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Manganese in PDB 5tis: Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

Enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

All present enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.V.Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.-C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Braeuer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Watermann, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.870, 223.140, 310.710, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 5tis:

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex (pdb code 5tis). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5tis

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Manganese binding site 1 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:33.4
occ:1.00
 MN1 A:OEX601 0.0 33.4 1.0
OE2 A:GLU189 1.7 40.3 1.0
O3 A:OEX601 2.0 34.4 0.8
O1 A:OEX601 2.0 32.1 1.0
OD2 A:ASP342 2.1 32.4 1.0
NE2 A:HIS332 2.2 37.7 1.0
MN2 A:OEX601 2.7 35.1 1.0
O5 A:OEX601 2.8 39.1 1.0
CD A:GLU189 2.8 35.6 1.0
CD2 A:HIS332 3.1 31.8 1.0
CG A:ASP342 3.1 35.3 1.0
CE1 A:HIS332 3.2 31.6 1.0
MN3 A:OEX601 3.3 34.4 1.0
OE1 A:GLU189 3.4 41.5 1.0
OD1 A:ASP342 3.4 34.5 1.0
CA1 A:OEX601 3.5 41.3 1.0
O2 A:OEX601 3.6 32.2 1.0
OE1 A:GLU333 4.0 38.4 1.0
CG A:GLU189 4.1 38.5 1.0
NE2 A:HIS337 4.1 36.7 1.0
OXT A:ALA344 4.1 34.6 1.0
CG A:HIS332 4.2 36.4 1.0
ND1 A:HIS332 4.3 30.9 1.0
CB A:ASP342 4.5 33.8 1.0
CG1 A:VAL185 4.5 35.1 1.0
OE1 C:GLU354 4.5 35.7 1.0
O A:HOH780 4.5 47.0 1.0
OE2 C:GLU354 4.6 38.2 1.0
CE1 A:HIS337 4.7 36.5 1.0
CD A:GLU333 4.7 37.2 1.0
O A:HOH772 4.8 29.4 1.0
C A:ALA344 4.8 41.2 1.0
O A:ALA344 4.8 34.8 1.0
O4 A:OEX601 4.9 36.2 1.0
MN4 A:OEX601 4.9 40.5 1.0
CD C:GLU354 5.0 33.6 1.0
OE2 A:GLU333 5.0 38.0 1.0

Manganese binding site 2 out of 8 in 5tis

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Manganese binding site 2 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:35.1
occ:1.00
 MN2 A:OEX601 0.0 35.1 1.0
O1 A:OEX601 1.8 32.1 1.0
O2 A:OEX601 1.8 32.2 1.0
OXT A:ALA344 1.9 34.6 1.0
O3 A:OEX601 2.0 34.4 0.8
OD1 A:ASP342 2.1 34.5 1.0
OE1 C:GLU354 2.1 35.7 1.0
MN3 A:OEX601 2.7 34.4 1.0
MN1 A:OEX601 2.7 33.4 1.0
CD C:GLU354 2.9 33.6 1.0
CG A:ASP342 2.9 35.3 1.0
C A:ALA344 2.9 41.2 1.0
OE2 C:GLU354 3.0 38.2 1.0
OD2 A:ASP342 3.0 32.4 1.0
O A:ALA344 3.4 34.8 1.0
CA1 A:OEX601 3.4 41.3 1.0
O5 A:OEX601 3.7 39.1 1.0
NE2 A:HIS337 3.8 36.7 1.0
O A:HOH771 4.0 37.0 1.0
OE2 A:GLU189 4.0 40.3 1.0
O4 A:OEX601 4.1 36.2 1.0
CA A:ALA344 4.2 32.4 1.0
OE1 A:GLU333 4.3 38.4 1.0
N A:ALA344 4.3 40.2 1.0
CG C:GLU354 4.4 32.9 1.0
CD2 A:HIS337 4.4 31.5 1.0
CB A:ASP342 4.4 33.8 1.0
NE2 A:HIS332 4.5 37.7 1.0
NH2 C:ARG357 4.8 33.0 1.0
CA A:ASP342 4.8 31.9 1.0
CB C:GLU354 4.9 36.0 1.0
CD A:GLU189 4.9 35.6 1.0
O A:HOH780 4.9 47.0 1.0
C A:ASP342 4.9 40.0 1.0
OD1 A:ASP170 5.0 39.1 1.0
CE1 A:HIS337 5.0 36.5 1.0
OE1 A:GLU189 5.0 41.5 1.0

