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Chlorine in PDB 7d1u: Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution:
1.10.3.9;

Other elements in 7d1u:

The structure of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution (pdb code 7d1u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution, PDB code: 7d1u:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7d1u

Go back to Chlorine Binding Sites List in 7d1u
Chlorine binding site 1 out of 4 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:13.1
occ:1.00
 O D:HOH554 3.0 12.4 1.0
OD1 A:ASN181 3.1 8.0 1.0
O A:HOH583 3.2 12.3 1.0
NZ D:LYS317 3.6 11.5 1.0
N A:GLU333 3.6 12.9 1.0
CA A:HIS332 3.8 12.7 1.0
CB A:HIS332 3.8 12.6 1.0
CE D:LYS317 4.0 11.4 1.0
CG A:ASN181 4.0 8.0 1.0
ND2 A:ASN181 4.1 8.0 1.0
CD2 D:LEU321 4.1 10.7 1.0
CG2 A:VAL185 4.1 8.4 1.0
CB D:LYS317 4.2 11.3 1.0
CD1 D:LEU321 4.2 10.7 1.0
C A:HIS332 4.2 12.8 1.0
CG A:GLU333 4.2 13.0 1.0
O A:HOH594 4.3 13.4 1.0
CG D:LEU321 4.3 10.7 1.0
O D:LYS317 4.4 11.1 1.0
CA A:GLU333 4.6 13.0 1.0
CG D:LYS317 4.6 11.3 1.0
C D:LYS317 4.8 11.1 1.0
O A:HOH526 4.9 14.0 1.0
CG A:HIS332 4.9 12.6 1.0
CA D:LYS317 4.9 11.2 1.0
CD D:LYS317 4.9 11.4 1.0
N A:HIS332 5.0 12.6 1.0

Chlorine binding site 2 out of 4 in 7d1u

Go back to Chlorine Binding Sites List in 7d1u
Chlorine binding site 2 out of 4 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:15.7
occ:1.00
 O C:HOH671 3.0 14.5 1.0
N A:ASN338 3.1 14.7 1.0
O A:HOH587 3.1 16.9 1.0
N C:GLU354 3.2 13.9 1.0
CA A:HIS337 3.6 14.4 1.0
CA C:GLY353 3.7 14.1 1.0
CD2 A:PHE339 3.8 15.1 1.0
C A:HIS337 3.9 14.6 1.0
N A:PHE339 3.9 15.1 1.0
CB C:GLU354 3.9 13.8 1.0
C C:GLY353 3.9 14.0 1.0
O A:ALA336 4.0 14.2 1.0
CA A:ASN338 4.0 14.9 1.0
CA C:GLU354 4.1 13.8 1.0
CB A:ASN338 4.2 14.9 1.0
O C:HOH727 4.3 15.1 1.0
CB A:HIS337 4.3 14.4 1.0
CG C:GLU354 4.4 13.9 1.0
CG A:PHE339 4.4 15.1 1.0
C A:ASN338 4.4 15.0 1.0
CE2 A:PHE339 4.4 15.1 1.0
CB A:PHE339 4.4 15.1 1.0
O C:HOH696 4.6 15.8 1.0
N A:HIS337 4.7 14.3 1.0
C A:ALA336 4.8 14.2 1.0
CA A:PHE339 4.8 15.2 1.0
N C:THR355 4.8 13.7 1.0
O C:HOH641 4.8 14.9 1.0
O A:PHE339 4.9 15.3 1.0
CG A:ASN338 4.9 14.9 1.0
N C:GLY353 5.0 14.2 1.0
O C:GLY352 5.0 14.3 1.0

Chlorine binding site 3 out of 4 in 7d1u

Go back to Chlorine Binding Sites List in 7d1u
Chlorine binding site 3 out of 4 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl403

b:13.1
occ:1.00
 O d:HOH555 3.0 12.4 1.0
OD1 a:ASN181 3.1 8.0 1.0
O a:HOH582 3.2 11.3 1.0
NZ d:LYS317 3.6 11.6 1.0
N a:GLU333 3.6 12.9 1.0
CA a:HIS332 3.8 12.7 1.0
CB a:HIS332 3.8 12.6 1.0
CE d:LYS317 4.0 11.5 1.0
CG a:ASN181 4.0 8.0 1.0
ND2 a:ASN181 4.1 8.0 1.0
CD2 d:LEU321 4.1 10.7 1.0
CG2 a:VAL185 4.1 8.4 1.0
CB d:LYS317 4.2 11.4 1.0
CD1 d:LEU321 4.2 10.7 1.0
C a:HIS332 4.2 12.8 1.0
CG a:GLU333 4.2 13.1 1.0
O a:HOH593 4.3 13.5 1.0
CG d:LEU321 4.3 10.7 1.0
O d:LYS317 4.4 11.2 1.0
CA a:GLU333 4.6 13.1 1.0
CG d:LYS317 4.6 11.4 1.0
C d:LYS317 4.8 11.2 1.0
O a:HOH526 4.9 13.6 1.0
CG a:HIS332 4.9 12.6 1.0
CA d:LYS317 4.9 11.3 1.0
CD d:LYS317 4.9 11.5 1.0
N a:HIS332 5.0 12.6 1.0

Chlorine binding site 4 out of 4 in 7d1u

Go back to Chlorine Binding Sites List in 7d1u
Chlorine binding site 4 out of 4 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl404

b:15.7
occ:1.00
 O c:HOH672 3.0 14.5 1.0
N a:ASN338 3.1 14.7 1.0
O a:HOH586 3.1 16.9 1.0
N c:GLU354 3.2 13.9 1.0
CA a:HIS337 3.6 14.5 1.0
CA c:GLY353 3.7 14.1 1.0
CD2 a:PHE339 3.8 15.1 1.0
C a:HIS337 3.9 14.6 1.0
N a:PHE339 3.9 15.1 1.0
CB c:GLU354 3.9 13.9 1.0
C c:GLY353 3.9 14.0 1.0
O a:ALA336 4.0 14.2 1.0
CA a:ASN338 4.0 14.9 1.0
CA c:GLU354 4.1 13.9 1.0
CB a:ASN338 4.2 14.9 1.0
O c:HOH727 4.3 14.9 1.0
CB a:HIS337 4.3 14.5 1.0
CG c:GLU354 4.4 13.9 1.0
CG a:PHE339 4.4 15.1 1.0
C a:ASN338 4.4 15.0 1.0
CE2 a:PHE339 4.4 15.1 1.0
CB a:PHE339 4.4 15.1 1.0
O c:HOH696 4.6 15.7 1.0
N a:HIS337 4.7 14.3 1.0
C a:ALA336 4.8 14.2 1.0
CA a:PHE339 4.8 15.1 1.0
N c:THR355 4.8 13.8 1.0
O c:HOH641 4.8 14.8 1.0
O a:PHE339 4.9 15.3 1.0
CG a:ASN338 4.9 14.9 1.0
N c:GLY353 5.0 14.3 1.0
O c:GLY352 5.0 14.4 1.0

Reference:

K.Kato, N.Miyazaki, T.Hamaguchi, Y.Nakajima, F.Akita, K.Yonekura, J.R.Shen. High-Resolution Cryo-Em Structure of Photosystem II Reveals Damage From High-Dose Electron Beams Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01919-3
Page generated: Mon Jul 29 19:57:22 2024

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