Atomistry » Chlorine » PDB 5k9v-5kge » 5kaf
Atomistry »
  Chlorine »
    PDB 5k9v-5kge »
      5kaf »

Chlorine in PDB 5kaf: Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, F.Fuller, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.-C.Weng, M.S.Hunter, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.12 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.731, 223.815, 330.818, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30.3

Other elements in 5kaf:

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution (pdb code 5kaf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5kaf

Go back to Chlorine Binding Sites List in 5kaf
Chlorine binding site 1 out of 4 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:43.5
occ:0.93
 N A:GLU333 3.3 38.0 1.0
NZ D:LYS317 3.3 38.4 1.0
CA A:HIS332 3.5 33.3 1.0
CB A:HIS332 3.6 41.7 1.0
ND2 A:ASN181 3.7 28.9 1.0
C A:HIS332 3.9 42.7 1.0
CE D:LYS317 4.0 27.1 1.0
CG A:GLU333 4.3 36.2 1.0
CA A:GLU333 4.4 38.4 1.0
OD1 A:ASN181 4.5 37.0 1.0
CD2 D:LEU321 4.5 31.5 1.0
CG A:ASN181 4.5 35.9 1.0
CG A:HIS332 4.6 38.3 1.0
CD1 D:LEU321 4.6 32.1 1.0
CB D:LYS317 4.6 28.7 1.0
CG2 A:VAL185 4.7 34.9 1.0
CG D:LEU321 4.7 30.6 1.0
O D:LYS317 4.8 38.5 1.0
N A:HIS332 4.8 34.1 1.0
CD2 A:HIS332 4.8 31.9 1.0
CB A:GLU333 4.9 36.1 1.0
O A:MET331 5.0 41.2 1.0

Chlorine binding site 2 out of 4 in 5kaf

Go back to Chlorine Binding Sites List in 5kaf
Chlorine binding site 2 out of 4 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:44.0
occ:1.00
 N A:ASN338 3.0 38.7 1.0
CD2 A:PHE339 3.4 42.7 1.0
N A:PHE339 3.4 36.4 1.0
CA A:HIS337 3.6 35.8 1.0
N C:GLU354 3.7 39.5 1.0
C A:HIS337 3.8 35.5 1.0
CA A:ASN338 4.0 33.0 1.0
CB A:PHE339 4.0 38.5 1.0
C A:ASN338 4.1 36.3 1.0
CA C:GLY353 4.1 28.9 1.0
CG A:PHE339 4.1 37.1 1.0
CB A:HIS337 4.2 45.6 1.0
O A:ALA336 4.2 42.4 1.0
CA A:PHE339 4.3 33.8 1.0
CE2 A:PHE339 4.3 32.9 1.0
CB A:ASN338 4.4 32.4 1.0
CB C:GLU354 4.4 44.3 1.0
C C:GLY353 4.5 35.0 1.0
O A:PHE339 4.5 40.2 1.0
CD2 A:HIS337 4.6 38.2 1.0
CA C:GLU354 4.7 37.5 1.0
N A:HIS337 4.7 36.6 1.0
CG A:HIS337 4.8 39.6 1.0
C A:PHE339 4.9 37.2 1.0
C A:ALA336 4.9 39.3 1.0
CG C:GLU354 4.9 33.6 1.0
CG A:ASN338 5.0 33.8 1.0
O A:HIS337 5.0 29.7 1.0

Chlorine binding site 3 out of 4 in 5kaf

Go back to Chlorine Binding Sites List in 5kaf
Chlorine binding site 3 out of 4 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl603

b:59.5
occ:1.00
 NZ d:LYS317 3.2 48.9 1.0
CA a:HIS332 3.5 32.8 1.0
O d:LYS317 3.5 30.0 1.0
N a:GLU333 3.6 39.9 1.0
ND2 a:ASN181 3.8 36.2 1.0
CD2 d:LEU321 3.9 31.3 1.0
CB d:LYS317 3.9 31.0 1.0
CB a:HIS332 3.9 35.0 1.0
CE d:LYS317 4.0 54.4 1.0
CG d:LEU321 4.0 29.6 1.0
C a:HIS332 4.1 36.4 1.0
CD1 d:LEU321 4.2 30.1 1.0
C d:LYS317 4.2 33.9 1.0
O a:MET331 4.3 38.2 1.0
CA d:LYS317 4.3 34.1 1.0
CG d:LYS317 4.4 37.0 1.0
N a:HIS332 4.5 36.1 1.0
CA a:GLU333 4.7 37.5 1.0
C a:MET331 4.8 40.5 1.0
CG a:ASN181 4.8 36.9 1.0
CD d:LYS317 4.9 47.8 1.0

Chlorine binding site 4 out of 4 in 5kaf

Go back to Chlorine Binding Sites List in 5kaf
Chlorine binding site 4 out of 4 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl604

b:42.4
occ:1.00
 N a:ASN338 3.2 34.5 1.0
CD2 a:PHE339 3.3 42.0 1.0
N a:PHE339 3.7 34.6 1.0
CA a:HIS337 3.7 34.5 1.0
N c:GLU354 3.7 31.3 1.0
C a:HIS337 4.0 33.2 1.0
CB a:PHE339 4.0 45.9 1.0
CG a:PHE339 4.1 43.9 1.0
CA c:GLY353 4.1 35.4 1.0
CE2 a:PHE339 4.2 37.7 1.0
CA a:ASN338 4.2 37.4 1.0
O a:ALA336 4.2 42.9 1.0
C a:ASN338 4.3 37.2 1.0
CB a:HIS337 4.3 38.1 1.0
CA a:PHE339 4.4 41.8 1.0
CB c:GLU354 4.4 42.0 1.0
O c:HOH606 4.4 34.5 1.0
C c:GLY353 4.5 32.4 1.0
CB a:ASN338 4.6 36.6 1.0
O a:PHE339 4.6 38.1 1.0
CD2 a:HIS337 4.6 38.8 1.0
CA c:GLU354 4.7 30.6 1.0
N a:HIS337 4.8 35.9 1.0
CG a:HIS337 4.9 35.9 1.0
C a:PHE339 4.9 43.7 1.0
C a:ALA336 5.0 37.3 1.0

Reference:

I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Brauer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano. Structure of Photosystem II and Substrate Binding at Room Temperature. Nature V. 540 453 2016.
ISSN: ESSN 1476-4687
PubMed: 27871088
DOI: 10.1038/NATURE20161
Page generated: Sat Jul 12 04:00:01 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