Chlorine in PDB 5tis: Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

Enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

All present enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.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.V.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.Braeuer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, 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.Watermann, 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, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.870, 223.140, 310.710, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 5tis:

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex 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 Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex (pdb code 5tis). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5tis

Go back to Chlorine Binding Sites List in 5tis
Chlorine binding site 1 out of 4 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:33.0
occ:1.00
O A:HOH734 3.0 35.2 1.0
O D:HOH530 3.2 29.8 1.0
NZ D:LYS317 3.2 37.1 1.0
ND2 A:ASN181 3.3 33.3 1.0
N A:GLU333 3.5 29.1 1.0
CE D:LYS317 3.8 38.1 1.0
CA A:HIS332 3.8 35.8 1.0
CB A:HIS332 3.8 30.3 1.0
CG A:GLU333 4.0 33.4 1.0
C A:HIS332 4.1 33.5 1.0
OD1 A:ASN181 4.1 36.7 1.0
CG A:ASN181 4.2 32.5 1.0
CG2 A:VAL185 4.3 31.5 1.0
O A:HOH730 4.4 40.8 1.0
CA A:GLU333 4.4 35.0 1.0
CD1 D:LEU321 4.6 25.2 1.0
CB D:LYS317 4.6 33.2 1.0
O A:HOH758 4.6 34.2 1.0
CD2 D:LEU321 4.6 31.8 1.0
CG D:LEU321 4.8 31.1 1.0
CB A:GLU333 4.8 33.7 1.0
CG A:HIS332 4.9 36.4 1.0
CD A:GLU333 4.9 37.2 1.0
CG D:LYS317 5.0 35.5 1.0

Chlorine binding site 2 out of 4 in 5tis

Go back to Chlorine Binding Sites List in 5tis
Chlorine binding site 2 out of 4 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:33.9
occ:1.00
O A:HOH773 2.9 31.6 1.0
O C:HOH654 3.1 34.1 1.0
N A:ASN338 3.2 44.5 1.0
CD2 A:PHE339 3.4 45.7 1.0
N C:GLU354 3.5 30.3 1.0
N A:PHE339 3.7 36.7 1.0
CA A:HIS337 3.8 30.1 1.0
CA C:GLY353 4.0 29.8 1.0
C A:HIS337 4.0 41.0 1.0
CA A:ASN338 4.1 38.0 1.0
CE2 A:PHE339 4.2 41.8 1.0
CG A:PHE339 4.2 46.8 1.0
CB C:GLU354 4.2 36.0 1.0
CB A:PHE339 4.2 38.5 1.0
C C:GLY353 4.2 33.5 1.0
O A:ALA336 4.3 35.2 1.0
C A:ASN338 4.3 37.9 1.0
CB A:HIS337 4.3 27.3 1.0
O C:HOH670 4.4 36.1 1.0
O A:HOH771 4.4 37.0 1.0
CB A:ASN338 4.4 38.9 1.0
CA C:GLU354 4.4 35.4 1.0
CA A:PHE339 4.5 39.2 1.0
O A:PHE339 4.7 42.1 1.0
CD2 A:HIS337 4.9 31.5 1.0
N A:HIS337 4.9 36.2 1.0
N C:THR355 4.9 29.5 1.0
CG A:HIS337 5.0 32.3 1.0

Chlorine binding site 3 out of 4 in 5tis

Go back to Chlorine Binding Sites List in 5tis
Chlorine binding site 3 out of 4 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl603

b:33.9
occ:1.00
O a:HOH746 3.0 30.1 1.0
O d:HOH568 3.1 35.4 1.0
NZ d:LYS317 3.3 35.9 1.0
N a:GLU333 3.4 23.5 1.0
ND2 a:ASN181 3.4 29.4 1.0
CA a:HIS332 3.7 32.5 1.0
CB a:HIS332 3.7 27.9 1.0
CE d:LYS317 3.9 32.1 1.0
C a:HIS332 4.0 27.5 1.0
CG a:GLU333 4.1 28.3 1.0
OD1 a:ASN181 4.3 28.1 1.0
O d:HOH529 4.3 29.4 1.0
CG a:ASN181 4.3 30.2 1.0
CG2 a:VAL185 4.3 31.4 1.0
CA a:GLU333 4.3 32.0 1.0
CD2 d:LEU321 4.5 31.4 1.0
CB d:LYS317 4.5 30.9 1.0
CD1 d:LEU321 4.6 37.2 1.0
CG a:HIS332 4.7 27.0 1.0
CG d:LEU321 4.8 28.9 1.0
CB a:GLU333 4.8 23.1 1.0
CG d:LYS317 4.8 31.8 1.0
O d:LYS317 4.9 32.4 1.0
N a:HIS332 5.0 28.5 1.0
CD d:LYS317 5.0 36.7 1.0

Chlorine binding site 4 out of 4 in 5tis

Go back to Chlorine Binding Sites List in 5tis
Chlorine binding site 4 out of 4 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl604

b:35.5
occ:1.00
O c:HOH667 3.0 34.1 1.0
N a:ASN338 3.1 35.4 1.0
O a:HOH763 3.2 37.8 0.9
N c:GLU354 3.4 32.8 1.0
CD2 a:PHE339 3.6 41.7 1.0
N a:PHE339 3.7 31.8 1.0
CA a:HIS337 3.7 30.9 1.0
C a:HIS337 3.9 32.8 1.0
CA c:GLY353 4.0 32.5 1.0
CA a:ASN338 4.0 36.8 1.0
CB c:GLU354 4.1 32.8 1.0
O a:ALA336 4.2 31.9 1.0
C c:GLY353 4.2 35.1 1.0
CB a:PHE339 4.2 37.3 1.0
C a:ASN338 4.3 35.0 1.0
CG a:PHE339 4.3 37.8 1.0
CB a:ASN338 4.3 32.8 1.0
CA c:GLU354 4.3 32.8 1.0
CB a:HIS337 4.3 29.1 1.0
CE2 a:PHE339 4.4 35.4 1.0
CA a:PHE339 4.5 38.2 1.0
O c:HOH652 4.5 35.0 1.0
O a:PHE339 4.7 33.4 1.0
N a:HIS337 4.8 31.4 1.0
N c:THR355 4.9 32.9 1.0
CD2 a:HIS337 4.9 32.2 1.0
C a:ALA336 4.9 37.6 1.0
CG a:ASN338 4.9 35.3 1.0
CG a:HIS337 5.0 31.5 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 Dec 12 12:28:36 2020

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