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Chlorine in PDB 4rvy: Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)

Enzymatic activity of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)

All present enzymatic activity of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3):
1.10.3.9;

Protein crystallography data

The structure of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3), PDB code: 4rvy 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.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) 102.30 / 5.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 136.610, 228.090, 308.680, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 29.1

Other elements in 4rvy:

The structure of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 8 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 S State After Two Flashes (S3) (pdb code 4rvy). 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 S State After Two Flashes (S3), PDB code: 4rvy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4rvy

Go back to Chlorine Binding Sites List in 4rvy
Chlorine binding site 1 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


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 S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:24.7
occ:1.00
 ND2 A:ASN181 3.3 19.1 1.0
NZ D:LYS317 3.3 24.2 1.0
N A:GLU333 3.4 20.8 1.0
CB A:HIS332 3.7 20.4 1.0
CA A:HIS332 3.7 21.0 1.0
CE D:LYS317 3.9 21.0 1.0
CG A:GLU333 4.0 21.6 1.0
C A:HIS332 4.1 20.9 1.0
OD1 A:ASN181 4.1 22.1 1.0
CG A:ASN181 4.1 19.8 1.0
CG2 A:VAL185 4.2 19.9 1.0
CD2 D:LEU321 4.2 19.1 1.0
CA A:GLU333 4.4 20.6 1.0
CD1 D:LEU321 4.4 18.9 1.0
CB D:LYS317 4.4 18.6 1.0
CG D:LEU321 4.5 18.8 1.0
CG D:LYS317 4.7 20.1 1.0
CG A:HIS332 4.8 20.4 1.0
CB A:GLU333 4.8 21.0 1.0
OE2 A:GLU333 4.8 22.1 1.0
O D:LYS317 4.8 18.9 1.0
CD A:GLU333 4.8 21.8 1.0
CD D:LYS317 5.0 19.2 1.0
N A:HIS332 5.0 20.9 1.0

Chlorine binding site 2 out of 6 in 4rvy

Go back to Chlorine Binding Sites List in 4rvy
Chlorine binding site 2 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


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 S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl611

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
N A:PHE339 3.7 21.6 1.0
CA A:HIS337 3.8 21.3 1.0
CA C:GLY353 3.8 22.6 1.0
C A:HIS337 4.0 21.3 1.0
C C:GLY353 4.0 22.6 1.0
CB C:GLU354 4.1 22.4 1.0
O A:ALA336 4.1 21.6 1.0
CA A:ASN338 4.2 21.7 1.0
CB A:HIS337 4.3 21.1 1.0
CB A:ASN338 4.3 22.2 1.0
CA C:GLU354 4.3 21.5 1.0
CB A:PHE339 4.3 21.9 1.0
CG A:PHE339 4.4 22.3 1.0
CE2 A:PHE339 4.4 22.3 1.0
CG C:GLU354 4.4 21.5 1.0
C A:ASN338 4.4 21.6 1.0
CA A:PHE339 4.6 21.8 1.0
O A:PHE339 4.7 22.2 1.0
O C:GLY352 4.8 22.5 1.0
N A:HIS337 4.9 21.0 1.0
N C:THR355 4.9 21.2 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
NE2 C:GLN313 5.0 21.2 1.0
CG A:HIS337 5.0 20.8 1.0

Chlorine binding site 3 out of 6 in 4rvy

Go back to Chlorine Binding Sites List in 4rvy
Chlorine binding site 3 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


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 S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl610

b:24.7
occ:1.00
 ND2 a:ASN181 3.3 19.1 1.0
NZ d:LYS317 3.3 24.2 1.0
N a:GLU333 3.4 20.8 1.0
CB a:HIS332 3.7 20.4 1.0
CA a:HIS332 3.7 21.0 1.0
CE d:LYS317 3.9 21.0 1.0
CG a:GLU333 4.0 21.6 1.0
C a:HIS332 4.1 20.9 1.0
OD1 a:ASN181 4.1 22.1 1.0
CG a:ASN181 4.1 19.8 1.0
CG2 a:VAL185 4.2 19.9 1.0
CD2 d:LEU321 4.2 19.1 1.0
CA a:GLU333 4.4 20.6 1.0
CD1 d:LEU321 4.4 18.9 1.0
CB d:LYS317 4.4 18.6 1.0
CG d:LEU321 4.5 18.8 1.0
CG d:LYS317 4.7 20.1 1.0
CG a:HIS332 4.8 20.4 1.0
CB a:GLU333 4.8 21.0 1.0
OE2 a:GLU333 4.8 22.1 1.0
O d:LYS317 4.8 18.9 1.0
CD a:GLU333 4.8 21.8 1.0
CD d:LYS317 5.0 19.2 1.0
N a:HIS332 5.0 20.9 1.0

Chlorine binding site 4 out of 6 in 4rvy

Go back to Chlorine Binding Sites List in 4rvy
Chlorine binding site 4 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


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 S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl611

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
N a:PHE339 3.7 21.6 1.0
CA a:HIS337 3.8 21.3 1.0
CA c:GLY353 3.8 22.6 1.0
C a:HIS337 4.0 21.3 1.0
C c:GLY353 4.0 22.6 1.0
CB c:GLU354 4.1 22.4 1.0
O a:ALA336 4.1 21.6 1.0
CA a:ASN338 4.2 21.7 1.0
CB a:HIS337 4.3 21.1 1.0
CB a:ASN338 4.3 22.2 1.0
CA c:GLU354 4.3 21.5 1.0
CB a:PHE339 4.3 21.9 1.0
CG a:PHE339 4.4 22.3 1.0
CE2 a:PHE339 4.4 22.3 1.0
CG c:GLU354 4.4 21.5 1.0
C a:ASN338 4.4 21.6 1.0
CA a:PHE339 4.6 21.8 1.0
O a:PHE339 4.7 22.2 1.0
O c:GLY352 4.8 22.5 1.0
N a:HIS337 4.9 21.0 1.0
N c:THR355 4.9 21.2 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
NE2 c:GLN313 5.0 21.2 1.0
CG a:HIS337 5.0 20.8 1.0

Chlorine binding site 5 out of 6 in 4rvy

Go back to Chlorine Binding Sites List in 4rvy
Chlorine binding site 5 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


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 S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl201

b:50.8
occ:1.00
 NZ U:LYS104 3.9 25.9 1.0
OD2 V:ASP53 4.4 26.7 1.0
CE U:LYS104 5.0 27.2 1.0

Chlorine binding site 6 out of 6 in 4rvy

Go back to Chlorine Binding Sites List in 4rvy
Chlorine binding site 6 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


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 S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
u:Cl201

b:50.8
occ:1.00
 NZ u:LYS104 3.9 25.9 1.0
OD2 v:ASP53 4.4 26.7 1.0
CE u:LYS104 5.0 27.2 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: ISSN 0028-0836
PubMed: 25043005
DOI: 10.1038/NATURE13453
Page generated: Sat Dec 12 11:12:23 2020

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