C a:ALA344 2.9 39.0 0.3
MN3 a:OEY602 2.9 38.7 0.3
CD c:GLU354 3.0 39.4 0.3
C a:ALA344 3.0 36.5 0.7
OE2 c:GLU354 3.0 34.9 0.7
CG a:ASP342 3.1 36.8 0.7
OD2 a:ASP342 3.1 37.5 0.3
O a:ALA344 3.3 40.6 0.3
O a:ALA344 3.3 33.7 0.7
OD2 a:ASP342 3.3 35.4 0.7
OE2 c:GLU354 3.3 38.1 0.3
CA1 a:OEY602 3.4 40.5 0.3
CA1 a:OEX601 3.4 36.5 0.7
O5 a:OEX601 3.7 36.8 0.7
NE2 a:HIS337 3.8 37.0 0.3
O5 a:OEY602 3.8 39.4 0.3
O c:HOH684 3.8 38.1 1.0
O6 a:OEY602 3.8 43.5 0.3
O a:HOH703 4.1 38.0 1.0
NE2 a:HIS337 4.1 32.1 0.7
OE2 a:GLU189 4.2 38.6 0.3
OE2 a:GLU189 4.2 32.4 0.7
CA a:ALA344 4.2 37.4 0.3
CG c:GLU354 4.2 34.4 0.7
CD2 a:HIS337 4.2 35.7 0.3
N a:ALA344 4.3 37.5 0.3
CB a:ASP342 4.3 40.2 0.3
CA a:ALA344 4.3 34.7 0.7
CG c:GLU354 4.3 36.2 0.3
CD2 a:HIS337 4.4 34.7 0.7
OE1 a:GLU333 4.4 32.3 0.7
N a:ALA344 4.4 37.2 0.7
CB a:ASP342 4.5 37.1 0.7
O4 a:OEX601 4.5 33.2 0.7
C a:ASP342 4.6 41.9 0.3
NE2 a:HIS332 4.6 33.5 0.7
O a:ASP342 4.6 37.8 0.3
OE1 a:GLU333 4.6 35.9 0.3
CA a:ASP342 4.6 38.5 0.3
O4 a:OEY602 4.7 37.1 0.3
NE2 a:HIS332 4.7 39.2 0.3
CD a:GLU189 4.7 29.4 0.7
CB c:GLU354 4.8 36.3 0.3
OD2 a:ASP170 4.8 37.3 0.7
OE1 a:GLU189 4.8 29.5 0.7
OE1 a:GLU189 4.8 40.8 0.3
NH2 c:ARG357 4.8 33.6 0.7
NH1 c:ARG357 4.8 34.5 0.7
NH1 c:ARG357 4.8 33.7 0.3
CB c:GLU354 4.8 32.6 0.7
C a:ASP342 4.8 36.9 0.7
CA a:ASP342 4.8 36.4 0.7
NH2 c:ARG357 4.9 37.3 0.3
OD2 a:ASP170 4.9 37.2 0.3
CD a:GLU189 4.9 39.6 0.3
CE1 a:HIS337 5.0 39.2 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 11:50:24 2024

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