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Chlorine in PDB 4ub6: Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6 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) 62.29 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.744, 229.989, 288.337, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.8

Other elements in 4ub6:

The structure of Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser (pdb code 4ub6). 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-1) By A Femtosecond X-Ray Laser, PDB code: 4ub6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ub6

Go back to Chlorine Binding Sites List in 4ub6
Chlorine binding site 1 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:18.8
occ:1.00
 O D:HOH578 3.0 13.8 1.0
NZ D:LYS317 3.3 15.4 1.0
ND2 A:ASN181 3.3 13.4 1.0
O A:HOH560 3.4 18.5 1.0
N A:GLU333 3.4 15.2 1.0
CB A:HIS332 3.7 14.6 1.0
CA A:HIS332 3.8 14.5 1.0
CG A:GLU333 3.9 14.8 1.0
CE D:LYS317 4.1 15.8 1.0
C A:HIS332 4.1 30.9 1.0
OD1 A:ASN181 4.2 15.0 1.0
CG2 A:VAL185 4.2 14.6 1.0
CG A:ASN181 4.2 13.3 1.0
CD2 D:LEU321 4.2 13.8 1.0
CD1 D:LEU321 4.3 14.3 1.0
O A:HOH559 4.4 18.9 1.0
CA A:GLU333 4.4 18.1 1.0
CB D:LYS317 4.5 16.5 1.0
CG D:LEU321 4.5 14.8 1.0
O A:HOH524 4.6 14.3 1.0
CG A:HIS332 4.8 14.7 1.0
CB A:GLU333 4.8 15.0 1.0
CG D:LYS317 4.9 15.9 1.0
CD A:GLU333 4.9 30.2 1.0
OE2 A:GLU333 4.9 22.1 1.0

Chlorine binding site 2 out of 6 in 4ub6

Go back to Chlorine Binding Sites List in 4ub6
Chlorine binding site 2 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:19.1
occ:1.00
 O C:HOH674 3.0 18.6 1.0
O A:HOH603 3.0 23.1 1.0
N A:ASN338 3.2 22.5 1.0
N C:GLU354 3.4 17.7 1.0
CA A:HIS337 3.7 28.3 1.0
N A:PHE339 3.8 21.0 1.0
CA C:GLY353 3.8 19.1 1.0
CD2 A:PHE339 3.9 18.9 1.0
C A:HIS337 3.9 17.2 1.0
C C:GLY353 4.1 17.8 1.0
O A:ALA336 4.1 16.8 1.0
CB C:GLU354 4.1 18.1 1.0
CA A:ASN338 4.2 21.8 1.0
CB A:HIS337 4.3 16.7 1.0
O C:HOH629 4.4 18.6 1.0
CA C:GLU354 4.4 17.8 1.0
CB A:PHE339 4.4 31.4 1.0
CB A:ASN338 4.5 20.9 1.0
C A:ASN338 4.5 27.2 1.0
CG A:PHE339 4.5 18.9 1.0
O A:PHE339 4.6 23.4 1.0
O A:HOH630 4.6 18.4 1.0
CA A:PHE339 4.7 18.4 1.0
CG C:GLU354 4.7 22.0 1.0
CE2 A:PHE339 4.7 19.2 1.0
N A:HIS337 4.8 16.6 1.0
CD2 A:HIS337 4.9 19.9 1.0
N C:THR355 4.9 17.9 1.0
C A:ALA336 4.9 25.4 1.0
CG A:HIS337 4.9 23.1 1.0
O C:GLY352 5.0 18.8 1.0
NE2 C:GLN313 5.0 19.8 1.0

Chlorine binding site 3 out of 6 in 4ub6

Go back to Chlorine Binding Sites List in 4ub6
Chlorine binding site 3 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl201

b:50.8
occ:1.00
 O U:HOH305 2.3 46.5 1.0
O V:HOH407 2.5 50.5 1.0
O U:HOH331 2.5 35.4 1.0
O V:HOH386 2.8 71.1 1.0
O V:HOH388 3.0 42.5 1.0
O V:HOH327 3.0 26.3 1.0
O B:HOH935 3.3 51.8 1.0
NZ U:LYS104 4.0 20.9 1.0
O B:HOH940 4.3 37.3 1.0
O V:HOH383 4.6 26.4 1.0
OD2 V:ASP53 4.6 21.3 1.0
O1 B:GOL630 4.8 40.9 1.0
O2 B:GOL630 4.8 26.3 1.0

