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Chlorine in PDB 5mx2: Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution

Enzymatic activity of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution

All present enzymatic activity of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution, PDB code: 5mx2 was solved by M.Zhang, M.Bommer, R.Chatterjee, R.Hussain, J.Kern, J.Yano, H.Dau, H.Dobbek, A.Zouni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.65 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.326, 219.617, 304.043, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26

Other elements in 5mx2:

The structure of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution (pdb code 5mx2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution, PDB code: 5mx2:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5mx2

Go back to Chlorine Binding Sites List in 5mx2
Chlorine binding site 1 out of 4 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:57.4
occ:1.00
 O A:HOH568 3.3 39.9 1.0
N A:GLU333 3.4 42.1 1.0
ND2 A:ASN181 3.6 22.7 1.0
CA A:HIS332 3.7 39.2 1.0
O A:HOH569 3.8 32.8 1.0
CB A:HIS332 4.0 39.0 1.0
C A:HIS332 4.1 40.5 1.0
OD1 A:ASN181 4.2 27.0 1.0
CE D:LYS317 4.2 34.9 1.0
CB D:LYS317 4.2 25.7 1.0
CG A:ASN181 4.4 22.1 1.0
CG2 A:VAL185 4.4 22.1 1.0
CG D:LYS317 4.4 28.6 1.0
CG A:GLU333 4.5 45.1 1.0
CA A:GLU333 4.5 44.3 1.0
CD1 D:LEU321 4.5 17.3 1.0
CD2 D:LEU321 4.6 21.8 1.0
NZ D:LYS317 4.6 31.3 1.0
O A:MET331 4.7 34.0 1.0
CD D:LYS317 4.7 29.2 1.0
CG D:LEU321 4.8 20.8 1.0
N A:HIS332 4.9 37.1 1.0

Chlorine binding site 2 out of 4 in 5mx2

Go back to Chlorine Binding Sites List in 5mx2
Chlorine binding site 2 out of 4 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:57.5
occ:1.00
 N A:ASN338 2.9 53.8 1.0
O C:HOH656 3.1 47.5 1.0
N C:GLU354 3.2 51.3 1.0
CG C:GLU354 3.5 68.2 1.0
CA A:HIS337 3.6 44.4 1.0
CD2 A:PHE339 3.6 43.6 1.0
N A:PHE339 3.6 46.8 1.0
C A:HIS337 3.7 47.2 1.0
CA A:ASN338 3.9 49.2 1.0
CA C:GLY353 3.9 38.9 1.0
O A:ALA336 3.9 51.0 1.0
CB C:GLU354 4.0 61.4 1.0
C C:GLY353 4.1 40.8 1.0
CB A:ASN338 4.1 44.1 1.0
C A:ASN338 4.2 44.7 1.0
CA C:GLU354 4.2 0.4 1.0
CB A:PHE339 4.3 46.4 1.0
CE2 A:PHE339 4.3 40.3 1.0
CG A:PHE339 4.3 46.2 1.0
CD C:GLU354 4.3 73.4 1.0
CB A:HIS337 4.3 48.3 1.0
CA A:PHE339 4.5 45.8 1.0
O A:PHE339 4.6 45.8 1.0
N A:HIS337 4.6 47.8 1.0
N C:THR355 4.7 48.9 1.0
C A:ALA336 4.7 53.0 1.0
OE2 C:GLU354 4.8 64.7 1.0
O C:HOH634 4.8 40.2 1.0
CG A:ASN338 4.8 47.0 1.0
C C:GLU354 4.9 1.0 1.0
O A:HIS337 5.0 43.9 1.0
CG A:HIS337 5.0 47.7 1.0

Chlorine binding site 3 out of 4 in 5mx2

Go back to Chlorine Binding Sites List in 5mx2
Chlorine binding site 3 out of 4 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl402

b:52.1
occ:1.00
 O d:HOH547 3.2 29.7 1.0
ND2 a:ASN181 3.3 20.1 1.0
O a:HOH567 3.6 42.0 1.0
N a:GLU333 3.6 36.5 1.0
CA a:HIS332 3.7 34.0 1.0
OD1 a:ASN181 3.7 18.0 1.0
CB a:HIS332 3.8 34.0 1.0
CG a:ASN181 3.9 17.7 1.0
CG2 a:VAL185 4.0 24.4 1.0
O a:HOH571 4.1 31.8 1.0
C a:HIS332 4.2 36.0 1.0
CE d:LYS317 4.3 34.4 1.0
CD2 d:LEU321 4.3 24.4 1.0
CB d:LYS317 4.4 27.3 1.0
CD1 d:LEU321 4.5 23.1 1.0
CD d:LYS317 4.6 27.1 1.0
CG d:LEU321 4.7 22.6 1.0
CA a:GLU333 4.7 39.8 1.0
O d:LYS317 4.7 26.2 1.0
CG d:LYS317 4.7 30.5 1.0
CG a:GLU333 4.8 44.3 1.0
N a:HIS332 4.9 30.7 1.0
CG a:HIS332 4.9 42.3 1.0

Chlorine binding site 4 out of 4 in 5mx2

Go back to Chlorine Binding Sites List in 5mx2
Chlorine binding site 4 out of 4 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl403

b:40.9
occ:1.00
 N a:ASN338 2.6 33.2 1.0
N a:PHE339 3.4 27.0 1.0
CA a:HIS337 3.4 29.8 1.0
C a:HIS337 3.4 31.2 1.0
N c:GLU354 3.4 32.6 1.0
CA a:ASN338 3.5 30.1 1.0
O c:HOH621 3.5 32.0 1.0
CD2 a:PHE339 3.6 29.0 1.0
CB a:ASN338 3.8 25.3 1.0
C a:ASN338 3.8 29.5 1.0
O a:ALA336 3.9 33.9 1.0
CB c:GLU354 3.9 33.8 1.0
CA c:GLY353 4.1 25.2 1.0
CB a:HIS337 4.1 28.3 1.0
CE2 a:PHE339 4.2 25.5 1.0
CG a:PHE339 4.3 31.4 1.0
C c:GLY353 4.3 28.2 1.0
CA c:GLU354 4.3 28.0 1.0
CA a:PHE339 4.4 28.9 1.0
CB a:PHE339 4.4 29.2 1.0
O a:PHE339 4.4 35.3 1.0
N a:HIS337 4.5 31.7 1.0
O c:HOH661 4.6 28.1 1.0
O a:HIS337 4.6 31.8 1.0
CG a:ASN338 4.6 28.9 1.0
C a:ALA336 4.6 33.6 1.0
CG a:HIS337 4.7 34.5 1.0
CD2 a:HIS337 4.9 37.8 1.0
C a:PHE339 4.9 30.7 1.0
OE1 c:GLU354 5.0 48.6 1.0

Reference:

M.Zhang, M.Bommer, R.Chatterjee, R.Hussein, J.Yano, H.Dau, J.Kern, H.Dobbek, A.Zouni. Structural Insights Into the Light-Driven Auto-Assembly Process of the Water-Oxidizing MN4CAO5-Cluster in Photosystem II. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28718766
DOI: 10.7554/ELIFE.26933
Page generated: Fri Jul 26 13:01:12 2024

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