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Chlorine 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
Calcium (Ca) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4pbu

Go back to Chlorine Binding Sites List in 4pbu
Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl603

b:24.7
occ:1.00
 ND2 A:ASN181 3.3 19.1 1.0
N A:GLU333 3.4 20.8 1.0
NZ D:LYS317 3.4 24.2 1.0
CB A:HIS332 3.7 20.4 1.0
CA A:HIS332 3.7 21.0 1.0
CG A:GLU333 4.0 21.6 1.0
CE D:LYS317 4.0 21.0 1.0
C A:HIS332 4.1 20.9 1.0
OD1 A:ASN181 4.1 22.1 1.0
CD2 D:LEU321 4.1 19.1 1.0
CG A:ASN181 4.1 19.8 1.0
CG2 A:VAL185 4.2 19.9 1.0
CD1 D:LEU321 4.2 18.9 1.0
CA A:GLU333 4.4 20.6 1.0
CB D:LYS317 4.4 18.6 1.0
CG D:LEU321 4.4 18.8 1.0
O D:LYS317 4.7 18.9 1.0
CG A:HIS332 4.8 20.4 1.0
CG D:LYS317 4.8 20.1 1.0
CB A:GLU333 4.8 21.0 1.0
OE2 A:GLU333 4.8 22.1 1.0
CD A:GLU333 4.8 21.8 1.0
N A:HIS332 5.0 20.9 1.0

Chlorine binding site 2 out of 6 in 4pbu

Go back to Chlorine Binding Sites List in 4pbu
Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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:Cl604

b:21.8
occ:1.00
 N A:ASN338 3.2 21.6 1.0
N C:GLU354 3.3 22.0 1.0
CD2 A:PHE339 3.7 21.7 1.0
CA C:GLY353 3.7 22.6 1.0
N A:PHE339 3.7 21.6 1.0
CA A:HIS337 3.8 21.3 1.0
C A:HIS337 4.0 21.3 1.0
C C:GLY353 4.0 22.6 1.0
O A:ALA336 4.1 21.6 1.0
CA A:ASN338 4.2 21.7 1.0
CB C:GLU354 4.3 22.4 1.0
CB A:HIS337 4.3 21.1 1.0
CB A:ASN338 4.3 22.2 1.0
CB A:PHE339 4.3 21.9 1.0
CG A:PHE339 4.4 22.3 1.0
CA C:GLU354 4.4 21.5 1.0
CE2 A:PHE339 4.4 22.3 1.0
C A:ASN338 4.4 21.6 1.0
CA A:PHE339 4.6 21.8 1.0
CG C:GLU354 4.6 21.5 1.0
O A:PHE339 4.7 22.2 1.0
O C:GLY352 4.7 22.5 1.0
N A:HIS337 4.9 21.0 1.0
N C:THR355 4.9 21.2 1.0
N C:GLY353 4.9 22.6 1.0
C A:ALA336 4.9 21.7 1.0
CG A:ASN338 5.0 22.3 1.0
CD2 A:HIS337 5.0 20.5 1.0
CG A:HIS337 5.0 20.8 1.0
NE2 C:GLN313 5.0 21.2 1.0

Chlorine binding site 3 out of 6 in 4pbu

Go back to Chlorine Binding Sites List in 4pbu
Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl 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
V:Cl201

b:50.8
occ:1.00
 NZ U:LYS104 4.4 25.9 1.0
OD2 V:ASP53 4.4 26.7 1.0
NH1 V:ARG55 4.8 25.1 1.0

Chlorine binding site 4 out of 6 in 4pbu

Go back to Chlorine Binding Sites List in 4pbu
Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl 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:Cl404

b:28.8
occ:1.00
 NZ d:LYS317 3.4 26.5 1.0
ND2 a:ASN181 3.4 21.0 1.0
N a:GLU333 3.4 22.7 1.0
CB a:HIS332 3.6 22.7 1.0
CA a:HIS332 3.7 22.7 1.0
CG a:GLU333 4.0 24.4 1.0
CD2 d:LEU321 4.0 20.5 1.0
OD1 a:ASN181 4.1 24.2 1.0
C a:HIS332 4.1 23.1 1.0
CG a:ASN181 4.2 23.1 1.0
CG2 a:VAL185 4.2 22.3 1.0
CE d:LYS317 4.2 25.1 1.0
CD1 d:LEU321 4.2 19.4 1.0
CG d:LEU321 4.4 19.9 1.0
CB d:LYS317 4.4 22.0 1.0
CA a:GLU333 4.4 23.3 1.0
O d:LYS317 4.6 22.1 1.0
CG a:HIS332 4.7 23.3 1.0
CG d:LYS317 4.8 22.6 1.0
OE2 a:GLU333 4.8 24.4 1.0
CB a:GLU333 4.8 23.6 1.0
CD a:GLU333 4.8 25.6 1.0
CD2 a:HIS332 4.9 22.9 1.0

Chlorine binding site 5 out of 6 in 4pbu

Go back to Chlorine Binding Sites List in 4pbu
Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl 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:Cl405

b:26.9
occ:1.00
 N a:ASN338 3.2 25.1 1.0
N c:GLU354 3.4 24.3 1.0
CA c:GLY353 3.6 24.5 1.0
CD2 a:PHE339 3.6 27.2 1.0
CA a:HIS337 3.7 24.2 1.0
N a:PHE339 3.7 26.0 1.0
C a:HIS337 3.9 24.9 1.0
C c:GLY353 4.0 24.0 1.0
CA a:ASN338 4.1 25.6 1.0
O a:ALA336 4.2 23.8 1.0
CB a:HIS337 4.3 24.3 1.0
CB a:ASN338 4.3 25.3 1.0
CE2 a:PHE339 4.3 28.0 1.0
CG a:PHE339 4.4 27.3 1.0
CB a:PHE339 4.4 26.4 1.0
CB c:GLU354 4.4 25.0 1.0
C a:ASN338 4.4 25.9 1.0
CA c:GLU354 4.5 24.7 1.0
CA a:PHE339 4.6 26.2 1.0
O c:GLY352 4.7 25.6 1.0
O a:PHE339 4.7 26.9 1.0
CG c:GLU354 4.8 25.5 1.0
N a:HIS337 4.8 23.5 1.0
N c:GLY353 4.8 25.0 1.0
CD2 a:HIS337 4.9 25.3 1.0
C a:ALA336 4.9 23.5 1.0
N c:THR355 4.9 24.8 1.0
CG a:HIS337 4.9 25.4 1.0
CG a:ASN338 4.9 26.1 1.0

Chlorine binding site 6 out of 6 in 4pbu

Go back to Chlorine Binding Sites List in 4pbu
Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl 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
v:Cl201

b:60.5
occ:1.00
 NZ u:LYS104 4.2 27.5 1.0
OD2 v:ASP53 4.3 32.5 1.0
NH1 v:ARG55 4.4 43.0 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: Thu Jul 25 23:55:14 2024

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