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Manganese in PDB 4ixr: Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State

Enzymatic activity of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State

All present enzymatic activity of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State:
1.10.3.9;

Protein crystallography data

The structure of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State, PDB code: 4ixr was solved by J.Kern, R.Alonso-Mori, R.Tran, J.Hattne, R.J.Gildea, N.Echols, C.Gloeckner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, S.Koroidov, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, D.W.Schafer, M.Messerschmidt, M.M.Seibert, J.E.Koglin, D.Sokaras, T.-C.Weng, J.Sellberg, M.J.Latimer, R.W.Grosse-Kunstleve, P.H.Zwart, W.E.White, P.Glatzel, P.D.Adams, M.J.Bogan, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, N.K.Sauter, V.K.Yachandra, U.Bergmann, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.97 / 5.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.976, 227.568, 306.994, 90.00, 90.00, 90.00
R / Rfree (%) 28.5 / 31.3

Other elements in 4ixr:

The structure of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State 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 Fs X-Ray Diffraction of Photosystem II, First Illuminated State (pdb code 4ixr). 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 Fs X-Ray Diffraction of Photosystem II, First Illuminated State, PDB code: 4ixr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ixr

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Manganese binding site 1 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:36.0
occ:1.00
 MN1 A:OEC409 0.0 36.0 1.0
OE2 A:GLU189 1.8 59.5 1.0
NE2 A:HIS332 2.3 54.4 1.0
OD2 A:ASP342 2.6 62.6 1.0
MN2 A:OEC409 2.6 45.6 1.0
CD A:GLU189 2.7 63.5 1.0
CD2 A:HIS332 3.1 57.9 1.0
OE1 A:GLU189 3.2 66.7 1.0
MN3 A:OEC409 3.3 44.6 1.0
CE1 A:HIS332 3.4 61.2 1.0
CA1 A:OEC409 3.4 57.8 1.0
CG A:ASP342 3.5 66.1 1.0
OD1 A:ASP342 3.7 64.5 1.0
OE1 A:GLU333 3.8 56.2 1.0
CG A:GLU189 3.9 60.6 1.0
NE2 A:HIS337 4.2 62.6 1.0
CG A:HIS332 4.3 60.5 1.0
OE2 C:GLU354 4.3 73.6 1.0
ND1 A:HIS332 4.4 59.9 1.0
CG1 A:VAL185 4.5 64.1 1.0
CE1 A:HIS337 4.6 62.7 1.0
CD A:GLU333 4.7 61.3 1.0
OE1 C:GLU354 4.8 66.0 1.0
O A:ALA344 4.8 77.2 1.0
CB A:ASP342 4.9 66.8 1.0
C A:ALA344 4.9 80.8 1.0

Manganese binding site 2 out of 8 in 4ixr

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Manganese binding site 2 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:45.6
occ:1.00
 MN2 A:OEC409 0.0 45.6 1.0
OD1 A:ASP342 2.3 64.5 1.0
C A:ALA344 2.4 80.8 1.0
O A:ALA344 2.6 77.2 1.0
MN1 A:OEC409 2.6 36.0 1.0
MN3 A:OEC409 2.7 44.6 1.0
OE2 C:GLU354 3.0 73.6 1.0
CG A:ASP342 3.1 66.1 1.0
OD2 A:ASP342 3.1 62.6 1.0
CA1 A:OEC409 3.2 57.8 1.0
OE2 A:GLU189 3.3 59.5 1.0
OE1 C:GLU354 3.4 66.0 1.0
CD C:GLU354 3.5 74.9 1.0
CA A:ALA344 3.7 90.7 1.0
N A:ALA344 3.9 86.4 1.0
CD A:GLU189 4.2 63.5 1.0
OE1 A:GLU189 4.2 66.7 1.0
NE2 A:HIS337 4.3 62.6 1.0
OE1 A:GLU333 4.3 56.2 1.0
CB A:ALA344 4.4 92.1 1.0
CB A:ASP342 4.5 66.8 1.0
NE2 A:HIS332 4.6 54.4 1.0
OD1 A:ASP170 4.7 90.2 1.0
CG C:GLU354 5.0 72.5 1.0

Manganese binding site 3 out of 8 in 4ixr

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Manganese binding site 3 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:44.6
occ:1.00
 MN3 A:OEC409 0.0 44.6 1.0
OE1 A:GLU333 2.2 56.2 1.0
OE2 C:GLU354 2.3 73.6 1.0
MN2 A:OEC409 2.7 45.6 1.0
MN4 A:OEC409 3.2 62.1 1.0
CD A:GLU333 3.2 61.3 1.0
MN1 A:OEC409 3.3 36.0 1.0
CA1 A:OEC409 3.3 57.8 1.0
CD C:GLU354 3.5 74.9 1.0
OE2 A:GLU333 3.7 62.2 1.0
OD2 A:ASP170 3.7 80.5 1.0
OD1 A:ASP170 3.8 90.2 1.0
C A:ALA344 4.1 80.8 1.0
O A:ALA344 4.1 77.2 1.0
OE1 C:GLU354 4.1 66.0 1.0
CG A:ASP170 4.2 83.6 1.0
NH2 C:ARG357 4.4 69.1 1.0
CG A:GLU333 4.5 62.1 1.0
NE2 A:HIS332 4.6 54.4 1.0
OE2 A:GLU189 4.7 59.5 1.0
CG C:GLU354 4.7 72.5 1.0
OD1 A:ASP342 4.7 64.5 1.0
CD2 A:HIS332 4.8 57.9 1.0
NE2 A:HIS337 4.9 62.6 1.0
OD2 A:ASP342 4.9 62.6 1.0

Manganese binding site 4 out of 8 in 4ixr

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Manganese binding site 4 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:62.1
occ:1.00
 MN4 A:OEC409 0.0 62.1 1.0
OD2 A:ASP170 2.3 80.5 1.0
OE2 A:GLU333 2.4 62.2 1.0
CD A:GLU333 3.0 61.3 1.0
MN3 A:OEC409 3.2 44.6 1.0
OE1 A:GLU333 3.3 56.2 1.0
CG A:ASP170 3.5 83.6 1.0
OD1 A:ASP170 4.2 90.2 1.0
OD1 A:ASP61 4.3 59.9 1.0
CG A:GLU333 4.3 62.1 1.0
O A:SER169 4.5 65.8 1.0
CA A:ASP170 4.5 64.6 1.0
CA1 A:OEC409 4.6 57.8 1.0
CB A:ASP170 4.7 72.7 1.0

Manganese binding site 5 out of 8 in 4ixr

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Manganese binding site 5 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:36.0
occ:1.00
 MN1 a:OEC411 0.0 36.0 1.0
OE2 a:GLU189 1.8 64.5 1.0
NE2 a:HIS332 2.5 57.9 1.0
OD2 a:ASP342 2.6 51.6 1.0
MN2 a:OEC411 2.6 45.6 1.0
CD a:GLU189 2.7 75.8 1.0
OE1 a:GLU189 3.1 83.0 1.0
CD2 a:HIS332 3.2 58.0 1.0
MN3 a:OEC411 3.3 44.6 1.0
CA1 a:OEC411 3.4 68.3 1.0
CG a:ASP342 3.4 56.7 1.0
OD1 a:ASP342 3.5 57.8 1.0
CE1 a:HIS332 3.6 55.7 1.0
OE1 a:GLU333 3.8 65.9 1.0
CG a:GLU189 4.0 76.2 1.0
NE2 a:HIS337 4.2 76.2 1.0
OE2 c:GLU354 4.4 69.5 1.0
CG a:HIS332 4.5 53.0 1.0
OE1 c:GLU354 4.6 71.3 1.0
ND1 a:HIS332 4.6 50.9 1.0
CG1 a:VAL185 4.6 56.7 1.0
CD a:GLU333 4.7 70.5 1.0
CE1 a:HIS337 4.7 73.3 1.0
O a:ALA344 4.7 83.2 1.0
C a:ALA344 4.9 83.2 1.0
CB a:ASP342 4.9 60.3 1.0
CD c:GLU354 4.9 71.9 1.0

