Chlorine in PDB 8irc: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation):
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation), PDB code: 8irc was solved by H.Li, M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.77, 231.76, 288.58, 90, 90, 90
R / Rfree (%) 14.1 / 17.6

Other elements in 8irc:

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) (pdb code 8irc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation), PDB code: 8irc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8irc

Go back to Chlorine Binding Sites List in 8irc
Chlorine binding site 1 out of 4 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:42.4
occ:1.00
 O D:HOH550 3.1 40.4 1.0
NZ D:LYS317 3.1 45.6 1.0
N A:GLU333 3.3 40.3 1.0
O A:HOH534 3.4 44.9 1.0
ND2 A:ASN181 3.4 39.0 1.0
CE D:LYS317 3.8 45.1 1.0
CA A:HIS332 3.8 42.3 1.0
CB A:HIS332 3.8 40.0 1.0
CG A:GLU333 3.9 42.9 1.0
C A:HIS332 4.0 42.8 1.0
OD1 A:ASN181 4.1 42.2 1.0
O D:HOH512 4.1 42.0 1.0
CG A:ASN181 4.2 43.8 1.0
CA A:GLU333 4.3 45.4 1.0
CG2 A:VAL185 4.3 37.9 1.0
CD1 D:LEU321 4.4 39.2 1.0
O A:HOH569 4.4 47.0 1.0
CB D:LYS317 4.5 43.2 1.0
CD2 D:LEU321 4.5 42.0 1.0
CB A:GLU333 4.7 42.7 1.0
CG D:LEU321 4.8 43.0 1.0
CG A:HIS332 4.8 46.2 1.0
CG D:LYS317 4.8 43.9 1.0
O D:LYS317 4.9 43.5 1.0
CD D:LYS317 4.9 43.6 1.0
CD A:GLU333 4.9 45.5 1.0
OE2 A:GLU333 5.0 47.2 1.0
CD2 A:HIS332 5.0 44.2 1.0

Chlorine binding site 2 out of 4 in 8irc

Go back to Chlorine Binding Sites List in 8irc
Chlorine binding site 2 out of 4 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:46.3
occ:1.00
 O C:HOH702 3.1 44.5 1.0
N A:ASN338 3.1 46.2 1.0
O A:HOH583 3.2 51.5 1.0
N C:GLU354 3.3 49.1 1.0
N A:PHE339 3.6 46.2 1.0
CA A:HIS337 3.7 46.8 1.0
CA C:GLY353 3.8 45.3 1.0
CD2 A:PHE339 3.8 51.4 1.0
C A:HIS337 3.9 50.5 1.0
C C:GLY353 4.1 48.2 1.0
CA A:ASN338 4.1 49.1 1.0
CB C:GLU354 4.2 45.9 1.0
CB A:HIS337 4.2 45.6 1.0
O A:ALA336 4.2 50.2 1.0
CB A:PHE339 4.3 48.3 1.0
CA C:GLU354 4.3 47.3 1.0
C A:ASN338 4.3 48.4 1.0
CB A:ASN338 4.4 46.4 1.0
O C:HOH691 4.4 45.1 1.0
CG A:PHE339 4.4 51.9 1.0
CA A:PHE339 4.5 49.2 1.0
O A:PHE339 4.5 47.0 1.0
O C:HOH737 4.5 51.5 1.0
CE2 A:PHE339 4.7 46.4 1.0
N A:HIS337 4.8 42.4 1.0
N C:THR355 4.8 42.8 1.0
CD2 A:HIS337 4.8 46.0 1.0
CG A:HIS337 4.9 50.6 1.0
C A:PHE339 5.0 48.8 1.0
NE2 C:GLN313 5.0 46.4 1.0
CG A:ASN338 5.0 49.8 1.0
C A:ALA336 5.0 45.7 1.0
O C:GLY352 5.0 45.7 1.0

