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Manganese in PDB 4fby: Fs X-Ray Diffraction of Photosystem II

Enzymatic activity of Fs X-Ray Diffraction of Photosystem II

All present enzymatic activity of Fs X-Ray Diffraction of Photosystem II:
1.10.3.9;

Protein crystallography data

The structure of Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby was solved by J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Gloeckner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.-C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, 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) 85.89 / 6.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 130.783, 227.764, 308.630, 90.00, 90.00, 90.00
R / Rfree (%) 36.6 / 38.5

Other elements in 4fby:

The structure of Fs X-Ray Diffraction of Photosystem II also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Fs X-Ray Diffraction of Photosystem II (pdb code 4fby). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4fby

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Manganese binding site 1 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.9
occ:1.00
 MN1 A:OEC412 0.0 0.9 1.0
MN2 A:OEC412 2.4 0.5 1.0
NE2 A:HIS332 2.6 0.7 1.0
MN3 A:OEC412 2.7 0.2 1.0
CD2 A:HIS332 2.8 0.9 1.0
CA1 A:OEC412 2.9 0.5 1.0
OE2 A:GLU189 3.0 0.4 1.0
OE1 A:GLU333 3.2 0.2 1.0
MN4 A:OEC412 3.7 0.1 1.0
CD A:GLU189 3.7 0.3 1.0
CD A:GLU333 3.7 0.4 1.0
OE1 A:GLU189 3.9 0.9 1.0
CE1 A:HIS332 3.9 0.9 1.0
CG A:GLU333 4.0 0.9 1.0
OD2 A:ASP342 4.0 0.2 1.0
CG1 A:VAL185 4.2 0.7 1.0
CG A:HIS332 4.2 0.3 1.0
OE2 C:GLU354 4.2 0.8 1.0
OXT A:ALA344 4.5 0.7 1.0
OE2 A:GLU333 4.5 0.7 1.0
NE2 A:HIS337 4.6 0.8 1.0
ND1 A:HIS332 4.7 0.7 1.0
CE1 A:HIS337 4.7 1.0 1.0
OD1 A:ASP342 4.7 0.7 1.0
CG A:ASP342 4.8 0.6 1.0
CG A:GLU189 4.8 0.3 1.0
O A:ALA344 4.9 0.9 1.0
OE1 C:GLU354 5.0 0.0 1.0
CB A:GLU333 5.0 0.1 1.0

Manganese binding site 2 out of 8 in 4fby

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Manganese binding site 2 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.5
occ:1.00
 MN2 A:OEC412 0.0 0.5 1.0
MN1 A:OEC412 2.4 0.9 1.0
OD1 A:ASP342 2.5 0.7 1.0
OXT A:ALA344 2.5 0.7 1.0
OD2 A:ASP342 2.8 0.2 1.0
MN3 A:OEC412 2.8 0.2 1.0
CG A:ASP342 3.0 0.6 1.0
OE1 C:GLU354 3.0 0.0 1.0
OE2 A:GLU189 3.2 0.4 1.0
OE2 C:GLU354 3.2 0.8 1.0
C A:ALA344 3.4 0.1 1.0
NE2 A:HIS337 3.5 0.8 1.0
CD C:GLU354 3.5 0.6 1.0
O A:ALA344 3.6 0.9 1.0
CA1 A:OEC412 3.7 0.5 1.0
NE2 A:HIS332 3.8 0.7 1.0
OE1 A:GLU333 4.1 0.2 1.0
CD A:GLU189 4.2 0.3 1.0
CE1 A:HIS337 4.2 1.0 1.0
OE1 A:GLU189 4.4 0.9 1.0
CB A:ASP342 4.5 0.4 1.0
CD2 A:HIS337 4.5 0.2 1.0
CA A:ALA344 4.6 1.0 1.0
CD2 A:HIS332 4.7 0.9 1.0
CE1 A:HIS332 4.7 0.9 1.0
N A:ALA344 4.7 0.7 1.0

