Atomistry » Chlorine » PDB 8ihb-8it5 » 8irc
Atomistry »
  Chlorine »
    PDB 8ihb-8it5 »
      8irc »

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: Sun Jul 13 12:21:23 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy