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Calcium 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
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 9 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4pbu

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Calcium binding site 1 out of 9 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 Calcium with other atoms in the Ca 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:Ca601

b:24.6
occ:1.00
 CA1 A:OEX601 0.0 24.6 1.0
O1 A:OEX601 2.3 22.5 1.0
OD2 A:ASP170 2.4 23.9 1.0
O2 A:OEX601 2.5 25.2 1.0
O5 A:OEX601 2.5 24.1 1.0
O A:ALA344 2.5 25.6 1.0
CG A:ASP170 3.2 22.6 1.0
OD1 A:ASP170 3.4 23.1 1.0
MN2 A:OEX601 3.4 22.9 1.0
OE1 A:GLU189 3.4 26.4 1.0
MN3 A:OEX601 3.4 23.5 1.0
C A:ALA344 3.5 25.1 1.0
MN1 A:OEX601 3.5 22.6 1.0
OXT A:ALA344 3.7 25.0 1.0
MN4 A:OEX601 3.8 26.3 1.0
O3 A:OEX601 3.9 23.3 1.0
O4 A:OEX601 4.0 26.6 1.0
NH1 C:ARG357 4.0 26.4 1.0
OE2 A:GLU189 4.1 25.1 1.0
CD A:GLU189 4.1 24.6 1.0
NH2 C:ARG357 4.2 23.9 1.0
CB A:ASP170 4.4 21.7 1.0
CZ C:ARG357 4.6 27.5 1.0
OH A:TYR161 4.8 22.4 1.0
OE1 A:GLN165 4.8 23.9 1.0
CA A:ALA344 4.8 24.7 1.0
OE1 C:GLU354 4.8 22.6 1.0
OE2 C:GLU354 5.0 23.1 1.0

Calcium binding site 2 out of 9 in 4pbu

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Calcium binding site 2 out of 9 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 Calcium with other atoms in the Ca 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
B:Ca601

b:76.3
occ:1.00
 OD1 B:ASN438 2.7 29.1 1.0
CG B:ASN438 3.9 27.1 1.0
O B:SER439 4.5 22.6 1.0
OE1 O:GLU181 4.6 47.5 1.0
CA B:ASN438 4.6 24.5 1.0
OE2 B:GLU435 4.6 33.7 1.0
ND2 B:ASN438 4.7 29.5 1.0
OE2 O:GLU181 4.8 46.2 1.0
C B:ASN438 4.8 23.9 1.0
CB B:ASN438 4.8 25.2 1.0
O B:ASN438 5.0 23.6 1.0

Calcium binding site 3 out of 9 in 4pbu

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Calcium binding site 3 out of 9 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 Calcium with other atoms in the Ca 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
F:Ca102

b:56.6
occ:1.00
 OXT F:ARG45 2.6 30.8 1.0
O F:ARG45 3.0 30.5 1.0
C F:ARG45 3.2 31.1 1.0
OE1 V:GLU23 4.2 45.7 1.0
OE2 V:GLU23 4.4 46.5 1.0
CD V:GLU23 4.5 44.0 1.0
O A:ALA309 4.7 28.4 1.0
CA F:ARG45 4.7 31.3 1.0

Calcium binding site 4 out of 9 in 4pbu

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Calcium binding site 4 out of 9 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 Calcium with other atoms in the Ca 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
O:Ca301

b:49.3
occ:1.00
 O O:THR138 2.5 43.6 1.0
O O:VAL201 2.5 39.5 1.0
OD1 O:ASN200 2.5 41.9 1.0
CG O:ASN200 3.6 40.6 1.0
C O:THR138 3.6 43.6 1.0
C O:VAL201 3.7 39.0 1.0
ND2 O:ASN200 4.0 42.7 1.0
N O:VAL201 4.3 38.3 1.0
CA O:SER139 4.4 43.6 1.0
N O:SER139 4.4 43.6 1.0
CA O:THR138 4.5 43.7 1.0
CA O:VAL201 4.6 38.6 1.0
N O:ALA202 4.6 39.6 1.0
CA O:ALA202 4.6 40.1 1.0
C O:ASN200 4.6 38.1 1.0
O O:THR140 4.7 42.2 1.0
CB O:THR138 4.8 43.6 1.0
C O:SER139 4.8 43.3 1.0
CB O:ASN200 4.9 38.6 1.0

Calcium binding site 5 out of 9 in 4pbu

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Calcium binding site 5 out of 9 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 Calcium with other atoms in the Ca 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:Ca401