Manganese binding site 3 out of 8 in 5tis

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Manganese binding site 3 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:34.4
occ:1.00
 MN3 A:OEX601 0.0 34.4 1.0
O4 A:OEX601 1.7 36.2 1.0
O2 A:OEX601 1.8 32.2 1.0
OE2 C:GLU354 2.0 38.2 1.0
O5 A:OEX601 2.1 39.1 1.0
OE1 A:GLU333 2.2 38.4 1.0
O3 A:OEX601 2.2 34.4 0.8
MN4 A:OEX601 2.6 40.5 1.0
MN2 A:OEX601 2.7 35.1 1.0
CD A:GLU333 2.9 37.2 1.0
OE2 A:GLU333 3.0 38.0 1.0
CD C:GLU354 3.0 33.6 1.0
MN1 A:OEX601 3.3 33.4 1.0
OE1 C:GLU354 3.4 35.7 1.0
CA1 A:OEX601 3.5 41.3 1.0
O1 A:OEX601 3.5 32.1 1.0
OD2 A:ASP170 3.9 35.6 1.0
O A:HOH710 4.0 36.1 1.0
NH2 C:ARG357 4.1 33.0 1.0
OXT A:ALA344 4.1 34.6 1.0
OD1 A:ASP170 4.2 39.1 1.0
NE2 A:HIS337 4.2 36.7 1.0
O A:HOH738 4.3 37.9 1.0
CG C:GLU354 4.4 32.9 1.0
NE2 A:HIS332 4.4 37.7 1.0
CG A:GLU333 4.4 33.4 1.0
O A:HOH723 4.4 36.2 1.0
CG A:ASP170 4.5 35.1 1.0
CD2 A:HIS332 4.5 31.8 1.0
OD1 A:ASP342 4.6 34.5 1.0
O A:ALA344 4.6 34.8 1.0
OD2 A:ASP342 4.7 32.4 1.0
OE2 A:GLU189 4.8 40.3 1.0
C A:ALA344 4.9 41.2 1.0
CE1 A:HIS337 4.9 36.5 1.0
O A:HOH772 4.9 29.4 1.0
CB A:GLU333 4.9 33.7 1.0

Manganese binding site 4 out of 8 in 5tis

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Manganese binding site 4 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:40.5
occ:1.00
 MN4 A:OEX601 0.0 40.5 1.0
O4 A:OEX601 1.8 36.2 1.0
OD2 A:ASP170 2.0 35.6 1.0
OE2 A:GLU333 2.0 38.0 1.0
O A:HOH738 2.1 37.9 1.0
O A:HOH723 2.2 36.2 1.0
O5 A:OEX601 2.3 39.1 1.0
MN3 A:OEX601 2.6 34.4 1.0
CD A:GLU333 3.0 37.2 1.0
CG A:ASP170 3.1 35.1 1.0
OE1 A:GLU333 3.4 38.4 1.0
O A:HOH710 3.5 36.1 1.0
OD1 A:ASP170 3.6 39.1 1.0
O2 A:OEX601 3.7 32.2 1.0
O A:HOH772 3.9 29.4 1.0
CA1 A:OEX601 3.9 41.3 1.0
OD1 A:ASP61 4.2 37.4 1.0
OE2 C:GLU354 4.2 38.2 1.0
CB A:ASP170 4.3 33.0 1.0
CG A:GLU333 4.4 33.4 1.0
O A:HOH734 4.4 35.2 1.0
NH2 C:ARG357 4.5 33.0 1.0
CA A:ASP170 4.5 37.1 1.0
O A:HOH755 4.5 45.5 1.0
O A:SER169 4.5 31.8 1.0
O3 A:OEX601 4.5 34.4 0.8
N A:ASP170 4.9 32.2 1.0
C A:SER169 4.9 32.0 1.0
O A:HOH730 4.9 40.8 1.0
MN1 A:OEX601 4.9 33.4 1.0
OG A:SER169 4.9 36.6 1.0

