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Manganese in PDB 4tnj: Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution, PDB code: 4tnj was solved by J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.Brewster, C.A.Stan, C.Gloeckner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.-C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.97 / 4.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.298, 228.713, 307.976, 90.00, 90.00, 90.00
R / Rfree (%) 27.6 / 28.4

Other elements in 4tnj:

The structure of Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution (pdb code 4tnj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution, PDB code: 4tnj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4tnj

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Manganese binding site 1 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.8
occ:1.00
 MN1 A:OEX412 0.0 0.8 1.0
O3 A:OEX412 1.9 0.7 1.0
O1 A:OEX412 1.9 0.9 1.0
O5 A:OEX412 1.9 0.2 1.0
OE2 A:GLU189 2.5 0.1 1.0
NE2 A:HIS332 2.5 0.1 1.0
MN3 A:OEX412 2.7 0.2 1.0
MN2 A:OEX412 2.7 0.8 1.0
OD2 A:ASP342 2.8 0.5 1.0
CD2 A:HIS332 3.2 0.3 1.0
CD A:GLU189 3.3 0.2 1.0
CA1 A:OEX412 3.4 0.7 1.0
OE1 A:GLU189 3.4 0.7 1.0
O2 A:OEX412 3.5 1.0 1.0
CE1 A:HIS332 3.7 0.1 1.0
CG A:ASP342 3.8 0.1 1.0
MN4 A:OEX412 3.8 0.2 1.0
OD1 A:ASP342 4.0 0.7 1.0
NE2 A:HIS337 4.2 0.9 1.0
O4 A:OEX412 4.2 0.1 1.0
OE1 A:GLU333 4.4 0.5 1.0
CG A:HIS332 4.4 0.8 1.0
OE2 C:GLU354 4.6 0.5 1.0
CG1 A:VAL185 4.6 0.9 1.0
OE1 C:GLU354 4.6 0.1 1.0
CE1 A:HIS337 4.6 0.1 1.0
CG A:GLU189 4.6 0.2 1.0
CD A:GLU333 4.7 0.9 1.0
ND1 A:HIS332 4.7 0.1 1.0
CG A:GLU333 4.8 0.8 1.0

Manganese binding site 2 out of 8 in 4tnj

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Manganese binding site 2 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.8
occ:1.00
 MN2 A:OEX412 0.0 0.8 1.0
O1 A:OEX412 1.9 0.9 1.0
O3 A:OEX412 1.9 0.7 1.0
O2 A:OEX412 2.0 1.0 1.0
OXT A:ALA344 2.6 0.4 1.0
OD1 A:ASP342 2.6 0.7 1.0
MN1 A:OEX412 2.7 0.8 1.0
MN3 A:OEX412 2.8 0.2 1.0
OE1 C:GLU354 2.8 0.1 1.0
C A:ALA344 3.0 0.6 1.0
O A:ALA344 3.0 0.5 1.0
OD2 A:ASP342 3.2 0.5 1.0
CG A:ASP342 3.3 0.1 1.0
CA1 A:OEX412 3.3 0.7 1.0
OE2 C:GLU354 3.3 0.5 1.0
CD C:GLU354 3.4 0.5 1.0
O5 A:OEX412 3.5 0.2 1.0
CA A:ALA344 4.2 0.1 1.0
N A:ALA344 4.2 0.3 1.0
OE2 A:GLU189 4.3 0.1 1.0
O4 A:OEX412 4.3 0.1 1.0
NE2 A:HIS337 4.3 0.9 1.0
OE1 A:GLU189 4.7 0.7 1.0
CB A:ASP342 4.7 0.8 1.0
OD1 A:ASP170 4.8 0.5 1.0
CG C:GLU354 4.8 0.2 1.0
OE1 A:GLU333 4.8 0.5 1.0
CD A:GLU189 4.9 0.2 1.0
NE2 A:HIS332 4.9 0.1 1.0
CB A:ALA344 4.9 0.8 1.0

