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Chlorine in PDB 4ub8: Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8 was solved by M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.90 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.807, 230.001, 288.502, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.5

Other elements in 4ub8:

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser (pdb code 4ub8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ub8

Go back to Chlorine Binding Sites List in 4ub8
Chlorine binding site 1 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:19.3
occ:1.00
 O D:HOH590 3.2 15.4 1.0
NZ D:LYS317 3.2 18.9 1.0
O A:HOH561 3.2 23.0 1.0
N A:GLU333 3.4 19.8 1.0
ND2 A:ASN181 3.4 16.7 1.0
CB A:HIS332 3.8 18.7 1.0
CA A:HIS332 3.9 19.9 1.0
CE D:LYS317 4.0 15.3 1.0
CG A:GLU333 4.0 17.7 1.0
OD1 A:ASN181 4.1 16.9 1.0
C A:HIS332 4.1 23.4 1.0
CG2 A:VAL185 4.2 16.7 1.0
CG A:ASN181 4.2 19.4 1.0
CD2 D:LEU321 4.3 18.2 1.0
O A:HOH560 4.3 21.0 1.0
CA A:GLU333 4.4 18.4 1.0
CD1 D:LEU321 4.4 15.1 1.0
CB D:LYS317 4.6 16.1 1.0
O A:HOH525 4.6 18.1 1.0
CG D:LEU321 4.6 20.6 1.0
O D:LYS317 4.7 22.2 1.0
CB A:GLU333 4.8 18.1 1.0
CG A:HIS332 4.8 17.5 1.0
OE2 A:GLU333 4.9 24.0 1.0
CD A:GLU333 4.9 30.2 1.0
CG D:LYS317 5.0 15.9 1.0

Chlorine binding site 2 out of 6 in 4ub8

Go back to Chlorine Binding Sites List in 4ub8
Chlorine binding site 2 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:23.4
occ:1.00
 O A:HOH604 3.0 24.1 1.0
O C:HOH669 3.0 21.0 1.0
N A:ASN338 3.2 20.0 1.0
N C:GLU354 3.4 24.3 1.0
CA A:HIS337 3.7 19.5 1.0
CA C:GLY353 3.8 19.4 1.0
CD2 A:PHE339 3.8 25.6 1.0
N A:PHE339 3.8 19.8 1.0
C A:HIS337 3.9 27.0 1.0
C C:GLY353 4.1 25.7 1.0
O A:ALA336 4.1 22.0 1.0
CA A:ASN338 4.2 19.4 1.0
CB A:HIS337 4.2 18.2 1.0
CB C:GLU354 4.3 28.6 1.0
O C:HOH625 4.3 20.1 1.0
CB A:PHE339 4.4 27.1 1.0
CA C:GLU354 4.4 18.8 1.0
CG A:PHE339 4.4 29.6 1.0
CB A:ASN338 4.5 25.3 1.0
O A:HOH632 4.5 22.3 1.0
C A:ASN338 4.5 19.8 1.0
O A:PHE339 4.6 22.9 1.0
CE2 A:PHE339 4.6 20.6 1.0
CG C:GLU354 4.6 27.4 1.0
CA A:PHE339 4.7 19.9 1.0
N A:HIS337 4.8 18.1 1.0
CD2 A:HIS337 4.8 17.9 1.0
CG A:HIS337 4.9 17.9 1.0
C A:ALA336 4.9 25.9 1.0
N C:THR355 4.9 19.4 1.0
O C:GLY352 4.9 24.4 1.0
NE2 C:GLN313 5.0 22.9 1.0

Chlorine binding site 3 out of 6 in 4ub8

Go back to Chlorine Binding Sites List in 4ub8
Chlorine binding site 3 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cl202

b:63.8
occ:1.00
 O U:HOH230 2.6 22.4 0.5
O U:HOH205 2.8 47.6 1.0
O V:HOH390 2.9 42.8 1.0
O V:HOH388 2.9 79.4 1.0
O V:HOH328 3.0 26.7 1.0
O V:HOH319 3.1 62.3 1.0
NZ U:LYS104 4.1 22.9 1.0
O U:HOH230 4.3 24.4 0.5
O V:HOH385 4.5 32.6 1.0
OD2 V:ASP53 4.6 22.8 1.0
O2 V:GOL201 4.8 35.3 1.0
O1 V:GOL201 4.9 41.4 1.0
NH1 V:ARG55 4.9 25.0 0.5