Manganese binding site 6 out of 8 in 4ixr

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Manganese binding site 6 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:45.6
occ:1.00
 MN2 a:OEC411 0.0 45.6 1.0
OD1 a:ASP342 2.3 57.8 1.0
C a:ALA344 2.3 83.2 1.0
O a:ALA344 2.6 83.2 1.0
MN1 a:OEC411 2.6 36.0 1.0
MN3 a:OEC411 2.7 44.6 1.0
OE2 c:GLU354 3.1 69.5 1.0
OE1 c:GLU354 3.1 71.3 1.0
CG a:ASP342 3.2 56.7 1.0
CA1 a:OEC411 3.3 68.3 1.0
OD2 a:ASP342 3.4 51.6 1.0
OE2 a:GLU189 3.4 64.5 1.0
CD c:GLU354 3.5 71.9 1.0
CA a:ALA344 3.6 91.3 1.0
N a:ALA344 3.9 91.4 1.0
OE1 a:GLU189 4.1 83.0 1.0
CD a:GLU189 4.2 75.8 1.0
OE1 a:GLU333 4.3 65.9 1.0
CB a:ALA344 4.3 89.4 1.0
NE2 a:HIS337 4.4 76.2 1.0
CB a:ASP342 4.6 60.3 1.0
OD1 a:ASP170 4.7 68.0 1.0
NE2 a:HIS332 4.9 57.9 1.0
CG c:GLU354 4.9 68.7 1.0

Manganese binding site 7 out of 8 in 4ixr

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Manganese binding site 7 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:44.6
occ:1.00
 MN3 a:OEC411 0.0 44.6 1.0
OE1 a:GLU333 2.2 65.9 1.0
OE2 c:GLU354 2.3 69.5 1.0
MN2 a:OEC411 2.7 45.6 1.0
MN4 a:OEC411 3.2 62.1 1.0
MN1 a:OEC411 3.3 36.0 1.0
CA1 a:OEC411 3.3 68.3 1.0
CD a:GLU333 3.3 70.5 1.0
CD c:GLU354 3.4 71.9 1.0
OD2 a:ASP170 3.6 65.1 1.0
OD1 a:ASP170 3.8 68.0 1.0
OE2 a:GLU333 3.8 68.7 1.0
O a:ALA344 3.9 83.2 1.0
C a:ALA344 3.9 83.2 1.0
OE1 c:GLU354 3.9 71.3 1.0
NH2 c:ARG357 4.0 76.2 1.0
CG a:ASP170 4.1 66.7 1.0
CG a:GLU333 4.6 70.7 1.0
CG c:GLU354 4.6 68.7 1.0
OD1 a:ASP342 4.8 57.8 1.0
OE2 a:GLU189 4.8 64.5 1.0
CZ c:ARG357 4.8 75.3 1.0
OE1 a:GLU189 4.9 83.0 1.0
NH1 c:ARG357 5.0 73.2 1.0

Manganese binding site 8 out of 8 in 4ixr

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Manganese binding site 8 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:62.1
occ:1.00
 MN4 a:OEC411 0.0 62.1 1.0
OD2 a:ASP170 2.3 65.1 1.0
OE2 a:GLU333 2.4 68.7 1.0
CD a:GLU333 3.0 70.5 1.0
OE1 a:GLU333 3.2 65.9 1.0
MN3 a:OEC411 3.2 44.6 1.0
CG a:ASP170 3.5 66.7 1.0
OD1 a:ASP61 4.1 56.4 1.0
OD1 a:ASP170 4.2 68.0 1.0
O a:SER169 4.2 66.4 1.0
CG a:GLU333 4.4 70.7 1.0
CA a:ASP170 4.4 60.0 1.0
CB a:ASP170 4.6 62.5 1.0
CA1 a:OEC411 4.6 68.3 1.0
NH2 c:ARG357 4.7 76.2 1.0
C a:SER169 4.8 63.3 1.0
N a:ASP170 4.9 61.5 1.0
OG a:SER169 4.9 72.0 1.0
OE2 c:GLU354 4.9 69.5 1.0

Reference:

J.Kern, R.Alonso-Mori, R.Tran, J.Hattne, R.J.Gildea, N.Echols, C.Glockner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, S.Koroidov, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, D.W.Schafer, M.Messerschmidt, M.M.Seibert, J.E.Koglin, D.Sokaras, T.C.Weng, J.Sellberg, M.J.Latimer, R.W.Grosse-Kunstleve, P.H.Zwart, W.E.White, P.Glatzel, P.D.Adams, M.J.Bogan, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, N.K.Sauter, V.K.Yachandra, U.Bergmann, J.Yano. Simultaneous Femtosecond X-Ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science V. 340 491 2013.
ISSN: ISSN 0036-8075
PubMed: 23413188
DOI: 10.1126/SCIENCE.1234273
Page generated: Sat Oct 5 19:55:43 2024

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