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Manganese in PDB 4pbu: Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State

Enzymatic activity of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State

All present enzymatic activity of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State:
1.10.3.9;

Protein crystallography data

The structure of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State, PDB code: 4pbu was solved by C.Kupitz, S.Basu, I.Grotjohann, R.Fromme, N.Zatsepin, K.N.Rendek, M.Hunter, R.L.Shoeman, T.A.White, D.Wang, D.James, J.H.Yang, D.E.Cobb, B.Reeder, R.G.Sierra, H.Liu, A.Barty, A.Aquila, D.Deponte, R.A.Kirian, S.Bari, J.J.Bergkamp, K.Beyerlein, M.J.Bogan, C.Caleman, T.-C.Chao, C.E.Conrad, K.M.Davis, H.Fleckenstein, L.Galli, S.P.Hau-Riege, S.Kassemeyer, H.Laksmono, M.Liang, L.Lomb, S.Marchesini, A.V.Martin, M.Messerschmidt, D.Milathianaki, K.Nass, A.Ros, S.Roy-Chowdhury, K.Schmidt, M.Seibert, J.Steinbrener, F.Stellato, L.Yan, C.Yoon, T.A.Moore, A.L.Moore, Y.Pushkar, G.J.Williams, S.Boutet, R.B.Doak, U.Weierstall, M.Frank, H.N.Chapman, J.C.H.Spence, P.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.64 / 5.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.250, 226.260, 307.090, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 26.2

Other elements in 4pbu:

The structure of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State also contains other interesting chemical elements:

Magnesium (Mg) 71 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms
Calcium (Ca) 9 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State (pdb code 4pbu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State, PDB code: 4pbu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4pbu

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Manganese binding site 1 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:22.6
occ:1.00
 MN1 A:OEX601 0.0 22.6 1.0
O3 A:OEX601 1.8 23.3 1.0
O1 A:OEX601 1.9 22.5 1.0
OE2 A:GLU189 1.9 25.1 1.0
NE2 A:HIS332 2.1 20.0 1.0
OD2 A:ASP342 2.3 23.5 1.0
O5 A:OEX601 2.6 24.1 1.0
MN2 A:OEX601 2.8 22.9 1.0
CD A:GLU189 2.9 24.6 1.0
CD2 A:HIS332 3.1 19.9 1.0
CE1 A:HIS332 3.1 22.8 1.0
CG A:ASP342 3.2 22.4 1.0
MN3 A:OEX601 3.3 23.5 1.0
OD1 A:ASP342 3.4 20.7 1.0
OE1 A:GLU189 3.5 26.4 1.0
CA1 A:OEX601 3.5 24.6 1.0
O2 A:OEX601 3.7 25.2 1.0
NE2 A:HIS337 3.9 22.7 1.0
OE1 A:GLU333 4.0 24.2 1.0
CG A:GLU189 4.1 23.9 1.0
ND1 A:HIS332 4.2 19.1 1.0
CG A:HIS332 4.2 20.4 1.0
OE1 C:GLU354 4.3 22.6 1.0
CG1 A:VAL185 4.5 20.3 1.0
OXT A:ALA344 4.5 25.0 1.0
OE2 C:GLU354 4.5 23.1 1.0
CB A:ASP342 4.5 22.0 1.0
CE1 A:HIS337 4.6 20.6 1.0
CD A:GLU333 4.8 21.8 1.0
CD C:GLU354 4.8 22.8 1.0
O A:ALA344 4.9 25.6 1.0
CD2 A:HIS337 5.0 20.5 1.0
MN4 A:OEX601 5.0 26.3 1.0

Manganese binding site 2 out of 8 in 4pbu

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Manganese binding site 2 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:22.9
occ:1.00
 MN2 A:OEX601 0.0 22.9 1.0
OE1 C:GLU354 1.9 22.6 1.0
OXT A:ALA344 2.0 25.0 1.0
O1 A:OEX601 2.1 22.5 1.0
O3 A:OEX601 2.1 23.3 1.0
O2 A:OEX601 2.1 25.2 1.0
OD1 A:ASP342 2.1 20.7 1.0
CD C:GLU354 2.8 22.8 1.0
MN1 A:OEX601 2.8 22.6 1.0
MN3 A:OEX601 2.9 23.5 1.0
C A:ALA344 3.0 25.1 1.0
CG A:ASP342 3.1 22.4 1.0
OE2 C:GLU354 3.2 23.1 1.0
OD2 A:ASP342 3.3 23.5 1.0
O A:ALA344 3.3 25.6 1.0
CA1 A:OEX601 3.4 24.6 1.0
O5 A:OEX601 3.8 24.1 1.0
NE2 A:HIS337 3.8 22.7 1.0
CG C:GLU354 4.2 21.5 1.0
CA A:ALA344 4.3 24.7 1.0
N A:ALA344 4.3 24.7 1.0
CD2 A:HIS337 4.3 20.5 1.0
OE2 A:GLU189 4.4 25.1 1.0
CB A:ASP342 4.5 22.0 1.0
O4 A:OEX601 4.5 26.6 1.0
CB C:GLU354 4.6 22.4 1.0
OE1 A:GLU333 4.6 24.2 1.0
NE2 A:HIS332 4.6 20.0 1.0
NH2 C:ARG357 4.6 23.9 1.0
NH1 C:ARG357 4.8 26.4 1.0
CA A:ASP342 4.8 22.5 1.0
C A:ASP342 5.0 22.6 1.0
CZ C:ARG357 5.0 27.5 1.0

Manganese binding site 3 out of 8 in 4pbu

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Manganese binding site 3 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:23.5
occ:1.00
 MN3 A:OEX601 0.0 23.5 1.0
O2 A:OEX601 1.9 25.2 1.0
OE2 C:GLU354 2.0 23.1 1.0
OE1 A:GLU333 2.1 24.2 1.0
O4 A:OEX601 2.1 26.6 1.0
O3 A:OEX601 2.1 23.3 1.0
O5 A:OEX601 2.4 24.1 1.0
MN2 A:OEX601 2.9 22.9 1.0
CD C:GLU354 2.9 22.8 1.0
MN4 A:OEX601 3.0 26.3 1.0
CD A:GLU333 3.0 21.8 1.0
OE1 C:GLU354 3.2 22.6 1.0
MN1 A:OEX601 3.3 22.6 1.0
OE2 A:GLU333 3.3 22.1 1.0
CA1 A:OEX601 3.4 24.6 1.0
O1 A:OEX601 3.5 22.5 1.0
NH2 C:ARG357 3.9 23.9 1.0
NE2 A:HIS337 4.1 22.7 1.0
OD1 A:ASP170 4.2 23.1 1.0
NE2 A:HIS332 4.2 20.0 1.0
CG C:GLU354 4.3 21.5 1.0
CG A:GLU333 4.4 21.6 1.0
OD2 A:ASP170 4.4 23.9 1.0
OXT A:ALA344 4.4 25.0 1.0
CD2 A:HIS332 4.5 19.9 1.0
OD1 A:ASP342 4.7 20.7 1.0
CE1 A:HIS337 4.7 20.6 1.0
CG A:ASP170 4.7 22.6 1.0
CB A:GLU333 4.8 21.0 1.0
O A:ALA344 4.8 25.6 1.0
OD2 A:ASP342 4.9 23.5 1.0
OE2 A:GLU189 4.9 25.1 1.0
CZ C:ARG357 5.0 27.5 1.0

Manganese binding site 4 out of 8 in 4pbu

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Manganese binding site 4 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:26.3
occ:1.00
 MN4 A:OEX601 0.0 26.3 1.0
OD1 A:ASP170 2.1 23.1 1.0
O4 A:OEX601 2.1 26.6 1.0
OE2 A:GLU333 2.2 22.1 1.0
O5 A:OEX601 2.5 24.1 1.0
MN3 A:OEX601 3.0 23.5 1.0
CD A:GLU333 3.1 21.8 1.0
CG A:ASP170 3.2 22.6 1.0
OE1 A:GLU333 3.3 24.2 1.0
OD2 A:ASP170 3.8 23.9 1.0
O2 A:OEX601 3.8 25.2 1.0
CA1 A:OEX601 3.8 24.6 1.0
OD1 A:ASP61 4.1 23.3 1.0
O A:SER169 4.3 20.6 1.0
CB A:ASP170 4.5 21.7 1.0
CG A:GLU333 4.5 21.6 1.0
NH2 C:ARG357 4.5 23.9 1.0
CA A:ASP170 4.5 21.5 1.0
OE2 C:GLU354 4.6 23.1 1.0
O3 A:OEX601 4.7 23.3 1.0
C A:SER169 4.9 20.3 1.0
N A:ASP170 5.0 20.9 1.0
MN1 A:OEX601 5.0 22.6 1.0
CG A:ASP61 5.0 22.7 1.0

