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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: Fri Jul 26 10:34:14 2024

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