Chlorine binding site 3 out of 4 in 8irc

Go back to Chlorine Binding Sites List in 8irc
Chlorine binding site 3 out of 4 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl402

b:49.0
occ:1.00
 NZ d:LYS317 3.1 46.1 1.0
O d:HOH560 3.2 53.4 1.0
O a:HOH558 3.3 48.6 1.0
N a:GLU333 3.3 42.5 1.0
ND2 a:ASN181 3.5 44.5 1.0
CA a:HIS332 3.8 48.4 1.0
CB a:HIS332 3.8 47.2 1.0
CE d:LYS317 3.8 45.8 1.0
CG a:GLU333 3.9 48.2 1.0
C a:HIS332 4.0 46.7 1.0
OD1 a:ASN181 4.1 44.8 1.0
CG2 a:VAL185 4.2 44.6 1.0
CG a:ASN181 4.2 46.5 1.0
O d:HOH527 4.3 49.2 1.0
CA a:GLU333 4.3 49.0 1.0
CD1 d:LEU321 4.4 43.5 1.0
CD2 d:LEU321 4.5 43.7 1.0
O a:HOH567 4.5 51.0 1.0
CB d:LYS317 4.6 44.2 1.0
CB a:GLU333 4.7 46.8 1.0
CG a:HIS332 4.7 50.1 1.0
CG d:LEU321 4.7 50.0 1.0
CG d:LYS317 4.8 43.9 1.0
CD2 a:HIS332 4.9 47.2 1.0
CD a:GLU333 4.9 48.1 1.0
OE2 a:GLU333 4.9 48.6 1.0
CD d:LYS317 4.9 47.7 1.0
O d:LYS317 4.9 46.9 1.0

Chlorine binding site 4 out of 4 in 8irc

Go back to Chlorine Binding Sites List in 8irc
Chlorine binding site 4 out of 4 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl403

b:55.5
occ:1.00
 O a:HOH602 2.9 56.6 1.0
O c:HOH670 3.0 54.5 1.0
N a:ASN338 3.2 51.8 1.0
N c:GLU354 3.4 51.8 1.0
N a:PHE339 3.6 53.5 1.0
CA a:HIS337 3.6 49.2 1.0
CD2 a:PHE339 3.7 52.8 1.0
CA c:GLY353 3.9 49.3 1.0
C a:HIS337 3.9 48.9 1.0
C c:GLY353 4.1 52.8 1.0
CB a:HIS337 4.1 41.8 1.0
CA a:ASN338 4.1 53.7 1.0
O a:ALA336 4.2 55.4 1.0
CB c:GLU354 4.2 49.5 1.0
CB a:PHE339 4.3 50.1 1.0
C a:ASN338 4.4 54.0 1.0
CA c:GLU354 4.4 51.3 1.0
CG a:PHE339 4.4 54.3 1.0
CB a:ASN338 4.4 52.6 1.0
O c:HOH679 4.4 48.8 1.0
CA a:PHE339 4.5 56.2 1.0
CE2 a:PHE339 4.5 55.8 1.0
O a:PHE339 4.5 58.2 1.0
O c:HOH739 4.6 58.4 1.0
N a:HIS337 4.8 47.5 1.0
CG a:HIS337 4.9 50.6 1.0
CD2 a:HIS337 4.9 48.5 1.0
C a:ALA336 4.9 53.5 1.0
N c:THR355 4.9 46.0 1.0
C a:PHE339 5.0 54.5 1.0
CG c:GLU354 5.0 49.9 1.0
NE2 c:GLN313 5.0 51.5 1.0

Reference:

H.Li, Y.Nakajima, E.Nango, S.Owada, D.Yamada, K.Hashimoto, F.Luo, R.Tanaka, F.Akita, K.Kato, J.M.Kang, Y.Saitoh, S.Kishi, H.Yu, N.Matsubara, H.Fujii, M.Sugahara, M.Suzuki, T.Masuda, T.Kimura, T.N.Thao, S.Yonekura, L.J.Yu, T.Tosha, K.Tono, Y.Joti, T.Hatsui, M.Yabashi, M.Kubo, S.Iwata, H.Isobe, K.Yamaguchi, M.Suga, J.R.Shen. Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Tue Jul 30 10:37:38 2024

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