Manganese binding site 5 out of 8 in 4pbu

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Manganese binding site 5 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:26.0
occ:1.00
 MN1 a:OEX401 0.0 26.0 1.0
OE2 a:GLU189 1.8 26.6 1.0
O1 a:OEX401 1.8 25.1 1.0
O3 a:OEX401 1.8 27.1 1.0
NE2 a:HIS332 2.2 24.2 1.0
OD2 a:ASP342 2.3 25.4 1.0
O5 a:OEX401 2.6 28.1 1.0
MN2 a:OEX401 2.8 26.7 1.0
CD a:GLU189 2.8 27.2 1.0
CE1 a:HIS332 3.1 24.0 1.0
CG a:ASP342 3.1 24.2 1.0
CD2 a:HIS332 3.2 22.9 1.0
OD1 a:ASP342 3.3 24.4 1.0
MN3 a:OEX401 3.3 25.5 1.0
OE1 a:GLU189 3.3 28.6 1.0
CA1 a:OEX401 3.5 27.5 1.0
O2 a:OEX401 3.7 27.3 1.0
NE2 a:HIS337 3.9 27.0 1.0
CG a:GLU189 4.1 25.8 1.0
OE1 a:GLU333 4.1 27.2 1.0
OE1 c:GLU354 4.2 26.2 1.0
ND1 a:HIS332 4.2 23.2 1.0
OXT a:ALA344 4.3 29.4 1.0
CG a:HIS332 4.3 23.3 1.0
OE2 c:GLU354 4.4 25.8 1.0
CB a:ASP342 4.5 25.2 1.0
CG1 a:VAL185 4.5 22.2 1.0
CE1 a:HIS337 4.6 27.4 1.0
CD c:GLU354 4.7 26.4 1.0
O a:ALA344 4.7 29.4 1.0
CD a:GLU333 4.8 25.6 1.0
C a:ALA344 4.9 29.3 1.0
MN4 a:OEX401 5.0 28.7 1.0
CD2 a:HIS337 5.0 25.3 1.0

Manganese binding site 6 out of 8 in 4pbu

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Manganese binding site 6 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:26.7
occ:1.00
 MN2 a:OEX401 0.0 26.7 1.0
OE1 c:GLU354 1.9 26.2 1.0
OXT a:ALA344 1.9 29.4 1.0
O1 a:OEX401 2.0 25.1 1.0
O2 a:OEX401 2.1 27.3 1.0
O3 a:OEX401 2.1 27.1 1.0
OD1 a:ASP342 2.1 24.4 1.0
MN1 a:OEX401 2.8 26.0 1.0
CD c:GLU354 2.8 26.4 1.0
C a:ALA344 2.9 29.3 1.0
MN3 a:OEX401 2.9 25.5 1.0
CG a:ASP342 3.1 24.2 1.0
OE2 c:GLU354 3.1 25.8 1.0
O a:ALA344 3.1 29.4 1.0
CA1 a:OEX401 3.3 27.5 1.0
OD2 a:ASP342 3.3 25.4 1.0
NE2 a:HIS337 3.8 27.0 1.0
O5 a:OEX401 3.9 28.1 1.0
CG c:GLU354 4.2 25.5 1.0
CA a:ALA344 4.2 28.9 1.0
OE2 a:GLU189 4.3 26.6 1.0
N a:ALA344 4.3 28.3 1.0
CD2 a:HIS337 4.3 25.3 1.0
CB a:ASP342 4.5 25.2 1.0
NH2 c:ARG357 4.5 30.8 1.0
CB c:GLU354 4.5 25.0 1.0
OE1 a:GLU333 4.5 27.2 1.0
O4 a:OEX401 4.5 27.7 1.0
NE2 a:HIS332 4.6 24.2 1.0
CA a:ASP342 4.9 25.3 1.0
NH1 c:ARG357 4.9 31.8 1.0
CD a:GLU189 4.9 27.2 1.0
OD2 a:ASP170 4.9 26.2 1.0
OE1 a:GLU189 5.0 28.6 1.0
CZ c:ARG357 5.0 30.5 1.0
C a:ASP342 5.0 25.9 1.0