Manganese binding site 3 out of 8 in 4tnj

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Manganese binding site 3 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.2
occ:1.00
 MN3 A:OEX412 0.0 0.2 1.0
O5 A:OEX412 1.9 0.2 1.0
O4 A:OEX412 1.9 0.1 1.0
O2 A:OEX412 1.9 1.0 1.0
O3 A:OEX412 1.9 0.7 1.0
OE1 A:GLU333 2.5 0.5 1.0
MN4 A:OEX412 2.7 0.2 1.0
MN1 A:OEX412 2.7 0.8 1.0
OE2 C:GLU354 2.7 0.5 1.0
MN2 A:OEX412 2.8 0.8 1.0
O1 A:OEX412 3.0 0.9 1.0
CD A:GLU333 3.1 0.9 1.0
CA1 A:OEX412 3.5 0.7 1.0
OE2 A:GLU333 3.5 0.2 1.0
CD C:GLU354 3.7 0.5 1.0
OE1 C:GLU354 3.9 0.1 1.0
OD2 A:ASP170 4.0 0.5 1.0
OD1 A:ASP170 4.0 0.5 1.0
CG A:GLU333 4.1 0.8 1.0
OXT A:ALA344 4.3 0.4 1.0
CG A:ASP170 4.5 0.3 1.0
NE2 A:HIS332 4.5 0.1 1.0
CD2 A:HIS332 4.6 0.3 1.0
NH2 C:ARG357 4.7 0.6 1.0
NE2 A:HIS337 4.8 0.9 1.0
OD2 A:ASP342 4.8 0.5 1.0
O A:ALA344 4.9 0.5 1.0
CE1 A:HIS337 4.9 0.1 1.0
CB A:GLU333 4.9 0.2 1.0
OD1 A:ASP342 5.0 0.7 1.0

Manganese binding site 4 out of 8 in 4tnj

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Manganese binding site 4 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.2
occ:1.00
 MN4 A:OEX412 0.0 0.2 1.0
O4 A:OEX412 1.9 0.1 1.0
O5 A:OEX412 1.9 0.2 1.0
MN3 A:OEX412 2.7 0.2 1.0
OE2 A:GLU333 2.7 0.2 1.0
OD2 A:ASP170 2.7 0.5 1.0
CD A:GLU333 3.2 0.9 1.0
OE1 A:GLU333 3.6 0.5 1.0
CG A:ASP170 3.8 0.3 1.0
MN1 A:OEX412 3.8 0.8 1.0
CA1 A:OEX412 3.8 0.7 1.0
O2 A:OEX412 3.9 1.0 1.0
CG A:GLU333 4.0 0.8 1.0
O3 A:OEX412 4.2 0.7 1.0
OD1 A:ASP170 4.2 0.5 1.0
CG1 A:VAL185 4.3 0.9 1.0
O1 A:OEX412 4.3 0.9 1.0
CD2 A:HIS332 4.6 0.3 1.0

Manganese binding site 5 out of 8 in 4tnj

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Manganese binding site 5 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn414

b:0.5
occ:1.00
 MN1 a:OEX414 0.0 0.5 1.0
O3 a:OEX414 1.9 0.8 1.0
O1 a:OEX414 1.9 0.8 1.0
O5 a:OEX414 1.9 0.8 1.0
OE2 a:GLU189 2.5 0.3 1.0
NE2 a:HIS332 2.5 0.0 1.0
MN3 a:OEX414 2.7 0.2 1.0
MN2 a:OEX414 2.7 0.0 1.0
OD2 a:ASP342 2.8 0.6 1.0
CD2 a:HIS332 3.1 0.5 1.0
CD a:GLU189 3.2 0.6 1.0
OE1 a:GLU189 3.3 0.0 1.0
CA1 a:OEX414 3.4 0.8 1.0
O2 a:OEX414 3.5 0.0 1.0
CE1 a:HIS332 3.7 0.6 1.0
CG a:ASP342 3.7 0.2 1.0
MN4 a:OEX414 3.8 0.5 1.0
OD1 a:ASP342 3.9 0.1 1.0
NE2 a:HIS337 4.1 0.5 1.0
O4 a:OEX414 4.2 0.4 1.0
CG a:HIS332 4.4 0.6 1.0
OE1 a:GLU333 4.4 0.9 1.0
OE1 c:GLU354 4.5 0.1 1.0
OE2 c:GLU354 4.5 1.0 1.0
CG1 a:VAL185 4.6 0.9 1.0
CE1 a:HIS337 4.6 0.7 1.0
CG a:GLU189 4.6 0.4 1.0
ND1 a:HIS332 4.7 0.7 1.0
CD a:GLU333 4.7 0.2 1.0
CG a:GLU333 4.8 1.0 1.0
CD c:GLU354 5.0 0.5 1.0

