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Manganese in PDB 4ixq: Rt Fs X-Ray Diffraction of Photosystem II, Dark State

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

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

Protein crystallography data

The structure of Rt Fs X-Ray Diffraction of Photosystem II, Dark State, PDB code: 4ixq 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) 82.94 / 5.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.864, 227.511, 307.219, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.4

Other elements in 4ixq:

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

Manganese binding site 1 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 1 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 61.9 1.0
NE2 A:HIS332 2.4 57.7 1.0
OD2 A:ASP342 2.5 63.1 1.0
MN2 A:OEC409 2.6 45.6 1.0
CD A:GLU189 2.8 65.1 1.0
CD2 A:HIS332 3.2 61.6 1.0
MN3 A:OEC409 3.3 44.6 1.0
OE1 A:GLU189 3.3 63.2 1.0
CA1 A:OEC409 3.4 46.3 1.0
CG A:ASP342 3.4 70.1 1.0
CE1 A:HIS332 3.5 57.2 1.0
OD1 A:ASP342 3.6 68.3 1.0
OE1 A:GLU333 3.8 65.5 1.0
CG A:GLU189 4.0 60.9 1.0
NE2 A:HIS337 4.1 62.0 1.0
OE2 C:GLU354 4.3 68.1 1.0
CG A:HIS332 4.4 58.8 1.0
ND1 A:HIS332 4.5 55.4 1.0
CE1 A:HIS337 4.5 62.8 1.0
OE1 C:GLU354 4.6 64.5 1.0
CG1 A:VAL185 4.6 60.7 1.0
CD A:GLU333 4.6 68.8 1.0
O A:ALA344 4.7 75.4 1.0
CB A:ASP342 4.8 74.2 1.0
C A:ALA344 4.9 78.8 1.0
CD C:GLU354 4.9 69.6 1.0

Manganese binding site 2 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 2 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 68.3 1.0
C A:ALA344 2.3 78.8 1.0
O A:ALA344 2.6 75.4 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 68.1 1.0
CG A:ASP342 3.1 70.1 1.0
OD2 A:ASP342 3.2 63.1 1.0
OE1 C:GLU354 3.2 64.5 1.0
CA1 A:OEC409 3.3 46.3 1.0
OE2 A:GLU189 3.4 61.9 1.0
CD C:GLU354 3.5 69.6 1.0
CA A:ALA344 3.6 85.6 1.0
N A:ALA344 3.8 80.8 1.0
NE2 A:HIS337 4.2 62.0 1.0
OE1 A:GLU333 4.3 65.5 1.0
CB A:ALA344 4.3 87.5 1.0
CD A:GLU189 4.3 65.1 1.0
OE1 A:GLU189 4.3 63.2 1.0
CB A:ASP342 4.6 74.2 1.0
OD1 A:ASP170 4.7 83.0 1.0
NE2 A:HIS332 4.8 57.7 1.0
CG C:GLU354 4.9 72.2 1.0

Manganese binding site 3 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 3 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 65.5 1.0
OE2 C:GLU354 2.3 68.1 1.0
MN2 A:OEC409 2.7 45.6 1.0
CD A:GLU333 3.2 68.8 1.0
MN4 A:OEC409 3.2 62.1 1.0
MN1 A:OEC409 3.3 36.0 1.0
CA1 A:OEC409 3.3 46.3 1.0
CD C:GLU354 3.5 69.6 1.0
OE2 A:GLU333 3.6 69.8 1.0
OD2 A:ASP170 3.7 73.9 1.0
OD1 A:ASP170 3.8 83.0 1.0
C A:ALA344 4.0 78.8 1.0
O A:ALA344 4.0 75.4 1.0
OE1 C:GLU354 4.0 64.5 1.0
CG A:ASP170 4.2 78.6 1.0
NH2 C:ARG357 4.3 70.2 1.0
CG A:GLU333 4.5 66.0 1.0
OE2 A:GLU189 4.6 61.9 1.0
CG C:GLU354 4.7 72.2 1.0
OD1 A:ASP342 4.7 68.3 1.0
NE2 A:HIS332 4.8 57.7 1.0
NE2 A:HIS337 4.8 62.0 1.0
OD2 A:ASP342 5.0 63.1 1.0
CD2 A:HIS332 5.0 61.6 1.0

Manganese binding site 4 out of 8 in 4ixq

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Manganese binding site 4 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 73.9 1.0
OE2 A:GLU333 2.4 69.8 1.0
CD A:GLU333 3.1 68.8 1.0
MN3 A:OEC409 3.2 44.6 1.0
OE1 A:GLU333 3.4 65.5 1.0
CG A:ASP170 3.5 78.6 1.0
OD1 A:ASP170 4.2 83.0 1.0
OD1 A:ASP61 4.3 60.3 1.0
CG A:GLU333 4.3 66.0 1.0
O A:SER169 4.4 71.3 1.0
CA A:ASP170 4.5 66.5 1.0
CA1 A:OEC409 4.6 46.3 1.0
CB A:ASP170 4.7 72.7 1.0
C A:SER169 5.0 66.8 1.0