Chlorine binding site 4 out of 6 in 4ub8

Go back to Chlorine Binding Sites List in 4ub8
Chlorine binding site 4 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl404

b:20.1
occ:1.00
 NZ d:LYS317 3.0 25.2 1.0
O d:HOH580 3.2 19.9 1.0
O a:HOH518 3.3 25.4 1.0
N a:GLU333 3.4 25.2 1.0
ND2 a:ASN181 3.5 20.8 1.0
CB a:HIS332 3.7 19.6 1.0
CA a:HIS332 3.8 22.1 1.0
CG a:GLU333 3.8 27.8 1.0
CE d:LYS317 3.9 18.9 1.0
C a:HIS332 4.1 22.1 1.0
CG2 a:VAL185 4.2 19.2 1.0
OD1 a:ASN181 4.2 18.9 1.0
CG a:ASN181 4.3 21.1 1.0
CA a:GLU333 4.3 19.6 1.0
O a:HOH517 4.3 21.9 1.0
CD2 d:LEU321 4.4 19.0 1.0
O a:HOH602 4.5 19.0 1.0
CB d:LYS317 4.5 22.5 1.0
CD1 d:LEU321 4.5 18.5 1.0
CB a:GLU333 4.7 20.3 1.0
CG a:HIS332 4.7 20.4 1.0
CG d:LEU321 4.7 18.6 1.0
OE2 a:GLU333 4.8 23.4 1.0
CD a:GLU333 4.8 25.0 1.0
CG d:LYS317 4.8 17.7 1.0
CD2 a:HIS332 4.9 20.1 1.0
CD d:LYS317 5.0 19.3 1.0
O d:HOH608 5.0 22.9 1.0

Chlorine binding site 5 out of 6 in 4ub8

Go back to Chlorine Binding Sites List in 4ub8
Chlorine binding site 5 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl405

b:26.0
occ:1.00
 O a:HOH562 3.2 26.3 1.0
O c:HOH670 3.2 23.8 1.0
N a:ASN338 3.2 22.9 1.0
CA a:HIS337 3.6 22.1 1.0
N c:GLU354 3.6 23.2 1.0
N a:PHE339 3.6 23.8 1.0
CD2 a:PHE339 3.7 24.5 1.0
C a:HIS337 3.9 22.5 1.0
CA c:GLY353 4.0 24.4 1.0
CB a:HIS337 4.1 22.1 1.0
CA a:ASN338 4.1 23.4 1.0
O a:ALA336 4.1 24.8 1.0
C c:GLY353 4.3 22.7 1.0
CB a:PHE339 4.3 28.3 1.0
CB a:ASN338 4.3 23.6 1.0
CB c:GLU354 4.4 27.8 1.0
CG a:PHE339 4.4 38.0 1.0
C a:ASN338 4.4 29.5 1.0
CA a:PHE339 4.5 26.3 1.0
CE2 a:PHE339 4.5 30.7 1.0
O c:HOH623 4.5 25.4 1.0
O a:PHE339 4.5 25.7 1.0
O c:HOH671 4.6 25.1 1.0
CA c:GLU354 4.6 22.6 1.0
CG c:GLU354 4.7 32.3 1.0
N a:HIS337 4.8 23.4 1.0
CG a:HIS337 4.8 23.7 1.0
CD2 a:HIS337 4.9 21.7 1.0
C a:ALA336 4.9 22.0 1.0
C a:PHE339 5.0 24.1 1.0

Chlorine binding site 6 out of 6 in 4ub8

Go back to Chlorine Binding Sites List in 4ub8
Chlorine binding site 6 out of 6 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
u:Cl201

b:63.2
occ:1.00
 O u:HOH337 2.4 52.8 1.0
O v:HOH301 2.5 57.4 1.0
O v:HOH317 2.9 38.5 1.0
NZ u:LYS104 4.0 29.6 1.0
O v:HOH374 4.2 57.8 1.0
OD2 v:ASP53 4.4 31.9 1.0
O v:HOH368 4.4 40.1 1.0
O v:HOH323 4.7 30.6 1.0
O v:HOH373 4.7 76.7 1.0
O1 v:GOL201 4.8 50.7 1.0
NH1 v:ARG55 4.8 63.5 1.0
O v:HOH357 4.9 48.7 1.0
O2 v:GOL201 5.0 42.5 1.0
CE u:LYS104 5.0 27.4 1.0

Reference:

M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen. Native Structure of Photosystem II at 1.95A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13991
Page generated: Fri Jul 11 21:59:54 2025

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