Manganese binding site 7 out of 8 in 4pbu

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Manganese binding site 7 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:25.5
occ:1.00
 MN3 a:OEX401 0.0 25.5 1.0
OE2 c:GLU354 1.9 25.8 1.0
O2 a:OEX401 1.9 27.3 1.0
OE1 a:GLU333 2.0 27.2 1.0
O3 a:OEX401 2.0 27.1 1.0
O4 a:OEX401 2.1 27.7 1.0
O5 a:OEX401 2.4 28.1 1.0
CD c:GLU354 2.8 26.4 1.0
MN4 a:OEX401 2.9 28.7 1.0
MN2 a:OEX401 2.9 26.7 1.0
CD a:GLU333 3.0 25.6 1.0
OE1 c:GLU354 3.2 26.2 1.0
OE2 a:GLU333 3.3 24.4 1.0
MN1 a:OEX401 3.3 26.0 1.0
CA1 a:OEX401 3.4 27.5 1.0
O1 a:OEX401 3.6 25.1 1.0
NH2 c:ARG357 3.8 30.8 1.0
OD1 a:ASP170 4.1 25.9 1.0
NE2 a:HIS337 4.1 27.0 1.0
NE2 a:HIS332 4.2 24.2 1.0
CG c:GLU354 4.2 25.5 1.0
OD2 a:ASP170 4.3 26.2 1.0
CG a:GLU333 4.3 24.4 1.0
OXT a:ALA344 4.4 29.4 1.0
CD2 a:HIS332 4.5 22.9 1.0
CG a:ASP170 4.7 25.1 1.0
CB a:GLU333 4.7 23.6 1.0
OD1 a:ASP342 4.7 24.4 1.0
CE1 a:HIS337 4.7 27.4 1.0
O a:ALA344 4.7 29.4 1.0
OE2 a:GLU189 4.9 26.6 1.0
CZ c:ARG357 4.9 30.5 1.0
OD2 a:ASP342 5.0 25.4 1.0

Manganese binding site 8 out of 8 in 4pbu

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Manganese binding site 8 out of 8 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:28.7
occ:1.00
 MN4 a:OEX401 0.0 28.7 1.0
OD1 a:ASP170 2.0 25.9 1.0
O4 a:OEX401 2.1 27.7 1.0
OE2 a:GLU333 2.1 24.4 1.0
O5 a:OEX401 2.5 28.1 1.0
MN3 a:OEX401 2.9 25.5 1.0
CD a:GLU333 3.0 25.6 1.0
CG a:ASP170 3.2 25.1 1.0
OE1 a:GLU333 3.2 27.2 1.0
OD2 a:ASP170 3.7 26.2 1.0
CA1 a:OEX401 3.8 27.5 1.0
O2 a:OEX401 3.8 27.3 1.0
OD1 a:ASP61 4.1 27.2 1.0
CB a:ASP170 4.4 23.9 1.0
O a:SER169 4.4 23.2 1.0
CG a:GLU333 4.4 24.4 1.0
NH2 c:ARG357 4.5 30.8 1.0
OE2 c:GLU354 4.5 25.8 1.0
O3 a:OEX401 4.5 27.1 1.0
CA a:ASP170 4.5 23.4 1.0
C a:SER169 4.9 22.7 1.0
MN1 a:OEX401 5.0 26.0 1.0
N a:ASP170 5.0 22.6 1.0

Reference:

C.Kupitz, S.Basu, I.Grotjohann, R.Fromme, N.A.Zatsepin, K.N.Rendek, M.S.Hunter, R.L.Shoeman, T.A.White, D.Wang, D.James, J.H.Yang, D.E.Cobb, B.Reeder, R.G.Sierra, H.Liu, A.Barty, A.L.Aquila, D.Deponte, R.A.Kirian, S.Bari, J.J.Bergkamp, K.R.Beyerlein, M.J.Bogan, C.Caleman, T.C.Chao, C.E.Conrad, K.M.Davis, H.Fleckenstein, L.Galli, S.P.Hau-Riege, S.Kassemeyer, H.Laksmono, M.Liang, L.Lomb, S.Marchesini, A.V.Martin, M.Messerschmidt, D.Milathianaki, K.Nass, A.Ros, S.Roy-Chowdhury, K.Schmidt, M.Seibert, J.Steinbrener, F.Stellato, L.Yan, C.Yoon, T.A.Moore, A.L.Moore, Y.Pushkar, G.J.Williams, S.Boutet, R.B.Doak, U.Weierstall, M.Frank, H.N.Chapman, J.C.Spence, P.Fromme. Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. Nature V. 513 261 2014.
ISSN: ESSN 1476-4687
PubMed: 25043005
DOI: 10.1038/NATURE13453
Page generated: Sat Oct 5 20:44:56 2024

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