b:27.5
occ:1.00
 CA1 a:OEX401 0.0 27.5 1.0
OD2 a:ASP170 2.4 26.2 1.0
O1 a:OEX401 2.4 25.1 1.0
O a:ALA344 2.5 29.4 1.0
O2 a:OEX401 2.5 27.3 1.0
O5 a:OEX401 2.8 28.1 1.0
CG a:ASP170 3.2 25.1 1.0
OE1 a:GLU189 3.2 28.6 1.0
MN2 a:OEX401 3.3 26.7 1.0
MN3 a:OEX401 3.4 25.5 1.0
C a:ALA344 3.4 29.3 1.0
MN1 a:OEX401 3.5 26.0 1.0
OD1 a:ASP170 3.5 25.9 1.0
OXT a:ALA344 3.7 29.4 1.0
MN4 a:OEX401 3.8 28.7 1.0
O3 a:OEX401 3.9 27.1 1.0
O4 a:OEX401 4.0 27.7 1.0
CD a:GLU189 4.0 27.2 1.0
NH1 c:ARG357 4.0 31.8 1.0
OE2 a:GLU189 4.1 26.6 1.0
NH2 c:ARG357 4.2 30.8 1.0
CB a:ASP170 4.5 23.9 1.0
CZ c:ARG357 4.6 30.5 1.0
OE1 a:GLN165 4.6 25.1 1.0
OH a:TYR161 4.7 23.5 1.0
OE1 c:GLU354 4.8 26.2 1.0
CA a:ALA344 4.8 28.9 1.0
OE2 c:GLU354 4.9 25.8 1.0
OD1 a:ASP342 5.0 24.4 1.0

Calcium binding site 6 out of 9 in 4pbu

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Calcium binding site 6 out of 9 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 Calcium with other atoms in the Ca 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
b:Ca601

b:77.2
occ:1.00
 OD1 b:ASN438 2.6 31.5 1.0
CG b:ASN438 3.8 28.2 1.0
ND2 b:ASN438 4.6 28.8 1.0
OE1 o:GLU181 4.7 46.0 1.0
CA b:ASN438 4.7 25.8 1.0
O b:SER439 4.7 23.8 1.0
CB b:ASN438 4.8 25.9 1.0
C b:ASN438 5.0 25.1 1.0

Calcium binding site 7 out of 9 in 4pbu

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Calcium binding site 7 out of 9 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 Calcium with other atoms in the Ca 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
c:Ca901

b:46.5
occ:1.00
 O c:THR24 2.4 44.6 1.0
OE1 c:GLU29 2.4 41.9 1.0
OG c:SER30 2.4 38.9 1.0
O c:PHE22 2.4 49.6 1.0
OD2 c:ASP27 2.5 39.6 1.0
OD1 c:ASP27 2.6 38.1 1.0
CG c:ASP27 2.9 39.4 1.0
C c:PHE22 3.5 49.7 1.0
CB c:SER30 3.5 37.8 1.0
CD c:GLU29 3.6 41.0 1.0
C c:THR24 3.6 44.4 1.0
N c:SER30 4.0 38.0 1.0
CA c:PHE22 4.1 50.5 1.0
OE2 c:GLU29 4.2 42.0 1.0
CB c:PHE22 4.2 50.6 1.0
N c:THR24 4.3 46.5 1.0
CA c:SER30 4.3 37.6 1.0
CA c:ASN25 4.4 42.4 1.0
C c:ALA23 4.4 47.4 1.0
CB c:ASP27 4.4 39.8 1.0
N c:ASN25 4.4 43.2 1.0
N c:ALA23 4.5 48.8 1.0
CA c:THR24 4.6 45.3 1.0
CB c:GLU29 4.7 39.4 1.0
CG c:GLU29 4.7 40.7 1.0
O c:ALA23 4.7 47.6 1.0
C c:ASN25 4.8 41.9 1.0
CA c:ALA23 4.8 48.1 1.0
C c:GLU29 4.9 38.5 1.0

Calcium binding site 8 out of 9 in 4pbu

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Calcium binding site 8 out of 9 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 Calcium with other atoms in the Ca 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
f:Ca102

b:58.4
occ:1.00
 OXT f:ARG45 2.5 38.0 1.0
O f:ARG45 3.0 38.5 1.0
C f:ARG45 3.2 38.3 1.0
OE2 v:GLU23 3.3 53.4 1.0
CD v:GLU23 4.3 52.6 1.0
OE1 v:GLU23 4.5 53.2 1.0
O a:ALA309 4.6 34.1 1.0
CA f:ARG45 4.7 38.2 1.0

Calcium binding site 9 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 9 out of 9 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 Calcium with other atoms in the Ca binding site number 9 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
o:Ca301

b:51.6
occ:1.00
 O o:THR138 2.3 48.8 1.0
O o:VAL201 2.5 43.4 1.0
OD1 o:ASN200 2.6 44.1 1.0
C o:THR138 3.3 49.0 1.0
CG o:ASN200 3.6 43.8 1.0
C o:VAL201 3.7 43.3 1.0
ND2 o:ASN200 4.1 44.4 1.0
N o:SER139 4.1 48.8 1.0
CA o:SER139 4.1 48.5 1.0
CA o:THR138 4.3 49.1 1.0
N o:VAL201 4.4 42.7 1.0
O o:THR140 4.5 46.8 1.0
N o:ALA202 4.6 43.8 1.0
CA o:VAL201 4.6 42.7 1.0
CA o:ALA202 4.6 44.5 1.0
C o:SER139 4.6 48.2 1.0
CB o:THR138 4.6 49.1 1.0
C o:ASN200 4.7 42.1 1.0
CB o:ASN200 5.0 41.9 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: Sun Jul 14 11:42:17 2024

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