Chlorine binding site 4 out of 6 in 4ub6

Go back to Chlorine Binding Sites List in 4ub6
Chlorine binding site 4 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl404

b:20.9
occ:1.00
 NZ d:LYS317 3.0 16.8 1.0
N a:GLU333 3.3 18.1 1.0
O a:HOH519 3.3 20.2 1.0
O d:HOH575 3.3 19.4 1.0
ND2 a:ASN181 3.5 16.5 1.0
CB a:HIS332 3.6 18.2 1.0
CA a:HIS332 3.8 18.2 1.0
CG a:GLU333 3.8 18.8 1.0
CE d:LYS317 3.9 16.4 1.0
C a:HIS332 4.0 25.7 1.0
CG2 a:VAL185 4.1 17.6 1.0
O a:HOH518 4.2 20.2 1.0
CD2 d:LEU321 4.2 17.6 1.0
OD1 a:ASN181 4.2 19.7 1.0
CA a:GLU333 4.3 26.2 1.0
CG a:ASN181 4.3 19.6 1.0
O a:HOH603 4.5 18.5 1.0
CD1 d:LEU321 4.5 17.1 1.0
CB a:GLU333 4.6 18.4 1.0
CB d:LYS317 4.6 16.2 1.0
CG a:HIS332 4.6 18.8 1.0
CG d:LEU321 4.7 17.2 1.0
OE2 a:GLU333 4.7 21.1 1.0
CD a:GLU333 4.8 21.1 1.0
CG d:LYS317 4.9 16.2 1.0
CD2 a:HIS332 4.9 18.7 1.0

Chlorine binding site 5 out of 6 in 4ub6

Go back to Chlorine Binding Sites List in 4ub6
Chlorine binding site 5 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl405

b:26.1
occ:1.00
 O a:HOH563 3.0 21.4 1.0
O c:HOH1069 3.0 22.3 1.0
N a:ASN338 3.2 27.0 1.0
N c:GLU354 3.6 21.0 1.0
N a:PHE339 3.7 27.1 1.0
CD2 a:PHE339 3.7 30.9 1.0
CA a:HIS337 3.7 20.7 1.0
CA c:GLY353 3.9 21.5 1.0
C a:HIS337 3.9 21.1 1.0
CA a:ASN338 4.1 22.0 1.0
C c:GLY353 4.2 22.3 1.0
CB a:HIS337 4.2 20.7 1.0
O a:ALA336 4.2 20.3 1.0
O c:HOH1025 4.3 24.6 1.0
CB a:PHE339 4.4 27.4 1.0
CG a:PHE339 4.4 26.4 1.0
CB c:GLU354 4.4 24.2 1.0
CE2 a:PHE339 4.4 25.8 1.0
C a:ASN338 4.4 22.4 1.0
CB a:ASN338 4.4 22.2 1.0
O a:PHE339 4.5 31.7 1.0
CA a:PHE339 4.5 24.9 1.0
CA c:GLU354 4.6 26.0 1.0
O c:HOH1070 4.6 22.6 1.0
CG c:GLU354 4.8 21.7 1.0
N a:HIS337 4.8 20.3 1.0
CD2 a:HIS337 4.9 20.3 1.0
CG a:HIS337 4.9 20.3 1.0
O c:GLY352 4.9 22.5 1.0
C a:ALA336 5.0 37.1 1.0
N c:THR355 5.0 23.3 1.0
C a:PHE339 5.0 28.8 1.0

Chlorine binding site 6 out of 6 in 4ub6

Go back to Chlorine Binding Sites List in 4ub6
Chlorine binding site 6 out of 6 in the Native Structure of Photosystem II (Dataset-1) 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-1) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Cl201

b:62.4
occ:1.00
 O b:HOH754 2.4 53.7 1.0
O u:HOH242 2.5 44.0 1.0
O v:HOH319 2.8 35.1 1.0
O v:HOH375 3.7 44.7 1.0
NZ u:LYS104 4.0 26.5 1.0
OD2 v:ASP53 4.3 29.5 1.0
O v:HOH369 4.4 29.2 1.0
O v:HOH325 4.7 28.4 1.0
O v:HOH359 4.7 48.8 1.0
O v:HOH374 4.8 61.6 1.0
O2 b:GOL630 4.9 39.5 1.0
O1 b:GOL630 4.9 50.8 1.0
NH1 v:ARG55 4.9 51.8 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 26 02:09:57 2024

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