Manganese binding site 5 out of 8 in 5tis

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Manganese binding site 5 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:32.4
occ:1.00
 MN1 a:OEX601 0.0 32.4 1.0
OE2 a:GLU189 1.8 37.3 1.0
O3 a:OEX601 1.9 33.5 1.0
O1 a:OEX601 1.9 31.2 1.0
OD2 a:ASP342 2.1 31.1 1.0
NE2 a:HIS332 2.2 30.0 1.0
O5 a:OEX601 2.6 33.6 1.0
MN2 a:OEX601 2.7 32.6 1.0
CD a:GLU189 3.0 35.4 1.0
CG a:ASP342 3.1 35.9 1.0
CD2 a:HIS332 3.1 36.0 1.0
CE1 a:HIS332 3.2 28.9 1.0
MN3 a:OEX601 3.2 32.9 1.0
OD1 a:ASP342 3.3 32.9 1.0
CA1 a:OEX601 3.4 42.4 1.0
O2 a:OEX601 3.6 28.8 1.0
OE1 a:GLU189 3.6 38.8 1.0
NE2 a:HIS337 3.8 32.5 1.0
OE1 a:GLU333 4.0 33.9 1.0
CG a:GLU189 4.1 41.0 1.0
OXT a:ALA344 4.2 32.4 1.0
O a:HOH739 4.2 40.0 1.0
ND1 a:HIS332 4.3 34.8 1.0
CG a:HIS332 4.3 27.0 1.0
CE1 a:HIS337 4.4 34.2 1.0
CB a:ASP342 4.4 34.0 1.0
OE2 c:GLU354 4.4 32.6 1.0
OE1 c:GLU354 4.5 38.1 1.0
O a:ALA344 4.6 38.1 1.0
CG1 a:VAL185 4.7 33.0 1.0
CD a:GLU333 4.7 28.0 1.0
C a:ALA344 4.8 34.7 1.0
O a:HOH779 4.9 33.5 1.0
CD c:GLU354 4.9 39.0 1.0
MN4 a:OEX601 4.9 35.8 1.0
OE2 a:GLU333 4.9 36.0 1.0
CD2 a:HIS337 5.0 32.2 1.0

Manganese binding site 6 out of 8 in 5tis

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Manganese binding site 6 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:32.6
occ:1.00
 MN2 a:OEX601 0.0 32.6 1.0
OXT a:ALA344 1.8 32.4 1.0
O1 a:OEX601 1.8 31.2 1.0
O2 a:OEX601 2.0 28.8 1.0
O3 a:OEX601 2.1 33.5 1.0
OE1 c:GLU354 2.1 38.1 1.0
OD1 a:ASP342 2.2 32.9 1.0
MN3 a:OEX601 2.7 32.9 1.0
MN1 a:OEX601 2.7 32.4 1.0
CD c:GLU354 2.8 39.0 1.0
C a:ALA344 2.8 34.7 1.0
OE2 c:GLU354 2.9 32.6 1.0
CG a:ASP342 3.0 35.9 1.0
O a:ALA344 3.1 38.1 1.0
OD2 a:ASP342 3.2 31.1 1.0
CA1 a:OEX601 3.4 42.4 1.0
O5 a:OEX601 3.6 33.6 1.0
NE2 a:HIS337 3.7 32.5 1.0
OE2 a:GLU189 4.0 37.3 1.0
CA a:ALA344 4.1 33.3 1.0
CG c:GLU354 4.1 41.4 1.0
N a:ALA344 4.2 35.6 1.0
OE1 a:GLU333 4.3 33.9 1.0
O a:HOH739 4.4 40.0 1.0
CD2 a:HIS337 4.4 32.2 1.0
CB a:ASP342 4.5 34.0 1.0
O4 a:OEX601 4.5 35.4 1.0
NE2 a:HIS332 4.6 30.0 1.0
NH2 c:ARG357 4.7 33.9 1.0
CE1 a:HIS337 4.8 34.2 1.0
CD a:GLU189 4.9 35.4 1.0
C a:ASP342 4.9 31.8 1.0
CA a:ASP342 4.9 33.9 1.0
OD1 a:ASP170 4.9 37.4 1.0
O a:ASP342 4.9 35.6 1.0
NH1 c:ARG357 5.0 28.8 1.0
CB c:GLU354 5.0 32.8 1.0