Manganese binding site 3 out of 8 in 4fby

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Manganese binding site 3 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.2
occ:1.00
 MN3 A:OEC412 0.0 0.2 1.0
OE2 C:GLU354 2.6 0.8 1.0
OE1 A:GLU333 2.6 0.2 1.0
MN4 A:OEC412 2.6 0.1 1.0
MN1 A:OEC412 2.7 0.9 1.0
MN2 A:OEC412 2.8 0.5 1.0
CA1 A:OEC412 3.0 0.5 1.0
OXT A:ALA344 3.2 0.7 1.0
CD A:GLU333 3.5 0.4 1.0
CD C:GLU354 3.7 0.6 1.0
OD2 A:ASP170 3.7 0.5 1.0
O A:ALA344 3.9 0.9 1.0
C A:ALA344 3.9 0.1 1.0
OD1 A:ASP170 4.0 0.1 1.0
OE2 A:GLU333 4.0 0.7 1.0
NH2 C:ARG357 4.1 0.0 1.0
OE1 C:GLU354 4.1 0.0 1.0
CG A:ASP170 4.3 0.6 1.0
CG A:GLU333 4.7 0.9 1.0
CZ C:ARG357 4.8 0.2 1.0
NH1 C:ARG357 4.8 0.3 1.0
CG C:GLU354 4.9 0.6 1.0
OE2 A:GLU189 5.0 0.4 1.0

Manganese binding site 4 out of 8 in 4fby

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Manganese binding site 4 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.1
occ:1.00
 MN4 A:OEC412 0.0 0.1 1.0
MN3 A:OEC412 2.6 0.2 1.0
OE2 A:GLU333 2.6 0.7 1.0
OD2 A:ASP170 2.7 0.5 1.0
CD A:GLU333 3.0 0.4 1.0
OE1 A:GLU333 3.0 0.2 1.0
CA1 A:OEC412 3.6 0.5 1.0
MN1 A:OEC412 3.7 0.9 1.0
CG A:ASP170 3.8 0.6 1.0
CG A:GLU333 4.2 0.9 1.0
OD1 A:ASP170 4.3 0.1 1.0
OD1 A:ASP61 4.5 0.1 1.0
OE2 C:GLU354 4.6 0.8 1.0
O A:SER169 4.7 0.1 1.0
NH2 C:ARG357 4.8 0.0 1.0
CA A:ASP170 4.9 0.7 1.0
CB A:ASP170 5.0 0.9 1.0

Manganese binding site 5 out of 8 in 4fby

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Manganese binding site 5 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn413

b:0.5
occ:1.00
 MN1 G:OEC413 0.0 0.5 1.0
MN2 G:OEC413 2.5 0.8 1.0
MN3 G:OEC413 2.7 0.2 1.0
NE2 G:HIS332 2.8 0.4 1.0
CD2 G:HIS332 2.9 0.1 1.0
OE1 G:GLU333 2.9 0.6 1.0
CA1 G:OEC413 2.9 0.4 1.0
OE2 G:GLU189 3.3 0.3 1.0
CD G:GLU333 3.4 0.8 1.0
MN4 G:OEC413 3.4 92.0 1.0
CG G:GLU333 3.7 0.7 1.0
CD G:GLU189 3.9 0.3 1.0
OE2 P:GLU354 4.1 0.7 1.0
OE1 G:GLU189 4.1 0.9 1.0
CE1 G:HIS332 4.1 0.7 1.0
OE2 G:GLU333 4.1 0.8 1.0
CG1 G:VAL185 4.1 0.4 1.0
CG G:HIS332 4.2 0.9 1.0
OD2 G:ASP342 4.3 0.5 1.0
OXT G:ALA344 4.6 0.8 1.0
CB G:GLU333 4.7 0.5 1.0
NE2 G:HIS337 4.8 0.1 1.0
ND1 G:HIS332 4.8 0.1 1.0
OD2 G:ASP170 4.8 0.9 1.0
CE1 G:HIS337 4.8 0.9 1.0
OD1 G:ASP342 5.0 0.1 1.0
O G:ALA344 5.0 0.2 1.0
CD P:GLU354 5.0 0.3 1.0