Manganese binding site 5 out of 8 in 4ixq

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Manganese binding site 5 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 59.9 1.0
NE2 a:HIS332 2.5 52.8 1.0
MN2 a:OEC411 2.6 45.6 1.0
OD2 a:ASP342 2.6 60.5 1.0
CD a:GLU189 2.7 68.3 1.0
OE1 a:GLU189 3.0 75.2 1.0
CD2 a:HIS332 3.2 55.0 1.0
MN3 a:OEC411 3.3 44.6 1.0
CA1 a:OEC411 3.4 62.4 1.0
CG a:ASP342 3.5 64.2 1.0
CE1 a:HIS332 3.6 52.6 1.0
OD1 a:ASP342 3.6 65.2 1.0
OE1 a:GLU333 3.7 61.0 1.0
CG a:GLU189 3.9 68.1 1.0
NE2 a:HIS337 4.2 71.7 1.0
OE2 c:GLU354 4.4 67.8 1.0
CG a:HIS332 4.4 50.8 1.0
CG1 a:VAL185 4.6 57.6 1.0
ND1 a:HIS332 4.6 48.4 1.0
CE1 a:HIS337 4.6 72.0 1.0
CD a:GLU333 4.6 67.0 1.0
OE1 c:GLU354 4.7 72.9 1.0
O a:ALA344 4.8 83.7 1.0
CB a:ASP342 4.9 62.9 1.0
C a:ALA344 4.9 87.0 1.0
CD c:GLU354 5.0 72.2 1.0

Manganese binding site 6 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 6 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 65.2 1.0
C a:ALA344 2.4 87.0 1.0
MN1 a:OEC411 2.6 36.0 1.0
O a:ALA344 2.7 83.7 1.0
MN3 a:OEC411 2.7 44.6 1.0
OE2 c:GLU354 3.1 67.8 1.0
CG a:ASP342 3.1 64.2 1.0
OE1 c:GLU354 3.2 72.9 1.0
CA1 a:OEC411 3.2 62.4 1.0
OD2 a:ASP342 3.3 60.5 1.0
OE2 a:GLU189 3.3 59.9 1.0
CD c:GLU354 3.5 72.2 1.0
CA a:ALA344 3.7 90.9 1.0
N a:ALA344 3.9 88.2 1.0
OE1 a:GLU189 4.0 75.2 1.0
CD a:GLU189 4.1 68.3 1.0
OE1 a:GLU333 4.3 61.0 1.0
NE2 a:HIS337 4.3 71.7 1.0
CB a:ALA344 4.4 86.8 1.0
CB a:ASP342 4.6 62.9 1.0
OD1 a:ASP170 4.8 72.0 1.0
NE2 a:HIS332 4.8 52.8 1.0
CG c:GLU354 5.0 70.6 1.0
C a:ASP342 5.0 65.8 1.0

Manganese binding site 7 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 7 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 61.0 1.0
OE2 c:GLU354 2.3 67.8 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
CD a:GLU333 3.3 67.0 1.0
CA1 a:OEC411 3.3 62.4 1.0
CD c:GLU354 3.4 72.2 1.0
OD2 a:ASP170 3.6 65.1 1.0
OE2 a:GLU333 3.7 66.7 1.0
OD1 a:ASP170 3.8 72.0 1.0
OE1 c:GLU354 4.0 72.9 1.0
C a:ALA344 4.0 87.0 1.0
O a:ALA344 4.0 83.7 1.0
NH2 c:ARG357 4.0 82.3 1.0
CG a:ASP170 4.1 69.3 1.0
CG a:GLU333 4.6 65.0 1.0
CG c:GLU354 4.6 70.6 1.0
OE2 a:GLU189 4.7 59.9 1.0
OD1 a:ASP342 4.7 65.2 1.0
CZ c:ARG357 4.9 77.7 1.0
OE1 a:GLU189 4.9 75.2 1.0
NE2 a:HIS332 5.0 52.8 1.0

Manganese binding site 8 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 8 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark 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, Dark 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 66.7 1.0
CD a:GLU333 3.1 67.0 1.0
MN3 a:OEC411 3.2 44.6 1.0
OE1 a:GLU333 3.2 61.0 1.0
CG a:ASP170 3.5 69.3 1.0
OD1 a:ASP61 4.2 58.0 1.0
O a:SER169 4.2 60.2 1.0
OD1 a:ASP170 4.2 72.0 1.0
CG a:GLU333 4.4 65.0 1.0
CA a:ASP170 4.4 58.9 1.0
CB a:ASP170 4.6 65.4 1.0
CA1 a:OEC411 4.6 62.4 1.0
C a:SER169 4.8 60.1 1.0
NH2 c:ARG357 4.8 82.3 1.0
N a:ASP170 4.9 59.4 1.0
OG a:SER169 4.9 70.4 1.0
OE2 c:GLU354 4.9 67.8 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 19:55:32 2024

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