Manganese binding site 7 out of 8 in 5tis

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Manganese binding site 7 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:32.9
occ:1.00
 MN3 a:OEX601 0.0 32.9 1.0
O2 a:OEX601 1.8 28.8 1.0
O3 a:OEX601 2.0 33.5 1.0
OE1 a:GLU333 2.1 33.9 1.0
OE2 c:GLU354 2.1 32.6 1.0
O4 a:OEX601 2.1 35.4 1.0
O5 a:OEX601 2.1 33.6 1.0
MN2 a:OEX601 2.7 32.6 1.0
MN4 a:OEX601 2.8 35.8 1.0
CD a:GLU333 2.9 28.0 1.0
OE2 a:GLU333 3.0 36.0 1.0
CD c:GLU354 3.1 39.0 1.0
MN1 a:OEX601 3.2 32.4 1.0
CA1 a:OEX601 3.4 42.4 1.0
OE1 c:GLU354 3.5 38.1 1.0
O1 a:OEX601 3.5 31.2 1.0
OD2 a:ASP170 4.0 34.3 1.0
NH2 c:ARG357 4.0 33.9 1.0
OXT a:ALA344 4.1 32.4 1.0
NE2 a:HIS337 4.2 32.5 1.0
OD1 a:ASP170 4.2 37.4 1.0
CG c:GLU354 4.3 41.4 1.0
NE2 a:HIS332 4.3 30.0 1.0
CG a:GLU333 4.3 28.3 1.0
O a:HOH734 4.3 37.8 1.0
CD2 a:HIS332 4.5 36.0 1.0
CG a:ASP170 4.6 36.2 1.0
O a:ALA344 4.6 38.1 1.0
OD1 a:ASP342 4.6 32.9 1.0
O a:HOH720 4.6 30.0 1.0
O a:HOH772 4.6 37.6 1.0
OE2 a:GLU189 4.7 37.3 1.0
OD2 a:ASP342 4.7 31.1 1.0
CE1 a:HIS337 4.7 34.2 1.0
CB a:GLU333 4.8 23.1 1.0
C a:ALA344 4.8 34.7 1.0
O a:HOH779 5.0 33.5 1.0

Manganese binding site 8 out of 8 in 5tis

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Manganese binding site 8 out of 8 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:35.8
occ:1.00
 MN4 a:OEX601 0.0 35.8 1.0
O4 a:OEX601 1.7 35.4 1.0
OE2 a:GLU333 2.0 36.0 1.0
OD2 a:ASP170 2.0 34.3 1.0
O a:HOH772 2.2 37.6 1.0
O a:HOH720 2.3 30.0 1.0
O5 a:OEX601 2.4 33.6 1.0
MN3 a:OEX601 2.8 32.9 1.0
CD a:GLU333 3.0 28.0 1.0
CG a:ASP170 3.1 36.2 1.0
OE1 a:GLU333 3.4 33.9 1.0
O2 a:OEX601 3.6 28.8 1.0
OD1 a:ASP170 3.7 37.4 1.0
O a:HOH779 3.8 33.5 1.0
CA1 a:OEX601 3.8 42.4 1.0
O a:HOH734 4.0 37.8 1.0
OD2 a:ASP61 4.1 30.7 1.0
O a:HOH776 4.3 31.3 0.8
CG a:GLU333 4.3 28.3 1.0
O a:HOH746 4.4 30.1 1.0
CB a:ASP170 4.4 29.8 1.0
O a:SER169 4.4 30.8 1.0
CA a:ASP170 4.5 25.5 1.0
O3 a:OEX601 4.6 33.5 1.0
OE2 c:GLU354 4.6 32.6 1.0
NH2 c:ARG357 4.6 33.9 1.0
O d:HOH529 4.8 29.4 1.0
C a:SER169 4.9 29.4 1.0
MN1 a:OEX601 4.9 32.4 1.0
N a:ASP170 5.0 28.8 1.0

Reference:

I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Brauer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano. Structure of Photosystem II and Substrate Binding at Room Temperature. Nature V. 540 453 2016.
ISSN: ESSN 1476-4687
PubMed: 27871088
DOI: 10.1038/NATURE20161
Page generated: Sun Oct 6 02:56:47 2024

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