Manganese binding site 6 out of 8 in 4tnj

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Manganese binding site 6 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn414

b:0.0
occ:1.00
 MN2 a:OEX414 0.0 0.0 1.0
O1 a:OEX414 1.9 0.8 1.0
O3 a:OEX414 1.9 0.8 1.0
O2 a:OEX414 2.0 0.0 1.0
OXT a:ALA344 2.6 1.0 1.0
OD1 a:ASP342 2.6 0.1 1.0
MN1 a:OEX414 2.7 0.5 1.0
OE1 c:GLU354 2.7 0.1 1.0
MN3 a:OEX414 2.8 0.2 1.0
C a:ALA344 3.0 0.9 1.0
O a:ALA344 3.1 0.2 1.0
OD2 a:ASP342 3.3 0.6 1.0
CG a:ASP342 3.3 0.2 1.0
OE2 c:GLU354 3.3 1.0 1.0
CA1 a:OEX414 3.3 0.8 1.0
CD c:GLU354 3.4 0.5 1.0
O5 a:OEX414 3.5 0.8 1.0
CA a:ALA344 4.2 0.0 1.0
N a:ALA344 4.2 0.1 1.0
O4 a:OEX414 4.3 0.4 1.0
OE2 a:GLU189 4.3 0.3 1.0
NE2 a:HIS337 4.4 0.5 1.0
OE1 a:GLU189 4.6 0.0 1.0
OD1 a:ASP170 4.7 0.4 1.0
CB a:ASP342 4.7 0.8 1.0
CG c:GLU354 4.8 0.9 1.0
OE1 a:GLU333 4.9 0.9 1.0
CD a:GLU189 4.9 0.6 1.0
CB a:ALA344 4.9 0.7 1.0
NE2 a:HIS332 4.9 0.0 1.0

Manganese binding site 7 out of 8 in 4tnj

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Manganese binding site 7 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn414

b:0.2
occ:1.00
 MN3 a:OEX414 0.0 0.2 1.0
O5 a:OEX414 1.9 0.8 1.0
O4 a:OEX414 1.9 0.4 1.0
O2 a:OEX414 1.9 0.0 1.0
O3 a:OEX414 1.9 0.8 1.0
OE1 a:GLU333 2.5 0.9 1.0
MN4 a:OEX414 2.6 0.5 1.0
OE2 c:GLU354 2.7 1.0 1.0
MN1 a:OEX414 2.7 0.5 1.0
MN2 a:OEX414 2.8 0.0 1.0
O1 a:OEX414 3.0 0.8 1.0
CD a:GLU333 3.1 0.2 1.0
CA1 a:OEX414 3.5 0.8 1.0
OE2 a:GLU333 3.6 0.5 1.0
CD c:GLU354 3.6 0.5 1.0
OE1 c:GLU354 3.9 0.1 1.0
OD2 a:ASP170 4.0 0.9 1.0
CG a:GLU333 4.1 1.0 1.0
OD1 a:ASP170 4.1 0.4 1.0
OXT a:ALA344 4.3 1.0 1.0
CG a:ASP170 4.5 0.9 1.0
NE2 a:HIS332 4.6 0.0 1.0
NH2 c:ARG357 4.6 0.8 1.0
CD2 a:HIS332 4.6 0.5 1.0
NE2 a:HIS337 4.7 0.5 1.0
OD2 a:ASP342 4.8 0.6 1.0
O a:ALA344 4.9 0.2 1.0
CB a:GLU333 4.9 0.1 1.0
CE1 a:HIS337 4.9 0.7 1.0
OD1 a:ASP342 5.0 0.1 1.0
CG c:GLU354 5.0 0.9 1.0

Manganese binding site 8 out of 8 in 4tnj

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Manganese binding site 8 out of 8 in the Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 4.5 A 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 500 Ms After the 2ND Illumination (2F) at 4.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn414

b:0.5
occ:1.00
 MN4 a:OEX414 0.0 0.5 1.0
O4 a:OEX414 1.9 0.4 1.0
O5 a:OEX414 1.9 0.8 1.0
MN3 a:OEX414 2.6 0.2 1.0
OD2 a:ASP170 2.7 0.9 1.0
OE2 a:GLU333 2.8 0.5 1.0
CD a:GLU333 3.2 0.2 1.0
OE1 a:GLU333 3.6 0.9 1.0
CG a:ASP170 3.8 0.9 1.0
MN1 a:OEX414 3.8 0.5 1.0
CA1 a:OEX414 3.8 0.8 1.0
O2 a:OEX414 3.9 0.0 1.0
CG a:GLU333 4.0 1.0 1.0
O3 a:OEX414 4.2 0.8 1.0
OD1 a:ASP170 4.2 0.4 1.0
O1 a:OEX414 4.3 0.8 1.0
CG1 a:VAL185 4.3 0.9 1.0
CD2 a:HIS332 4.6 0.5 1.0

Reference:

J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.S.Brewster, C.A.Stan, C.Glockner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra. Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-Ray Diffraction and Spectroscopy. Nat Commun V. 5 4371 2014.
ISSN: ESSN 2041-1723
PubMed: 25006873
DOI: 10.1038/NCOMMS5371
Page generated: Sat Oct 5 21:14:46 2024

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