Manganese binding site 6 out of 8 in 4fby

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Manganese binding site 6 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn413

b:0.8
occ:1.00
 MN2 G:OEC413 0.0 0.8 1.0
MN1 G:OEC413 2.5 0.5 1.0
OXT G:ALA344 2.6 0.8 1.0
OD1 G:ASP342 2.6 0.1 1.0
OE2 G:GLU189 2.8 0.3 1.0
OD2 G:ASP342 2.9 0.5 1.0
CG G:ASP342 3.1 0.4 1.0
C G:ALA344 3.3 0.1 1.0
O G:ALA344 3.3 0.2 1.0
CA1 G:OEC413 3.4 0.4 1.0
MN3 G:OEC413 3.4 0.2 1.0
OE2 P:GLU354 3.4 0.7 1.0
OE1 P:GLU354 3.4 0.7 1.0
CD G:GLU189 3.7 0.3 1.0
NE2 G:HIS332 3.8 0.4 1.0
CD P:GLU354 3.8 0.3 1.0
OE1 G:GLU189 3.9 0.9 1.0
NE2 G:HIS337 4.0 0.1 1.0
OE1 G:GLU333 4.2 0.6 1.0
CA G:ALA344 4.6 0.1 1.0
CB G:ASP342 4.6 0.8 1.0
CD2 G:HIS332 4.6 0.1 1.0
CE1 G:HIS337 4.6 0.9 1.0
CE1 G:HIS332 4.7 0.7 1.0
N G:ALA344 4.7 0.5 1.0
CD2 G:HIS337 5.0 0.5 1.0

Manganese binding site 7 out of 8 in 4fby

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Manganese binding site 7 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn413

b:0.2
occ:1.00
 MN3 G:OEC413 0.0 0.2 1.0
OE1 G:GLU333 2.6 0.6 1.0
MN1 G:OEC413 2.7 0.5 1.0
MN4 G:OEC413 2.7 92.0 1.0
CA1 G:OEC413 2.9 0.4 1.0
OE2 P:GLU354 3.0 0.7 1.0
OD2 G:ASP170 3.1 0.9 1.0
MN2 G:OEC413 3.4 0.8 1.0
CD G:GLU333 3.4 0.8 1.0
OD1 G:ASP170 3.6 0.2 1.0
OE2 G:GLU333 3.7 0.8 1.0
OXT G:ALA344 3.7 0.8 1.0
CG G:ASP170 3.7 0.7 1.0
NH2 P:ARG357 3.8 0.1 1.0
O G:ALA344 4.1 0.2 1.0
CD P:GLU354 4.2 0.3 1.0
C G:ALA344 4.4 0.1 1.0
CG G:GLU333 4.6 0.7 1.0
CZ P:ARG357 4.7 0.9 1.0
NH1 P:ARG357 4.7 1.0 1.0
OE1 P:GLU354 4.8 0.7 1.0

Manganese binding site 8 out of 8 in 4fby

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Manganese binding site 8 out of 8 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn413

b:92.0
occ:1.00
 MN4 G:OEC413 0.0 92.0 1.0
MN3 G:OEC413 2.7 0.2 1.0
OE2 G:GLU333 2.7 0.8 1.0
OD2 G:ASP170 2.7 0.9 1.0
CD G:GLU333 3.1 0.8 1.0
OE1 G:GLU333 3.4 0.6 1.0
MN1 G:OEC413 3.4 0.5 1.0
CA1 G:OEC413 3.7 0.4 1.0
CG G:ASP170 3.9 0.7 1.0
CG G:GLU333 4.2 0.7 1.0
OD1 G:ASP170 4.6 0.2 1.0
O G:SER169 4.7 0.5 1.0
CA G:ASP170 4.9 0.8 1.0
OD1 G:ASP61 4.9 0.9 1.0
CG1 G:VAL185 5.0 0.4 1.0

Reference:

J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Glockner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, U.Bergmann, J.Yano, V.K.Yachandra. Room Temperature Femtosecond X-Ray Diffraction of Photosystem II Microcrystals. Proc.Natl.Acad.Sci.Usa V. 109 9721 2012.
ISSN: ISSN 0027-8424
PubMed: 22665786
DOI: 10.1073/PNAS.1204598109
Page generated: Sat Oct 5 19:23:12 2024

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